CleftGeneDB-Search

Gene: MSX2

Basic information

Tag	Content
Uniprot ID	P35548; D3DQN1; Q53XM4; Q9UD60;
Entrez ID	4488
Genbank protein ID	AAH15509.1; CAA49156.1; BAA03611.1; AAB42178.1; AAP88816.1; EAW61382.1; AAB33867.1; BAA13949.1; BAA06549.1; EAW61381.1; AAD14169.1;
Genbank nucleotide ID	NM_002449.4
Ensembl protein ID	ENSP00000239243
Ensembl nucleotide ID	ENSG00000120149
Gene name	Homeobox protein MSX-2
Gene symbol	MSX2
Organism	Homo sapiens
NCBI taxa ID	9606
Cleft type
Developmental stage
Data sources	Manually collected
Reference	26602496
Functional description	Acts as a transcriptional regulator in bone development. Represses the ALPL promoter activity and antagonizes the stimulatory effect of DLX5 on ALPL expression during osteoblast differentiation. Probable morphogenetic role. May play a role in limb-pattern formation. In osteoblasts, suppresses transcription driven by the osteocalcin FGF response element (OCFRE). Binds to the homeodomain-response element of the ALPL promoter.
Sequence	MASPSKGNDL FSPDEEGPAV VAGPGPGPGG AEGAAEERRV KVSSLPFSVE ALMSDKKPPK 60 EASPLPAESA SAGATLRPLL LSGHGAREAH SPGPLVKPFE TASVKSENSE DGAAWMQEPG 120 RYSPPPRHMS PTTCTLRKHK TNRKPRTPFT TSQLLALERK FRQKQYLSIA ERAEFSSSLN 180 LTETQVKIWF QNRRAKAKRL QEAELEKLKM AAKPMLPSSF SLPFPISSPL QAASIYGASY 240 PFHRPVLPIP PVGLYATPVG YGMYHLS 267

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Gene expression information

Gene expression in different tissues (GTEx V7)

Gene expression in different tissues (ENCODE)

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Relation	Gene symbol	Entrez ID	UniProt ID	Cleft type	Species	Evidence	Details
1:1 ortholog	MSX2	540230	Q0P5C3		Bos taurus	Prediction	More>>
1:1 ortholog	MSX2	403663	Q9GK08		Canis lupus familiaris	Prediction	More>>
1:1 ortholog	MSX2	102169797	A0A452FSV2		Capra hircus	Prediction	More>>
1:1 ortholog	MSX2	4488	P35548		Homo sapiens	Publication	More>>
1:1 ortholog	Msx2	17702	Q03358	CPO	Mus musculus	Publication	More>>
1:1 ortholog	MSX2	744194	K7D1L0		Pan troglodytes	Prediction	More>>
1:1 ortholog	MSX2		A0A287BCF4		Sus scrofa	Prediction	More>>
1:1 ortholog	MSX2	100343959	G1SWN5		Oryctolagus cuniculus	Prediction	More>>
1:1 ortholog	Msx2	25483	G3V8D1		Rattus norvegicus	Prediction	More>>
1:1 ortholog	msx2a		A0A0J9YJ71		Danio rerio	Prediction	More>>

Identified variants/mutations related to cleft phenotype

Gene symbol	Significant Variants/SNPS	Methods	PubMed ID
MSX2	rs4868442*A	Genotyping	26602496

Other genetic variants/mutations

ID	Variant	Type	Disease	Chromosome\Coordinate	Evidence
rs201724372	p.Ser3Phe	missense variant	-	NC_000005.10:g.174724667C>T	ExAC,gnomAD
rs776192704	p.Pro4Leu	missense variant	-	NC_000005.10:g.174724670C>T	ExAC,gnomAD
rs768338363	p.Pro4Ala	missense variant	-	NC_000005.10:g.174724669C>G	ExAC,TOPMed,gnomAD
rs1353927283	p.Ser5Cys	missense variant	-	NC_000005.10:g.174724673C>G	gnomAD
rs764608651	p.Lys6Glu	missense variant	-	NC_000005.10:g.174724675A>G	ExAC,gnomAD
rs1304383366	p.Gly7Arg	missense variant	-	NC_000005.10:g.174724678G>C	TOPMed,gnomAD
rs367636705	p.Asn8Ser	missense variant	-	NC_000005.10:g.174724682A>G	1000Genomes,ESP,ExAC,TOPMed,gnomAD
rs1220617532	p.Asp14Glu	missense variant	-	NC_000005.10:g.174724701C>A	gnomAD
rs751397598	p.Glu16Val	missense variant	-	NC_000005.10:g.174724706A>T	ExAC,gnomAD
rs1470329113	p.Glu16Lys	missense variant	-	NC_000005.10:g.174724705G>A	TOPMed
rs754789827	p.Gly17Cys	missense variant	-	NC_000005.10:g.174724708G>T	ExAC,TOPMed,gnomAD
rs754789827	p.Gly17Ser	missense variant	-	NC_000005.10:g.174724708G>A	ExAC,TOPMed,gnomAD
rs1484867287	p.Val21Gly	missense variant	-	NC_000005.10:g.174724721T>G	TOPMed,gnomAD
rs1023578107	p.Val21Met	missense variant	-	NC_000005.10:g.174724720G>A	TOPMed,gnomAD
rs1023578107	p.Val21Leu	missense variant	-	NC_000005.10:g.174724720G>C	TOPMed,gnomAD
rs1023578107	p.Val21Leu	missense variant	-	NC_000005.10:g.174724720G>T	TOPMed,gnomAD
rs764356797	p.Ala22Thr	missense variant	-	NC_000005.10:g.174724723G>A	ExAC,gnomAD
rs754048064	p.Ala22Gly	missense variant	-	NC_000005.10:g.174724724C>G	ExAC,TOPMed,gnomAD
rs757530512	p.Gly23Arg	missense variant	-	NC_000005.10:g.174724726G>A	ExAC,TOPMed,gnomAD
rs1184315287	p.Gly23Val	missense variant	-	NC_000005.10:g.174724727G>T	gnomAD
rs778800326	p.Gly25Arg	missense variant	-	NC_000005.10:g.174724732G>C	ExAC,gnomAD
rs745950729	p.Pro26Leu	missense variant	-	NC_000005.10:g.174724736C>T	ExAC,TOPMed,gnomAD
rs1189500195	p.Pro26Ser	missense variant	-	NC_000005.10:g.174724735C>T	TOPMed,gnomAD
rs745950729	p.Pro26Arg	missense variant	-	NC_000005.10:g.174724736C>G	ExAC,TOPMed,gnomAD
rs939684065	p.Gly27Glu	missense variant	-	NC_000005.10:g.174724739G>A	TOPMed,gnomAD
rs1298578514	p.Pro28Ser	missense variant	-	NC_000005.10:g.174724741C>T	gnomAD
rs1361478485	p.Pro28Leu	missense variant	-	NC_000005.10:g.174724742C>T	gnomAD
rs1426493639	p.Gly29Glu	missense variant	-	NC_000005.10:g.174724745G>A	TOPMed,gnomAD
rs907900872	p.Ala31Gly	missense variant	-	NC_000005.10:g.174724751C>G	TOPMed
rs1220335673	p.Glu32Ter	stop gained	-	NC_000005.10:g.174724753G>T	gnomAD
rs780593593	p.Glu32Val	missense variant	-	NC_000005.10:g.174724754A>T	ExAC,TOPMed,gnomAD
rs1287168849	p.Ala35Val	missense variant	-	NC_000005.10:g.174724763C>T	gnomAD
rs1210698589	p.Ala35Thr	missense variant	-	NC_000005.10:g.174724762G>A	gnomAD
rs1210698589	p.Ala35Pro	missense variant	-	NC_000005.10:g.174724762G>C	gnomAD
rs1213128510	p.Glu36Lys	missense variant	-	NC_000005.10:g.174724765G>A	gnomAD
rs1385761840	p.Arg39Leu	missense variant	-	NC_000005.10:g.174724775G>T	gnomAD
rs1241043878	p.Arg39Cys	missense variant	-	NC_000005.10:g.174724774C>T	gnomAD
rs1192403644	p.Val42Ile	missense variant	-	NC_000005.10:g.174724783G>A	TOPMed,gnomAD
rs1192403644	p.Val42Phe	missense variant	-	NC_000005.10:g.174724783G>T	TOPMed,gnomAD
rs1393270252	p.Ser43Cys	missense variant	-	NC_000005.10:g.174724787C>G	gnomAD
rs1455201588	p.Ser44Gly	missense variant	-	NC_000005.10:g.174724789A>G	TOPMed
rs560526842	p.Ser44Asn	missense variant	-	NC_000005.10:g.174724790G>A	1000Genomes
rs781641392	p.Pro46Arg	missense variant	-	NC_000005.10:g.174724796C>G	ExAC,gnomAD
rs781641392	p.Pro46Leu	missense variant	-	NC_000005.10:g.174724796C>T	ExAC,gnomAD
rs1253038650	p.Val49Leu	missense variant	-	NC_000005.10:g.174724804G>C	TOPMed
rs1316428923	p.Glu50Val	missense variant	-	NC_000005.10:g.174724808A>T	gnomAD
rs1402690905	p.Glu50Ter	stop gained	-	NC_000005.10:g.174724807G>T	gnomAD
rs1344807799	p.Ala51Glu	missense variant	-	NC_000005.10:g.174724811C>A	gnomAD
rs932163493	p.Met53Val	missense variant	-	NC_000005.10:g.174724816A>G	TOPMed
rs1327996982	p.Ser54Phe	missense variant	-	NC_000005.10:g.174724820C>T	TOPMed,gnomAD
rs1050530108	p.Asp55Tyr	missense variant	-	NC_000005.10:g.174724822G>T	TOPMed
rs1216322113	p.Lys56Gln	missense variant	-	NC_000005.10:g.174724825A>C	TOPMed
rs1311328596	p.Lys56Arg	missense variant	-	NC_000005.10:g.174724826A>G	TOPMed
rs1393259421	p.Pro58Thr	missense variant	-	NC_000005.10:g.174724831C>A	TOPMed,gnomAD
rs747702409	p.Pro59Leu	missense variant	-	NC_000005.10:g.174724835C>T	ExAC,gnomAD
rs1353231469	p.Lys60Gln	missense variant	-	NC_000005.10:g.174724837A>C	gnomAD
rs769505079	p.Glu61Asp	missense variant	-	NC_000005.10:g.174724842G>T	ExAC,gnomAD
rs1283173223	p.Ala62Ser	missense variant	-	NC_000005.10:g.174724843G>T	gnomAD
rs890715736	p.Ala62Gly	missense variant	-	NC_000005.10:g.174724844C>G	TOPMed
rs1223205776	p.Pro64Leu	missense variant	-	NC_000005.10:g.174724850C>T	gnomAD
rs944917896	p.Pro64Ser	missense variant	-	NC_000005.10:g.174724849C>T	TOPMed,gnomAD
rs1041962845	p.Leu65Val	missense variant	-	NC_000005.10:g.174724852C>G	TOPMed,gnomAD
rs527786984	p.Pro66Arg	missense variant	-	NC_000005.10:g.174724856C>G	1000Genomes,ExAC,TOPMed,gnomAD
rs527786984	p.Pro66Leu	missense variant	-	NC_000005.10:g.174724856C>T	1000Genomes,ExAC,TOPMed,gnomAD
rs552575619	p.Ala67Val	missense variant	-	NC_000005.10:g.174724859C>T	1000Genomes,TOPMed,gnomAD
rs1157748986	p.Glu68Lys	missense variant	-	NC_000005.10:g.174724861G>A	gnomAD
rs1436246950	p.Glu68Gly	missense variant	-	NC_000005.10:g.174724862A>G	TOPMed
rs1407617887	p.Ser69Gly	missense variant	-	NC_000005.10:g.174724864A>G	gnomAD
rs1167204448	p.Ala70Ser	missense variant	-	NC_000005.10:g.174724867G>T	gnomAD
rs1392292724	p.Ser71Leu	missense variant	-	NC_000005.10:g.174724871C>T	TOPMed,gnomAD
rs1392292724	p.Ser71Trp	missense variant	-	NC_000005.10:g.174724871C>G	TOPMed,gnomAD
rs1007791560	p.Ala72Thr	missense variant	-	NC_000005.10:g.174724873G>A	TOPMed,gnomAD
rs1338021252	p.Ala72Gly	missense variant	-	NC_000005.10:g.174724874C>G	TOPMed,gnomAD
rs1279326834	p.Gly73Arg	missense variant	-	NC_000005.10:g.174724876G>C	gnomAD
NCI-TCGA novel	p.Gly73Arg	missense variant	-	NC_000005.10:g.174724876G>A	NCI-TCGA
rs1356629730	p.Thr75Ala	missense variant	-	NC_000005.10:g.174724882A>G	TOPMed,gnomAD
rs1333463536	p.Pro78Ser	missense variant	-	NC_000005.10:g.174724891C>T	gnomAD
rs1180890060	p.Gly85Asp	missense variant	-	NC_000005.10:g.174724913G>A	gnomAD
rs765510086	p.Ala86Ser	missense variant	-	NC_000005.10:g.174724915G>T	ExAC
rs750488190	p.Arg87Trp	missense variant	-	NC_000005.10:g.174724918C>T	ExAC,TOPMed,gnomAD
rs758520726	p.Arg87Gln	missense variant	-	NC_000005.10:g.174724919G>A	ExAC,gnomAD
rs121912971	p.Ala89Ter	stop gained	-	NC_000005.10:g.174724924_174724925delinsTA	-
rs1461027798	p.Ala89Val	missense variant	-	NC_000005.10:g.174724925C>T	gnomAD
RCV000018478	p.Ala89Ter	nonsense	Parietal foramina 1 (PFM1)	NC_000005.10:g.174724924_174724925delinsTA	ClinVar
rs1415931146	p.Ala89Thr	missense variant	-	NC_000005.10:g.174724924G>A	gnomAD
rs752778789	p.His90Gln	missense variant	-	NC_000005.10:g.174724929C>G	ExAC,TOPMed,gnomAD
rs751966362	p.Ser91Gly	missense variant	-	NC_000005.10:g.174724930A>G	ExAC,gnomAD
rs751966362	p.Ser91Cys	missense variant	-	NC_000005.10:g.174724930A>T	ExAC,gnomAD
rs1341406944	p.Pro92Arg	missense variant	-	NC_000005.10:g.174724934C>G	gnomAD
rs1416271501	p.Gly93Arg	missense variant	-	NC_000005.10:g.174724936G>C	gnomAD
rs748554134	p.Pro94Ser	missense variant	-	NC_000005.10:g.174724939C>T	ExAC,TOPMed,gnomAD
rs769329948	p.Val96Leu	missense variant	-	NC_000005.10:g.174724945G>T	ExAC,TOPMed,gnomAD
rs777629041	p.Pro98Leu	missense variant	-	NC_000005.10:g.174724952C>T	ExAC,gnomAD
rs1486500587	p.Glu100Lys	missense variant	-	NC_000005.10:g.174724957G>A	gnomAD
rs1255761029	p.Glu100Asp	missense variant	-	NC_000005.10:g.174724959G>T	gnomAD
rs774030950	p.Glu100Ala	missense variant	-	NC_000005.10:g.174724958A>C	ExAC,gnomAD
rs550184107	p.Thr101Ala	missense variant	-	NC_000005.10:g.174724960A>G	1000Genomes,ExAC,gnomAD
rs772051040	p.Ala102Thr	missense variant	-	NC_000005.10:g.174724963G>A	ExAC,gnomAD
rs1474731724	p.Ser103Trp	missense variant	-	NC_000005.10:g.174724967C>G	gnomAD
rs760574628	p.Lys105Asn	missense variant	-	NC_000005.10:g.174724974G>C	ExAC,gnomAD
rs1437011923	p.Lys105Gln	missense variant	-	NC_000005.10:g.174724972A>C	gnomAD
rs765421666	p.Ser106Leu	missense variant	-	NC_000005.10:g.174724976C>T	ExAC,TOPMed,gnomAD
rs1374535151	p.Ser106Pro	missense variant	-	NC_000005.10:g.174724975T>C	TOPMed,gnomAD
rs766394089	p.Asp111Val	missense variant	-	NC_000005.10:g.174724991A>T	ExAC,gnomAD
rs367897914	p.Ala113Val	missense variant	-	NC_000005.10:g.174724997C>T	ESP,ExAC,TOPMed
rs367897914	p.Ala113Val	missense variant	-	NC_000005.10:g.174724997C>T	NCI-TCGA,NCI-TCGA Cosmic
RCV000018479	p.Ala114Ter	nonsense	Parietal foramina 1 (PFM1)	NC_000005.10:g.174725004del	ClinVar
rs781782134	p.Met116Ile	missense variant	-	NC_000005.10:g.174725007G>T	ExAC,gnomAD
rs781782134	p.Met116Ile	missense variant	-	NC_000005.10:g.174725007G>A	ExAC,gnomAD
rs752992492	p.Gln117Glu	missense variant	-	NC_000005.10:g.174725008C>G	ExAC,gnomAD
rs752992492	p.Gln117Lys	missense variant	-	NC_000005.10:g.174725008C>A	ExAC,gnomAD
rs777537313	p.Pro119His	missense variant	-	NC_000005.10:g.174725015C>A	ExAC,gnomAD
rs777537313	p.Pro119Leu	missense variant	-	NC_000005.10:g.174725015C>T	ExAC,gnomAD
rs1263972828	p.Gly120Ser	missense variant	-	NC_000005.10:g.174725017G>A	gnomAD
rs771889290	p.Arg121Leu	missense variant	-	NC_000005.10:g.174725021G>T	ExAC,TOPMed,gnomAD
rs771889290	p.Arg121Gln	missense variant	-	NC_000005.10:g.174725021G>A	ExAC,TOPMed,gnomAD
COSM3410148	p.Ser123Leu	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000005.10:g.174725027C>T	NCI-TCGA Cosmic
rs746748359	p.Pro125Leu	missense variant	-	NC_000005.10:g.174725033C>T	ExAC,gnomAD
rs372131169	p.Pro125Ser	missense variant	-	NC_000005.10:g.174725032C>T	ESP,ExAC,TOPMed,gnomAD
rs1172179431	p.Pro126Ser	missense variant	-	NC_000005.10:g.174725035C>T	gnomAD
rs776428406	p.Arg127Gly	missense variant	-	NC_000005.10:g.174725038A>G	ExAC,gnomAD
rs1430264873	p.His128Gln	missense variant	-	NC_000005.10:g.174729163T>G	TOPMed,gnomAD
rs1405669891	p.His128Pro	missense variant	-	NC_000005.10:g.174729162A>C	TOPMed
rs4242182	p.Met129Thr	missense variant	-	NC_000005.10:g.174729165T>C	1000Genomes,ESP,ExAC,TOPMed,gnomAD
rs186769394	p.Met129Ile	missense variant	-	NC_000005.10:g.174729166G>C	1000Genomes,ExAC,TOPMed,gnomAD
rs4242182	p.Met129Lys	missense variant	-	NC_000005.10:g.174729165T>A	1000Genomes,ESP,ExAC,TOPMed,gnomAD
RCV000325806	p.Met129Thr	missense variant	Enlarged parietal foramina	NC_000005.10:g.174729165T>C	ClinVar
RCV000270658	p.Met129Thr	missense variant	-	NC_000005.10:g.174729165T>C	ClinVar
rs4242182	p.Met129Arg	missense variant	-	NC_000005.10:g.174729165T>G	1000Genomes,ESP,ExAC,TOPMed,gnomAD
rs186769394	p.Met129Ile	missense variant	-	NC_000005.10:g.174729166G>A	1000Genomes,ExAC,TOPMed,gnomAD
RCV000246108	p.Met129Thr	missense variant	-	NC_000005.10:g.174729165T>C	ClinVar
rs765584496	p.Pro131Arg	missense variant	-	NC_000005.10:g.174729171C>G	ExAC
rs1435145956	p.Pro131Ser	missense variant	-	NC_000005.10:g.174729170C>T	gnomAD
rs1314483278	p.Thr135Asn	missense variant	-	NC_000005.10:g.174729183C>A	TOPMed,gnomAD
NCI-TCGA novel	p.Arg137Lys	missense variant	-	NC_000005.10:g.174729189G>A	NCI-TCGA
COSM737675	p.Arg137Met	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000005.10:g.174729189G>T	NCI-TCGA Cosmic
NCI-TCGA novel	p.Lys140Asn	missense variant	-	NC_000005.10:g.174729199G>C	NCI-TCGA
rs762595550	p.Asn142Ser	missense variant	-	NC_000005.10:g.174729204A>G	ExAC,gnomAD
rs751060486	p.Arg143Gln	missense variant	-	NC_000005.10:g.174729207G>A	ExAC,TOPMed,gnomAD
rs1216385486	p.Arg143Trp	missense variant	-	NC_000005.10:g.174729206C>T	TOPMed,gnomAD
rs754536048	p.Pro145Leu	missense variant	-	NC_000005.10:g.174729213C>T	ExAC,gnomAD
rs756030049	p.Arg146Cys	missense variant	-	NC_000005.10:g.174729215C>T	ExAC,gnomAD
rs1201449653	p.Arg146His	missense variant	-	NC_000005.10:g.174729216G>A	TOPMed
rs1484486574	p.Thr147Met	missense variant	-	NC_000005.10:g.174729219C>T	gnomAD
rs104893895	p.Pro148Leu	missense variant	Craniosynostosis 2 (CRS2)	NC_000005.10:g.174729222C>T	UniProt,dbSNP
VAR_071634	p.Pro148Leu	missense variant	Craniosynostosis 2 (CRS2)	NC_000005.10:g.174729222C>T	UniProt
rs104893895	p.Pro148Leu	missense variant	-	NC_000005.10:g.174729222C>T	-
rs104893895	p.Pro148His	missense variant	Craniosynostosis 2 (CRS2)	NC_000005.10:g.174729222C>A	UniProt,dbSNP
VAR_003755	p.Pro148His	missense variant	Craniosynostosis 2 (CRS2)	NC_000005.10:g.174729222C>A	UniProt
rs104893895	p.Pro148His	missense variant	-	NC_000005.10:g.174729222C>A	-
RCV000018474	p.Pro148His	missense variant	Craniosynostosis 2 (CRS2)	NC_000005.10:g.174729222C>A	ClinVar
RCV000690192	p.Pro148Leu	missense variant	Enlarged parietal foramina	NC_000005.10:g.174729222C>T	ClinVar
NCI-TCGA novel	p.Phe149Leu	missense variant	-	NC_000005.10:g.174729226T>G	NCI-TCGA
rs1055665549	p.Thr151Ala	missense variant	-	NC_000005.10:g.174729230A>G	TOPMed,gnomAD
rs780471460	p.Ser152Phe	missense variant	-	NC_000005.10:g.174729234C>T	ExAC,gnomAD
VAR_010786	p.Leu154Pro	Missense	Parietal foramina 1 (PFM1) [MIM:168500]	-	UniProt
rs747053672	p.Ala156Thr	missense variant	-	NC_000005.10:g.174729245G>A	ExAC,gnomAD
rs776872613	p.Arg159His	missense variant	-	NC_000005.10:g.174729255G>A	ExAC,TOPMed,gnomAD
rs773491812	p.Arg159Cys	missense variant	-	NC_000005.10:g.174729254C>T	ExAC,TOPMed,gnomAD
rs776872613	p.Arg159Leu	missense variant	-	NC_000005.10:g.174729255G>T	ExAC,TOPMed,gnomAD
VAR_010200	p.Arg159_Lys160del	inframe_deletion	Parietal foramina 1 (PFM1) [MIM:168500]	-	UniProt
rs770204721	p.Lys160Thr	missense variant	-	NC_000005.10:g.174729258A>C	ExAC,TOPMed,gnomAD
rs770204721	p.Lys160Arg	missense variant	-	NC_000005.10:g.174729258A>G	ExAC,TOPMed,gnomAD
rs200519800	p.Phe161Tyr	missense variant	-	NC_000005.10:g.174729261T>A	1000Genomes,ExAC,gnomAD
rs766037353	p.Arg162His	missense variant	-	NC_000005.10:g.174729264G>A	ExAC,gnomAD
rs555293970	p.Arg162Cys	missense variant	-	NC_000005.10:g.174729263C>T	1000Genomes,ExAC,TOPMed,gnomAD
COSM449345	p.Gln163Ter	stop gained	Variant assessed as Somatic; HIGH impact.	NC_000005.10:g.174729266C>T	NCI-TCGA Cosmic
rs759220876	p.Gln165Leu	missense variant	-	NC_000005.10:g.174729273A>T	ExAC,gnomAD
rs759220876	p.Gln165Arg	missense variant	-	NC_000005.10:g.174729273A>G	ExAC,gnomAD
COSM1328902	p.Tyr166Asn	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000005.10:g.174729275T>A	NCI-TCGA Cosmic
COSM1065941	p.Tyr166His	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000005.10:g.174729275T>C	NCI-TCGA Cosmic
rs756013230	p.Ser168Phe	missense variant	-	NC_000005.10:g.174729282C>T	ExAC,gnomAD
rs1346104549	p.Ser168Ala	missense variant	-	NC_000005.10:g.174729281T>G	gnomAD
rs1428948082	p.Ala170Thr	missense variant	-	NC_000005.10:g.174729287G>A	TOPMed,gnomAD
RCV000018480	p.Ala170Ter	frameshift	Parietal foramina with cleidocranial dysplasia (PFMCCD)	NC_000005.10:g.174729284_174729287dup	ClinVar
rs1169833296	p.Glu171Asp	missense variant	-	NC_000005.10:g.174729292G>T	TOPMed
rs104893896	p.Arg172His	missense variant	-	NC_000005.10:g.174729294G>A	ExAC,gnomAD
rs104893896	p.Arg172His	missense variant	Parietal foramina 1 (PFM1)	NC_000005.10:g.174729294G>A	UniProt,dbSNP
VAR_010201	p.Arg172His	missense variant	Parietal foramina 1 (PFM1)	NC_000005.10:g.174729294G>A	UniProt
rs764005351	p.Arg172Cys	missense variant	-	NC_000005.10:g.174729293C>T	ExAC,gnomAD
rs764005351	p.Arg172Gly	missense variant	-	NC_000005.10:g.174729293C>G	ExAC,gnomAD
RCV000018476	p.Arg172His	missense variant	Parietal foramina 1 (PFM1)	NC_000005.10:g.174729294G>A	ClinVar
RCV000585463	p.Arg172Gly	missense variant	-	NC_000005.10:g.174729293C>G	ClinVar
rs1444546648	p.Ala173Thr	missense variant	-	NC_000005.10:g.174729296G>A	TOPMed
rs757042034	p.Glu174Ter	stop gained	-	NC_000005.10:g.174729299G>T	ExAC,gnomAD
rs1185740908	p.Ser176Pro	missense variant	-	NC_000005.10:g.174729305T>C	TOPMed
rs1195373061	p.Asn180Ser	missense variant	-	NC_000005.10:g.174729318A>G	TOPMed,gnomAD
rs1453621117	p.Thr182Ala	missense variant	-	NC_000005.10:g.174729323A>G	gnomAD
RCV000018481	p.Glu183Ter	frameshift	Parietal foramina 1 (PFM1)	NC_000005.10:g.174729327_174729334del	ClinVar
NCI-TCGA novel	p.Gln185His	missense variant	-	NC_000005.10:g.174729334G>T	NCI-TCGA
NCI-TCGA novel	p.Ile188SerPheSerTerUnkUnk	frameshift	-	NC_000005.10:g.174729338A>-	NCI-TCGA
rs781352134	p.Phe190Leu	missense variant	-	NC_000005.10:g.174729349C>G	ExAC,gnomAD
rs1203256966	p.Arg193Ter	stop gained	-	NC_000005.10:g.174729356C>T	TOPMed
NCI-TCGA novel	p.Arg194Thr	missense variant	-	NC_000005.10:g.174729360G>C	NCI-TCGA
rs1387945571	p.Ala195Gly	missense variant	-	NC_000005.10:g.174729363C>G	gnomAD
rs1328572937	p.Lys196Arg	missense variant	-	NC_000005.10:g.174729366A>G	gnomAD
rs770317741	p.Ala197Val	missense variant	-	NC_000005.10:g.174729369C>T	ExAC,gnomAD
rs770317741	p.Ala197Glu	missense variant	-	NC_000005.10:g.174729369C>A	ExAC,gnomAD
rs199732800	p.Arg199Ile	missense variant	-	NC_000005.10:g.174729375G>T	1000Genomes
rs1410308159	p.Leu200Pro	missense variant	-	NC_000005.10:g.174729378T>C	gnomAD
rs1375081991	p.Gln201Arg	missense variant	-	NC_000005.10:g.174729381A>G	gnomAD
rs182690432	p.Glu202Gln	missense variant	-	NC_000005.10:g.174729383G>C	1000Genomes,ExAC,gnomAD
rs111542301	p.Leu205Val	missense variant	-	NC_000005.10:g.174729392C>G	TOPMed,gnomAD
rs759131123	p.Met210Ile	missense variant	-	NC_000005.10:g.174729409G>A	ExAC,gnomAD
rs767161367	p.Ala211Gly	missense variant	-	NC_000005.10:g.174729411C>G	ExAC,TOPMed,gnomAD
rs775062909	p.Ala212Gly	missense variant	-	NC_000005.10:g.174729414C>G	ExAC,gnomAD
rs1467969048	p.Ala212Thr	missense variant	-	NC_000005.10:g.174729413G>A	TOPMed,gnomAD
rs1467969048	p.Ala212Ser	missense variant	-	NC_000005.10:g.174729413G>T	TOPMed,gnomAD
RCV000276654	p.Ala212Gly	missense variant	-	NC_000005.10:g.174729414C>G	ClinVar
COSM3853797	p.Ala212Val	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000005.10:g.174729414C>T	NCI-TCGA Cosmic
RCV000389679	p.Ala212Gly	missense variant	Enlarged parietal foramina	NC_000005.10:g.174729414C>G	ClinVar
rs1234326556	p.Pro214Leu	missense variant	-	NC_000005.10:g.174729420C>T	TOPMed,gnomAD
rs577629417	p.Met215Leu	missense variant	-	NC_000005.10:g.174729422A>T	1000Genomes,TOPMed,gnomAD
rs1297854733	p.Met215Ile	missense variant	-	NC_000005.10:g.174729424G>T	TOPMed
rs577629417	p.Met215Val	missense variant	-	NC_000005.10:g.174729422A>G	1000Genomes,TOPMed,gnomAD
NCI-TCGA novel	p.Pro217His	missense variant	-	NC_000005.10:g.174729429C>A	NCI-TCGA
NCI-TCGA novel	p.Pro217Ala	missense variant	-	NC_000005.10:g.174729428C>G	NCI-TCGA
rs760162567	p.Ser218Phe	missense variant	-	NC_000005.10:g.174729432C>T	ExAC,TOPMed,gnomAD
COSM1065942	p.Phe220Ser	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000005.10:g.174729438T>C	NCI-TCGA Cosmic
rs753676458	p.Ser221Gly	missense variant	-	NC_000005.10:g.174729440A>G	ExAC,gnomAD
rs1392988082	p.Pro225Leu	missense variant	-	NC_000005.10:g.174729453C>T	gnomAD
rs757239934	p.Ile226Val	missense variant	-	NC_000005.10:g.174729455A>G	ExAC,gnomAD
rs1330007091	p.Ser227Thr	missense variant	-	NC_000005.10:g.174729459G>C	gnomAD
rs373857075	p.Ser228Leu	missense variant	-	NC_000005.10:g.174729462C>T	ESP,ExAC,TOPMed,gnomAD
rs1287374727	p.Pro229His	missense variant	-	NC_000005.10:g.174729465C>A	gnomAD
rs1287374727	p.Pro229Leu	missense variant	-	NC_000005.10:g.174729465C>T	gnomAD
rs755243046	p.Gln231His	missense variant	-	NC_000005.10:g.174729472G>C	ExAC,gnomAD
rs781619692	p.Ala232Thr	missense variant	-	NC_000005.10:g.174729473G>A	ExAC,TOPMed,gnomAD
rs1165916964	p.Ala232Val	missense variant	-	NC_000005.10:g.174729474C>T	TOPMed
rs138053303	p.Ala233Val	missense variant	-	NC_000005.10:g.174729477C>T	ESP,ExAC,TOPMed,gnomAD
RCV000644909	p.Ala233Val	missense variant	Enlarged parietal foramina	NC_000005.10:g.174729477C>T	ClinVar
rs1196261944	p.Tyr236Cys	missense variant	-	NC_000005.10:g.174729486A>G	gnomAD
rs777944422	p.Gly237Glu	missense variant	-	NC_000005.10:g.174729489G>A	ExAC,gnomAD
NCI-TCGA novel	p.Ala238Ser	missense variant	-	NC_000005.10:g.174729491G>T	NCI-TCGA
rs1435910539	p.Ala238Thr	missense variant	-	NC_000005.10:g.174729491G>A	gnomAD
rs1176289041	p.Ser239Phe	missense variant	-	NC_000005.10:g.174729495C>T	TOPMed
rs368570722	p.Pro241Leu	missense variant	-	NC_000005.10:g.174729501C>T	ESP,ExAC,TOPMed,gnomAD
rs371825159	p.Phe242Leu	missense variant	-	NC_000005.10:g.174729505C>A	ESP,ExAC,gnomAD
rs1415719648	p.His243Pro	missense variant	-	NC_000005.10:g.174729507A>C	gnomAD
COSM1065943	p.Arg244Ile	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000005.10:g.174729510G>T	NCI-TCGA Cosmic
rs771700671	p.Val246Leu	missense variant	-	NC_000005.10:g.174729515G>C	ExAC,gnomAD
rs775044825	p.Leu247Pro	missense variant	-	NC_000005.10:g.174729519T>C	ExAC,gnomAD
rs374244313	p.Pro250Leu	missense variant	-	NC_000005.10:g.174729528C>T	ESP,gnomAD
rs1422233314	p.Pro250Ala	missense variant	-	NC_000005.10:g.174729527C>G	gnomAD
rs776218196	p.Pro251Ser	missense variant	-	NC_000005.10:g.174729530C>T	ExAC,gnomAD
NCI-TCGA novel	p.Val252AspPheSerTerUnkUnk	frameshift	-	NC_000005.10:g.174729533_174729534insA	NCI-TCGA
rs1339319232	p.Gly253Arg	missense variant	-	NC_000005.10:g.174729536G>A	gnomAD
rs750227762	p.Leu254Pro	missense variant	-	NC_000005.10:g.174729540T>C	ExAC,gnomAD
rs1227466459	p.Tyr255Cys	missense variant	-	NC_000005.10:g.174729543A>G	gnomAD
rs752824647	p.Thr257Met	missense variant	-	NC_000005.10:g.174729549C>T	ExAC,TOPMed,gnomAD
rs767820021	p.Thr257Ala	missense variant	-	NC_000005.10:g.174729548A>G	ExAC,TOPMed,gnomAD
COSM3776533	p.Pro258Leu	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000005.10:g.174729552C>T	NCI-TCGA Cosmic
rs528373280	p.Gly260Val	missense variant	-	NC_000005.10:g.174729558G>T	1000Genomes,ExAC,gnomAD
rs528373280	p.Gly260Glu	missense variant	-	NC_000005.10:g.174729558G>A	1000Genomes,ExAC,gnomAD
rs1441956714	p.Tyr261Cys	missense variant	-	NC_000005.10:g.174729561A>G	gnomAD
rs1193987566	p.Met263Val	missense variant	-	NC_000005.10:g.174729566A>G	gnomAD
rs199856192	p.Met263Ile	missense variant	-	NC_000005.10:g.174729568G>A	1000Genomes,ExAC,TOPMed,gnomAD
rs757757709	p.Met263Arg	missense variant	-	NC_000005.10:g.174729567T>G	ExAC,TOPMed,gnomAD
rs199856192	p.Met263Ile	missense variant	-	NC_000005.10:g.174729568G>T	1000Genomes,ExAC,TOPMed,gnomAD
rs1168359833	p.Tyr264Cys	missense variant	-	NC_000005.10:g.174729570A>G	gnomAD

Disease or phenotype associated information

Disease ID	Disease Name	Disease Type	Source
C0000768	Congenital Abnormality	group	BEFREE
C0004565	Melanoma, B16	disease	BEFREE
C0006142	Malignant neoplasm of breast	disease	BEFREE
C0008924	Cleft upper lip	disease	HPO
C0008928	Cleidocranial Dysplasia	disease	BEFREE
C0009402	Colorectal Carcinoma	disease	BEFREE
C0010054	Coronary Arteriosclerosis	disease	BEFREE
C0010278	Craniosynostosis	disease	BEFREE;GENOMICS_ENGLAND;MGD
C0011649	Dermoid Cyst	disease	HPO
C0011860	Diabetes Mellitus, Non-Insulin-Dependent	disease	BEFREE
C0011875	Diabetic Angiopathies	disease	BEFREE
C0013537	Eclampsia	disease	BEFREE
C0014065	Congenital cerebral hernia	disease	BEFREE;HPO
C0014544	Epilepsy	disease	HPO
C0015306	Hereditary Multiple Exostoses	disease	BEFREE
C0016037	Fibrodysplasia Ossificans Progressiva	disease	BEFREE
C0018681	Headache	phenotype	HPO;LHGDN
C0020538	Hypertensive disease	group	RGD
C0020608	Hypodontia	disease	BEFREE
C0023890	Liver Cirrhosis	disease	BEFREE
C0024623	Malignant neoplasm of stomach	disease	BEFREE
C0025202	melanoma	disease	BEFREE
C0027430	Nasal Polyps	disease	BEFREE
C0029408	Degenerative polyarthritis	disease	BEFREE
C0029463	Osteosarcoma	disease	BEFREE
C0029925	Ovarian Carcinoma	disease	BEFREE
C0030297	Pancreatic Neoplasm	disease	LHGDN
C0035078	Kidney Failure	disease	BEFREE
C0036572	Seizures	phenotype	HPO
C0039093	Congenital abnormal Synostosis	disease	BEFREE;LHGDN
C0085695	Chronic gastritis	disease	BEFREE
C0149521	Pancreatitis, Chronic	disease	BEFREE
C0151744	Myocardial Ischemia	disease	BEFREE
C0152423	Congenital small ears	disease	HPO
C0175699	Saethre-Chotzen Syndrome	disease	BEFREE
C0206721	Inverted Papilloma	disease	BEFREE;LHGDN
C0221354	Frontal bossing	disease	HPO
C0235974	Pancreatic carcinoma	disease	BEFREE
C0265535	Trigonocephaly	disease	HPO
C0278488	Carcinoma breast stage IV	disease	BEFREE
C0346163	Endometrioid carcinoma ovary	disease	BEFREE
C0346647	Malignant neoplasm of pancreas	disease	BEFREE
C0376634	Craniofacial Abnormalities	group	BEFREE;CTD_human
C0426799	Congenital hypoplasia of clavicle	disease	HPO
C0494165	Secondary malignant neoplasm of liver	disease	BEFREE
C0585442	Osteosarcoma of bone	disease	BEFREE
C0596263	Carcinogenesis	phenotype	BEFREE
C0677886	Epithelial ovarian cancer	disease	BEFREE
C0678222	Breast Carcinoma	disease	BEFREE
C0699791	Stomach Carcinoma	disease	BEFREE
C1140680	Malignant neoplasm of ovary	disease	BEFREE
C1290514	Familial hypodontia	disease	BEFREE
C1335302	Pancreatic Ductal Adenocarcinoma	disease	BEFREE
C1458155	Mammary Neoplasms	group	BEFREE
C1527249	Colorectal Cancer	disease	BEFREE
C1561643	Chronic Kidney Diseases	group	BEFREE
C1623038	Cirrhosis	disease	BEFREE
C1720887	Female Urogenital Diseases	group	CTD_human
C1832588	Chromosome 11p11.2 Deletion Syndrome	disease	BEFREE
C1849300	Widely patent fontanelles and sutures	phenotype	HPO
C1855496	Contiguous gene syndrome	disease	BEFREE
C1855698	Aplasia cutis congenita of scalp	disease	HPO
C1857484	Brachyturricephaly	phenotype	HPO
C1858160	CRANIOSYNOSTOSIS, TYPE 2	disease	BEFREE;CLINVAR;CTD_human;ORPHANET;UNIPROT
C1865045	Symmetrical, oval parietal bone defects	phenotype	HPO
C1868597	Parietal Foramina With Cleidocranial Dysplasia	disease	BEFREE;CTD_human;ORPHANET
C1868598	PARIETAL FORAMINA	disease	BEFREE;CTD_human;MGD;ORPHANET;UNIPROT
C1868599	PARIETAL FORAMINA 1	disease	CLINVAR;UNIPROT
C1881254	Inverted Squamous Cell Papilloma	disease	BEFREE
C1961099	Precursor T-Cell Lymphoblastic Leukemia-Lymphoma	disease	BEFREE
C2981150	Uranostaphyloschisis	disease	HPO
C3714756	Intellectual Disability	group	GENOMICS_ENGLAND
C3888194	MIXED LINEAGE LEUKEMIA	disease	BEFREE
C4020756	Unilateral coronal craniosynostosis	disease	HPO
C4021164	Bicoronal synostosis	disease	HPO
C4023418	Unicoronal synostosis	phenotype	HPO
C4025787	Calvarial skull defect	phenotype	BEFREE
C4048801	Scalp defect	phenotype	HPO
C4072857	Focal absence of scalp tissue	phenotype	HPO
C4072858	Solitary scalp defect	phenotype	HPO
C4083076	Increased head circumference	phenotype	HPO
C4255213	Increased size of skull	phenotype	HPO
C4280664	Big calvaria	phenotype	HPO
C4280665	Wedge shaped head	disease	HPO
C4280666	Triangular head shape	disease	HPO

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID	GO Term	Evidence
GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	IBA
GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	ISM
GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0001227	DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA
GO:0003712	transcription coregulator activity	ISS
GO:0005515	protein binding	IPI
GO:0008134	transcription factor binding	IEA
GO:0043565	sequence-specific DNA binding	IDA
GO:0044212	transcription regulatory region DNA binding	ISS

GO:Biological Process

GO ID	GO Term	Evidence
GO:0000122	negative regulation of transcription by RNA polymerase II	ISS
GO:0000122	negative regulation of transcription by RNA polymerase II	IMP
GO:0001649	osteoblast differentiation	ISS
GO:0002063	chondrocyte development	IEA
GO:0002076	osteoblast development	IEA
GO:0003148	outflow tract septum morphogenesis	IEA
GO:0003198	epithelial to mesenchymal transition involved in endocardial cushion formation	IEA
GO:0003416	endochondral bone growth	IEA
GO:0008285	negative regulation of cell population proliferation	IEA
GO:0009952	anterior/posterior pattern specification	IEA
GO:0023019	signal transduction involved in regulation of gene expression	IEA
GO:0030513	positive regulation of BMP signaling pathway	IEA
GO:0032792	negative regulation of CREB transcription factor activity	IEA
GO:0035115	embryonic forelimb morphogenesis	IEA
GO:0035116	embryonic hindlimb morphogenesis	IEA
GO:0035313	wound healing, spreading of epidermal cells	IEA
GO:0035880	embryonic nail plate morphogenesis	IEA
GO:0043066	negative regulation of apoptotic process	IEA
GO:0045599	negative regulation of fat cell differentiation	IEA
GO:0045617	negative regulation of keratinocyte differentiation	IEA
GO:0045669	positive regulation of osteoblast differentiation	IEA
GO:0045892	negative regulation of transcription, DNA-templated	ISS
GO:0048598	embryonic morphogenesis	IBA
GO:0048863	stem cell differentiation	IEA
GO:0051795	positive regulation of timing of catagen	IEA
GO:0060346	bone trabecula formation	IEA
GO:0060363	cranial suture morphogenesis	TAS
GO:0060364	frontal suture morphogenesis	IEA
GO:0060444	branching involved in mammary gland duct morphogenesis	IEA
GO:0061312	BMP signaling pathway involved in heart development	IEA
GO:0070166	enamel mineralization	IEA
GO:0071392	cellular response to estradiol stimulus	IEA
GO:0090427	activation of meiosis	IEA
GO:2000678	negative regulation of transcription regulatory region DNA binding	ISS
GO:2001055	positive regulation of mesenchymal cell apoptotic process	IEA

GO:Cellular Component

GO ID	GO Term	Evidence
GO:0000790	nuclear chromatin	ISA
GO:0005634	nucleus	IBA
GO:0005829	cytosol	IDA
GO:0016607	nuclear speck	IDA

Reactome Pathway

Reactome ID	Reactome Term	Evidence
R-HSA-212436	Generic Transcription Pathway	IEA
R-HSA-73857	RNA Polymerase II Transcription	IEA
R-HSA-74160	Gene expression (Transcription)	IEA
R-HSA-8878166	Transcriptional regulation by RUNX2	IEA
R-HSA-8939902	Regulation of RUNX2 expression and activity	IEA

Drugs and compounds information

ID	Drug Name	Action	PubMed
D015655	1-Methyl-4-phenylpyridinium	1-Methyl-4-phenylpyridinium results in decreased expression of MSX2 mRNA	28801915
C023514	2,6-dinitrotoluene	2,6-dinitrotoluene affects the expression of MSX2 mRNA	21346803
C034017	2-ethylhexanol	2-ethylhexanol results in increased expression of MSX2 mRNA	31445079
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	[NOG protein co-treated with belinostat co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	[NOG protein co-treated with mercuric bromide co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	[NOG protein co-treated with methylmercuric chloride co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	[NOG protein co-treated with Panobinostat co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	[NOG protein co-treated with p-Chloromercuribenzoic Acid co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	[NOG protein co-treated with Phenylmercuric Acetate co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	[NOG protein co-treated with trichostatin A co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	[NOG protein co-treated with Valproic Acid co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C496492	abrine	abrine results in increased expression of MSX2 mRNA	31054353
D020106	Acrylamide	Acrylamide results in decreased expression of MSX2 mRNA	28959563
D016604	Aflatoxin B1	Aflatoxin B1 results in decreased methylation of MSX2 gene	27153756
D000643	Ammonium Chloride	Ammonium Chloride affects the expression of MSX2 mRNA	16483693
D000935	Antifungal Agents	Antifungal Agents results in decreased expression of MSX2 mRNA	21254369
D000077237	Arsenic Trioxide	MSX2 protein results in decreased susceptibility to Arsenic Trioxide	20707922
C015001	arsenite	arsenite results in increased methylation of MSX2 promoter	23974009
D001205	Ascorbic Acid	[Ascorbic Acid co-treated with beta-glycerophosphoric acid co-treated with Dexamethasone] results in increased expression of MSX2 mRNA	28189605
D001205	Ascorbic Acid	cadmium sulfate inhibits the reaction [[Ascorbic Acid co-treated with beta-glycerophosphoric acid co-treated with Dexamethasone] results in increased expression of MSX2 mRNA]	28189605
D001280	Atrazine	Atrazine results in increased expression of MSX2 mRNA	29505797
C487081	belinostat	belinostat results in increased expression of MSX2 mRNA	26272509
C487081	belinostat	[NOG protein co-treated with belinostat co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
D001548	Benzalkonium Compounds	[IL6 protein affects the susceptibility to Benzalkonium Compounds] which affects the expression of MSX2 mRNA	30171875
D001564	Benzo(a)pyrene	Benzo(a)pyrene results in decreased expression of MSX2 mRNA	22228805
D001564	Benzo(a)pyrene	Benzo(a)pyrene results in increased expression of MSX2 mRNA	23735875
C026487	benzo(e)pyrene	benzo(e)pyrene results in decreased methylation of MSX2 intron	30157460
C031463	beta-glycerophosphoric acid	[Ascorbic Acid co-treated with beta-glycerophosphoric acid co-treated with Dexamethasone] results in increased expression of MSX2 mRNA	28189605
C031463	beta-glycerophosphoric acid	cadmium sulfate inhibits the reaction [[Ascorbic Acid co-treated with beta-glycerophosphoric acid co-treated with Dexamethasone] results in increased expression of MSX2 mRNA]	28189605
C543008	bis(4-hydroxyphenyl)sulfone	bis(4-hydroxyphenyl)sulfone results in increased expression of MSX2 mRNA	30951980
C006780	bisphenol A	bisphenol A results in decreased expression of MSX2 mRNA	22576693
C006780	bisphenol A	bisphenol A results in increased methylation of MSX2 gene	22576693
C006780	bisphenol A	bisphenol A affects the methylation of MSX2 promoter	27334623
C006780	bisphenol A	bisphenol A results in decreased expression of MSX2 mRNA	26063408
C006780	bisphenol A	bisphenol A results in increased expression of MSX2 mRNA	30951980
C006780	bisphenol A	bisphenol A results in decreased expression of MSX2 mRNA	25181051
C006780	bisphenol A	bisphenol A results in increased methylation of MSX2 gene	28505145
C000611646	bisphenol F	bisphenol F results in increased expression of MSX2 mRNA	30951980
C584509	C646 compound	C646 compound results in decreased expression of MSX2 mRNA	26191083
D019256	Cadmium Chloride	Cadmium Chloride results in decreased methylation of MSX2 promoter	22457795
C037123	cadmium sulfate	cadmium sulfate inhibits the reaction [[Ascorbic Acid co-treated with beta-glycerophosphoric acid co-treated with Dexamethasone] results in increased expression of MSX2 mRNA]	28189605
C055494	caffeic acid phenethyl ester	[Diethylnitrosamine co-treated with caffeic acid phenethyl ester] results in decreased expression of MSX2 mRNA	20360939
D002117	Calcitriol	Calcitriol results in increased expression of MSX2 mRNA	16002434
D002220	Carbamazepine	Carbamazepine affects the expression of MSX2 mRNA	25979313
C084597	chlorcyclizine	chlorcyclizine results in increased expression of MSX2 mRNA	21058326
C007076	citral	citral results in decreased expression of MSX2 mRNA	15581867
C018021	cobaltous chloride	cobaltous chloride results in increased expression of MSX2 mRNA	19376846
D003300	Copper	Copper results in increased expression of MSX2 mRNA	30556269
D003375	Coumestrol	Coumestrol results in decreased expression of MSX2 mRNA	19167446
D003471	Cuprizone	Cuprizone results in increased expression of MSX2 mRNA	26577399
D003907	Dexamethasone	[Ascorbic Acid co-treated with beta-glycerophosphoric acid co-treated with Dexamethasone] results in increased expression of MSX2 mRNA	28189605
D003907	Dexamethasone	cadmium sulfate inhibits the reaction [[Ascorbic Acid co-treated with beta-glycerophosphoric acid co-treated with Dexamethasone] results in increased expression of MSX2 mRNA]	28189605
D004041	Dietary Fats	Dietary Fats results in increased expression of MSX2 mRNA	25016146
D004052	Diethylnitrosamine	[Diethylnitrosamine co-treated with caffeic acid phenethyl ester] results in decreased expression of MSX2 mRNA	20360939
D004054	Diethylstilbestrol	Diethylstilbestrol results in decreased expression of MSX2 mRNA	16513791
D004054	Diethylstilbestrol	Diethylstilbestrol results in increased expression of MSX2 mRNA	17394237
D004054	Diethylstilbestrol	MSX2 affects the susceptibility to Diethylstilbestrol	15591538
D004054	Diethylstilbestrol	MSX2 protein results in decreased susceptibility to Diethylstilbestrol	16513791
C516138	dorsomorphin	[NOG protein co-treated with belinostat co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C516138	dorsomorphin	[NOG protein co-treated with mercuric bromide co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C516138	dorsomorphin	[NOG protein co-treated with methylmercuric chloride co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C516138	dorsomorphin	[NOG protein co-treated with Panobinostat co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C516138	dorsomorphin	[NOG protein co-treated with p-Chloromercuribenzoic Acid co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C516138	dorsomorphin	[NOG protein co-treated with Phenylmercuric Acetate co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C516138	dorsomorphin	[NOG protein co-treated with trichostatin A co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C516138	dorsomorphin	[NOG protein co-treated with Valproic Acid co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
D004317	Doxorubicin	Doxorubicin results in decreased expression of MSX2 mRNA	29803840
C118739	entinostat	entinostat results in increased expression of MSX2 mRNA	26272509
D004958	Estradiol	Estradiol results in decreased expression of MSX2 mRNA	19167446
D004958	Estradiol	Estradiol results in increased expression of MSX2 mRNA	17450229; 30077407;
D004958	Estradiol	[Polyphenols co-treated with Estradiol] results in decreased expression of MSX2 mRNA	30077407
D004967	Estrogens	[Estrogens co-treated with Progesterone] results in increased expression of MSX2 mRNA	17546050
D004967	Estrogens	Estrogens results in increased expression of MSX2 mRNA	17546050
D004997	Ethinyl Estradiol	Ethinyl Estradiol results in increased expression of MSX2 mRNA	17942748
D004997	Ethinyl Estradiol	[Tetrachlorodibenzodioxin co-treated with Ethinyl Estradiol] results in increased expression of MSX2 mRNA	17942748
D005459	Fluorides	Fluorides inhibits the reaction [potassium phosphate results in increased expression of MSX2 mRNA]	24561004
D005472	Fluorouracil	Fluorouracil results in decreased expression of MSX2 protein	15352031
D005472	Fluorouracil	MSX2 protein affects the susceptibility to Fluorouracil	15352031
C039281	furan	furan results in decreased expression of MSX2 mRNA	25539665
C577920	GSK126	GSK126 results in increased expression of MSX2 mRNA	26424790
C409722	hexaconazole	hexaconazole results in decreased expression of MSX2 mRNA	22045034
C492448	ICG 001	ICG 001 results in decreased expression of MSX2 mRNA	26191083
C561695	(+)-JQ1 compound	(+)-JQ1 compound results in increased expression of MSX2 mRNA	24796395
C008261	lead acetate	lead acetate results in decreased expression of MSX2 mRNA	22609695
C533894	LG 100815	LG 100815 results in decreased expression of MSX2 mRNA	16951191
D008070	Lipopolysaccharides	Lipopolysaccharides results in decreased expression of MSX2 mRNA	12057914
C025340	manganese chloride	manganese chloride results in decreased expression of MSX2 mRNA	28801915
D015122	Mercaptopurine	Mercaptopurine results in decreased expression of MSX2 mRNA	23358152
C042720	mercuric bromide	mercuric bromide results in increased expression of MSX2 mRNA	26272509
C042720	mercuric bromide	[NOG protein co-treated with mercuric bromide co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
D008701	Methapyrilene	Methapyrilene results in decreased methylation of MSX2 intron	30157460
C004925	methylmercuric chloride	methylmercuric chloride results in increased expression of MSX2 mRNA	23179753; 26272509; 28001369;
C004925	methylmercuric chloride	[NOG protein co-treated with methylmercuric chloride co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
D008777	Methyltestosterone	Methyltestosterone results in decreased expression of MSX2 mRNA	29191790
C500085	muraglitazar	muraglitazar results in increased expression of MSX2 mRNA	21515302
D037742	Nanotubes, Carbon	Nanotubes, Carbon analog affects the expression of MSX2 mRNA	21624382
C062198	octa-2,4,6-trienoic acid	octa-2,4,6-trienoic acid results in decreased expression of MSX2 mRNA	16951191
D010100	Oxygen	Oxygen deficiency results in decreased expression of MSX2 mRNA	24236059
D000077767	Panobinostat	[NOG protein co-treated with Panobinostat co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
D000077767	Panobinostat	Panobinostat results in increased expression of MSX2 mRNA	26272509
D020245	p-Chloromercuribenzoic Acid	[NOG protein co-treated with p-Chloromercuribenzoic Acid co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
D020245	p-Chloromercuribenzoic Acid	p-Chloromercuribenzoic Acid results in increased expression of MSX2 mRNA	26272509
C101814	perfluoro-n-undecanoic acid	perfluoro-n-undecanoic acid results in increased expression of MSX2 mRNA	23602845
D010662	Phenylmercuric Acetate	[NOG protein co-treated with Phenylmercuric Acetate co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
D010662	Phenylmercuric Acetate	Phenylmercuric Acetate results in increased expression of MSX2 mRNA	26272509
D059808	Polyphenols	[Polyphenols co-treated with Estradiol] results in decreased expression of MSX2 mRNA	30077407
D059808	Polyphenols	Polyphenols results in decreased expression of MSX2 mRNA	30077407
C013216	potassium phosphate	Fluorides inhibits the reaction [potassium phosphate results in increased expression of MSX2 mRNA]	24561004
C013216	potassium phosphate	potassium phosphate results in increased expression of MSX2 mRNA	24561004
D011374	Progesterone	[Estrogens co-treated with Progesterone] results in increased expression of MSX2 mRNA	17546050
D011374	Progesterone	Progesterone results in decreased expression of MSX2 mRNA	22238285
D011374	Progesterone	Progesterone results in increased expression of MSX2 mRNA	17546050
C009166	retinol acetate	retinol acetate results in increased expression of MSX2 mRNA	16772331
C513635	S-2-pentyl-4-pentynoic hydroxamic acid	S-2-pentyl-4-pentynoic hydroxamic acid results in increased expression of MSX2 mRNA	21427059
D012822	Silicon Dioxide	Silicon Dioxide analog results in increased expression of MSX2 mRNA	23806026
D000077210	Sunitinib	Sunitinib results in decreased expression of MSX2 mRNA	31533062
C087114	tebuconazole	tebuconazole results in decreased expression of MSX2 mRNA	30458266
C501413	tesaglitazar	tesaglitazar results in increased expression of MSX2 mRNA	21515302
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin affects the expression of MSX2 mRNA	24058054
D013749	Tetrachlorodibenzodioxin	[Tetrachlorodibenzodioxin co-treated with Ethinyl Estradiol] results in increased expression of MSX2 mRNA	17942748
D014212	Tretinoin	Tretinoin results in decreased expression of MSX2 mRNA	23724009
D014212	Tretinoin	Tretinoin results in increased expression of MSX2 mRNA	17138961; 21934132;
D014212	Tretinoin	Tretinoin results in increased expression of MSX2 mRNA	16604517
C032910	triadimefon	triadimefon results in decreased expression of MSX2 mRNA	21254369
C012589	trichostatin A	[NOG protein co-treated with trichostatin A co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
C012589	trichostatin A	trichostatin A results in increased expression of MSX2 mRNA	24935251; 26272509;
D000077288	Troglitazone	Troglitazone results in decreased expression of MSX2 mRNA	21515302
D014635	Valproic Acid	[NOG protein co-treated with Valproic Acid co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of MSX2 mRNA	27188386
D014635	Valproic Acid	Valproic Acid affects the expression of MSX2 mRNA	25979313
D014635	Valproic Acid	Valproic Acid results in decreased methylation of MSX2 gene	29154799
D014635	Valproic Acid	Valproic Acid results in increased expression of MSX2 mRNA	19101580; 23179753; 24383497; 24935251; 26272509; 27188386; 28001369;
D014635	Valproic Acid	Valproic Acid analog results in decreased expression of MSX2 mRNA	30578912
D014635	Valproic Acid	Valproic Acid results in decreased expression of MSX2 mRNA	22045034; 30578912;
D014635	Valproic Acid	Valproic Acid results in increased expression of MSX2 mRNA	19136453; 31445079;
D001335	Vehicle Emissions	Vehicle Emissions affects the methylation of MSX2 gene	25560391

Functional annotations

Keywords

Keyword ID	Keyword Term
KW-0989	Craniosynostosis
KW-0217	Developmental protein
KW-0225	Disease mutation
KW-0238	DNA-binding
KW-0371	Homeobox
KW-0539	Nucleus
KW-0892	Osteogenesis
KW-0621	Polymorphism
KW-1185	Reference proteome
KW-0678	Repressor
KW-0804	Transcription
KW-0805	Transcription regulation

Interpro

InterPro ID	InterPro Term
IPR009057	Homeobox-like_sf
IPR017970	Homeobox_CS
IPR001356	Homeobox_dom
IPR020479	Homeobox_metazoa

PROSITE

PROSITE ID	PROSITE Term
PS00027	HOMEOBOX_1
PS50071	HOMEOBOX_2

Pfam

Pfam ID	Pfam Term
PF00046	Homeodomain

Gene: MSX2

Basic information

Gene expression information

Gene expression in different tissues (GTEx V7)

Gene expression in different tissues (ENCODE)

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Identified variants/mutations related to cleft phenotype

Other genetic variants/mutations

Disease or phenotype associated information

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO:Biological Process

GO:Cellular Component

Reactome Pathway

Drugs and compounds information

Functional annotations

Keywords

Interpro

PROSITE

Pfam

Protein-protein interaction

Protein-miRNA interaction