CleftGeneDB-Search

Gene: VAX1

Basic information

Tag	Content
Uniprot ID	Q5SQQ9; B1AVW5; Q6ZSX0;
Entrez ID	11023
Genbank protein ID	AAI01695.1; EAW49433.1; AAI01697.1; BAC86826.1;
Genbank nucleotide ID	NM_199131.2; NM_001112704.1;
Ensembl protein ID	ENSP00000277905; ENSP00000358207;
Ensembl nucleotide ID	ENSG00000148704
Gene name	Ventral anterior homeobox 1
Gene symbol	VAX1
Organism	Homo sapiens
NCBI taxa ID	9606
Cleft type	CL/P
Developmental stage
Data sources	Manually collected
Reference	23463464; 26602496; 22095910;
Functional description	Transcription factor that may function in dorsoventral specification of the forebrain. Required for axon guidance and major tract formation in the developing forebrain. May contribute to the differentiation of the neuroretina, pigmented epithelium and optic stalk (By similarity).
Sequence	MFGKPDKMDV RCHSDAEAAR VSKNAHKESR ESKGAEGNLP AAFLKEPQGA FSASGAAEDC 60 NKSKSNSAAD PDYCRRILVR DAKGSIREII LPKGLDLDRP KRTRTSFTAE QLYRLEMEFQ 120 RCQYVVGRER TELARQLNLS ETQVKVWFQN RRTKQKKDQG KDSELRSVVS ETAATCSVLR 180 LLEQGRLLSP PGLPALLPPC ATGALGSALR GPSLPALGAG AAAGSAAAAA AAAPGPAGAA 240 SPHPPAVGGA PGPGPAGPGG LHAGAPAAGH SLFSLPVPSL LGSVASRLSS APLTMAGSLA 300 GNLQELSARY LSSSAFEPYS RTNNKEGAEK KALD 334

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	VAX1	486906	E2QUC0		Canis lupus familiaris	Prediction	More>>
1:1 ortholog	VAX1	102190017	A0A452DMM9		Capra hircus	Prediction	More>>
1:1 ortholog	VAX1	11023	Q5SQQ9	CL/P	Homo sapiens	Publication	More>>
1:1 ortholog	Vax1	22326	Q2NKI2	CPO	Mus musculus	Publication	More>>
1:1 ortholog	VAX1	740057	A0A2I3TJG6		Pan troglodytes	Prediction	More>>
1:1 ortholog	VAX1	100157019	F1S4S0		Sus scrofa	Prediction	More>>
1:1 ortholog	Vax1	64571	Q9JM00		Rattus norvegicus	Prediction	More>>
1:1 ortholog	vax1	373870	A0A0R4I9B5		Danio rerio	Prediction	More>>

Identified variants/mutations related to cleft phenotype

Gene symbol	Significant Variants/SNPS	Methods	PubMed ID
VAX1	c.453_454delinsAA; p.Arg152Ser	PCR; sequencing	22095910
VAX1	c.945C>T; p.Ala315Ala	PCR; sequencing	22095910
VAX1	rs4752028	Genotyping; direct sequencing; and TDT	23463464
VAX1	rs7078160	Genotyping; direct sequencing; and TDT	23463464
VAX1	rs14874160G>T	Genotyping; direct sequencing; and TDT	23463464
VAX1	c.898982>C	Genotyping; direct sequencing; and TDT	23463464
VAX1	rs148741605C>T	Genotyping; direct sequencing; and TDT	23463464
VAX1	c.840949G>A	Genotyping; direct sequencing; and TDT	23463464
VAX1	c.840439C>A	Genotyping; direct sequencing; and TDT	23463464
VAX1	c.897839C>T	Genotyping; direct sequencing; and TDT	23463464
VAX1	c.896171G>T	Genotyping; direct sequencing; and TDT	23463464
VAX1	c.896062T>G; p.M117R	Genotyping; direct sequencing; and TDT	23463464
VAX1	c.893947C>T	Genotyping; direct sequencing; and TDT	23463464
VAX1	c.893882G>T	Genotyping; direct sequencing; and TDT	23463464
VAX1	c.893824G>T; p.A233S	Genotyping; direct sequencing; and TDT	23463464
VAX1	rs7902527G>A	GWAS	31609978
VAX1	rs4752028T>C	GWAS	31609978
VAX1	rs4752028C>T	realtime-PCR	30633559
VAX1	rs7078160G>A (increasing risk)	realtime-PCR	30633559
VAX1	rs6585429A>G	GWAS	28232668
VAX1	rs7078160G>A (increasing risk)	SNPscan method and TDT	30048854
VAX1	rs7078160G>A (increasing risk)	PCR and Sanger sequencing	33132092
VAX1	rs7086344*T	Genotyping	26602496
VAX1	rs10886040	Genotyping and GWAS	27033726
VAX1	rs201128098	Genotyping and GWAS	27033726
VAX1	rs7072663	Genotyping and GWAS	27033726
VAX1	rs113339720	Genotyping and GWAS	27033726

Other genetic variants/mutations

ID	Variant	Type	Disease	Chromosome\Coordinate	Evidence
rs1407969897	p.Gly3Arg	missense variant	-	NC_000010.11:g.117138050C>T	TOPMed,gnomAD
rs1407969897	p.Gly3Arg	missense variant	-	NC_000010.11:g.117138050C>G	TOPMed,gnomAD
rs760200304	p.Pro5Leu	missense variant	-	NC_000010.11:g.117138043G>A	ExAC,gnomAD
rs369019203	p.Asp6Gly	missense variant	-	NC_000010.11:g.117138040T>C	ESP,ExAC,TOPMed,gnomAD
rs1028634962	p.Lys7Asn	missense variant	-	NC_000010.11:g.117138036T>A	TOPMed
NCI-TCGA novel	p.Asp9Val	missense variant	-	NC_000010.11:g.117138031T>A	NCI-TCGA
NCI-TCGA novel	p.Asp9Asn	missense variant	-	NC_000010.11:g.117138032C>T	NCI-TCGA
rs771996022	p.Val10Gly	missense variant	-	NC_000010.11:g.117138028A>C	ExAC,gnomAD
NCI-TCGA novel	p.Arg11Ter	stop gained	-	NC_000010.11:g.117138026G>A	NCI-TCGA
rs748062678	p.Arg11Gln	missense variant	-	NC_000010.11:g.117138025C>T	ExAC,gnomAD
rs1243275101	p.His13Leu	missense variant	-	NC_000010.11:g.117138019T>A	gnomAD
rs200217488	p.His13Gln	missense variant	-	NC_000010.11:g.117138018G>C	1000Genomes
rs372435563	p.Ser14Trp	missense variant	-	NC_000010.11:g.117138016G>C	ESP,TOPMed,gnomAD
rs372435563	p.Ser14Leu	missense variant	-	NC_000010.11:g.117138016G>A	ESP,TOPMed,gnomAD
rs768449638	p.Ala16Val	missense variant	-	NC_000010.11:g.117138010G>A	ExAC,TOPMed,gnomAD
rs1350198417	p.Ala16Thr	missense variant	-	NC_000010.11:g.117138011C>T	TOPMed
rs781390259	p.Glu17Gly	missense variant	-	NC_000010.11:g.117138007T>C	ExAC,TOPMed,gnomAD
rs1488626545	p.Glu17Lys	missense variant	-	NC_000010.11:g.117138008C>T	TOPMed
COSM1470301	p.Ala18Ser	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117138005C>A	NCI-TCGA Cosmic
COSM6064999	p.Ala19Gly	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117138001G>C	NCI-TCGA Cosmic
rs1363003041	p.Arg20Gln	missense variant	-	NC_000010.11:g.117137998C>T	TOPMed,gnomAD
rs757464020	p.Ser22Trp	missense variant	-	NC_000010.11:g.117137992G>C	ExAC,TOPMed,gnomAD
rs757464020	p.Ser22Leu	missense variant	-	NC_000010.11:g.117137992G>A	ExAC,TOPMed,gnomAD
NCI-TCGA novel	p.Lys23Asn	missense variant	-	NC_000010.11:g.117137988C>A	NCI-TCGA
rs1428776398	p.Ala25Pro	missense variant	-	NC_000010.11:g.117137984C>G	gnomAD
rs903654164	p.Ala25Val	missense variant	-	NC_000010.11:g.117137983G>A	TOPMed
NCI-TCGA novel	p.Lys27Asn	missense variant	-	NC_000010.11:g.117137976C>G	NCI-TCGA
rs376554237	p.Lys27Thr	missense variant	-	NC_000010.11:g.117137977T>G	ESP,ExAC,TOPMed,gnomAD
rs751640198	p.Lys27Glu	missense variant	-	NC_000010.11:g.117137978T>C	ExAC,gnomAD
rs376554237	p.Lys27Arg	missense variant	-	NC_000010.11:g.117137977T>C	ESP,ExAC,TOPMed,gnomAD
rs753261643	p.Glu28Gly	missense variant	-	NC_000010.11:g.117137974T>C	ExAC,gnomAD
rs759967956	p.Arg30Gln	missense variant	-	NC_000010.11:g.117137968C>T	ExAC,TOPMed,gnomAD
rs759967956	p.Arg30Leu	missense variant	-	NC_000010.11:g.117137968C>A	ExAC,TOPMed,gnomAD
rs759967956	p.Arg30Pro	missense variant	-	NC_000010.11:g.117137968C>G	ExAC,TOPMed,gnomAD
rs766031425	p.Glu31Lys	missense variant	-	NC_000010.11:g.117137966C>T	ExAC,TOPMed,gnomAD
rs766031425	p.Glu31Gln	missense variant	-	NC_000010.11:g.117137966C>G	ExAC,TOPMed,gnomAD
rs760266868	p.Gly34Asp	missense variant	-	NC_000010.11:g.117137956C>T	ExAC,gnomAD
rs760266868	p.Gly34Ala	missense variant	-	NC_000010.11:g.117137956C>G	ExAC,gnomAD
rs772737522	p.Ala35Thr	missense variant	-	NC_000010.11:g.117137954C>T	ExAC,gnomAD
COSM333504	p.Ala35Glu	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117137953G>T	NCI-TCGA Cosmic
rs369123910	p.Gly37Arg	missense variant	-	NC_000010.11:g.117137948C>T	ESP,ExAC,TOPMed,gnomAD
rs141168124	p.Pro40Arg	missense variant	-	NC_000010.11:g.117137938G>C	ESP,ExAC,TOPMed,gnomAD
rs141168124	p.Pro40Leu	missense variant	-	NC_000010.11:g.117137938G>A	ESP,ExAC,TOPMed,gnomAD
rs768646019	p.Ala41Gly	missense variant	-	NC_000010.11:g.117137935G>C	ExAC,TOPMed,gnomAD
rs938651186	p.Ala42Thr	missense variant	-	NC_000010.11:g.117137933C>T	NCI-TCGA Cosmic
rs938651186	p.Ala42Thr	missense variant	-	NC_000010.11:g.117137933C>T	TOPMed,gnomAD
rs938651186	p.Ala42Ser	missense variant	-	NC_000010.11:g.117137933C>A	TOPMed,gnomAD
rs771135577	p.Phe43Leu	missense variant	-	NC_000010.11:g.117137928G>T	ExAC,gnomAD
rs1250262155	p.Phe43Leu	missense variant	-	NC_000010.11:g.117137930A>G	TOPMed
rs1436374233	p.Leu44Phe	missense variant	-	NC_000010.11:g.117137927G>A	TOPMed
rs1179249319	p.Lys45Met	missense variant	-	NC_000010.11:g.117137923T>A	TOPMed
NCI-TCGA novel	p.Glu46Ter	stop gained	-	NC_000010.11:g.117137921C>A	NCI-TCGA
rs367560423	p.Glu46Lys	missense variant	-	NC_000010.11:g.117137921C>T	NCI-TCGA Cosmic
rs367560423	p.Glu46Lys	missense variant	-	NC_000010.11:g.117137921C>T	ESP,ExAC,TOPMed,gnomAD
rs367560423	p.Glu46Gln	missense variant	-	NC_000010.11:g.117137921C>G	ESP,ExAC,TOPMed,gnomAD
rs1302620952	p.Pro47Arg	missense variant	-	NC_000010.11:g.117137917G>C	gnomAD
rs1302620952	p.Pro47Gln	missense variant	-	NC_000010.11:g.117137917G>T	gnomAD
rs1462853173	p.Gln48His	missense variant	-	NC_000010.11:g.117137913C>G	gnomAD
rs1172446588	p.Gly49Asp	missense variant	-	NC_000010.11:g.117137911C>T	TOPMed
rs948925832	p.Ala53Pro	missense variant	-	NC_000010.11:g.117137900C>G	TOPMed
rs1427570227	p.Ala53Val	missense variant	-	NC_000010.11:g.117137899G>A	gnomAD
rs948925832	p.Ala53Thr	missense variant	-	NC_000010.11:g.117137900C>T	TOPMed
rs752885506	p.Ser54Leu	missense variant	-	NC_000010.11:g.117137896G>A	ExAC,gnomAD
rs755587809	p.Gly55Asp	missense variant	-	NC_000010.11:g.117137893C>T	ExAC,gnomAD
rs754203695	p.Ala56Ser	missense variant	-	NC_000010.11:g.117137891C>A	ExAC,TOPMed,gnomAD
rs754203695	p.Ala56Pro	missense variant	-	NC_000010.11:g.117137891C>G	ExAC,TOPMed,gnomAD
rs1196124925	p.Ala57Thr	missense variant	-	NC_000010.11:g.117137888C>T	gnomAD
rs1202619825	p.Asp59Gly	missense variant	-	NC_000010.11:g.117137881T>C	NCI-TCGA
rs1249422578	p.Asp59Asn	missense variant	-	NC_000010.11:g.117137882C>T	NCI-TCGA
rs1249422578	p.Asp59Asn	missense variant	-	NC_000010.11:g.117137882C>T	TOPMed,gnomAD
rs1202619825	p.Asp59Ala	missense variant	-	NC_000010.11:g.117137881T>G	gnomAD
rs1202619825	p.Asp59Gly	missense variant	-	NC_000010.11:g.117137881T>C	gnomAD
rs760308688	p.Cys60Ser	missense variant	-	NC_000010.11:g.117137878C>G	ExAC,TOPMed,gnomAD
rs760308688	p.Cys60Phe	missense variant	-	NC_000010.11:g.117137878C>A	ExAC,TOPMed,gnomAD
NCI-TCGA novel	p.Asn61Lys	missense variant	-	NC_000010.11:g.117137874G>C	NCI-TCGA
rs973817780	p.Ser63Asn	missense variant	-	NC_000010.11:g.117137869C>T	TOPMed
rs1004005013	p.Asn66Ser	missense variant	-	NC_000010.11:g.117137860T>C	TOPMed,gnomAD
rs750057346	p.Ser67Tyr	missense variant	-	NC_000010.11:g.117137857G>T	ExAC,TOPMed,gnomAD
rs750057346	p.Ser67Phe	missense variant	-	NC_000010.11:g.117137857G>A	ExAC,TOPMed,gnomAD
rs1239668375	p.Ala68Thr	missense variant	-	NC_000010.11:g.117137855C>T	TOPMed
rs767256510	p.Ala68Val	missense variant	-	NC_000010.11:g.117137854G>A	ExAC,gnomAD
rs767256510	p.Ala68Glu	missense variant	-	NC_000010.11:g.117137854G>T	ExAC,gnomAD
rs1027165059	p.Ala69Gly	missense variant	-	NC_000010.11:g.117137851G>C	gnomAD
rs1027165059	p.Ala69Glu	missense variant	-	NC_000010.11:g.117137851G>T	gnomAD
rs773894040	p.Asp70Glu	missense variant	-	NC_000010.11:g.117137847G>C	ExAC,TOPMed,gnomAD
rs773894040	p.Asp70Glu	missense variant	-	NC_000010.11:g.117137847G>T	ExAC,TOPMed,gnomAD
rs1428704285	p.Pro71Leu	missense variant	-	NC_000010.11:g.117137845G>A	gnomAD
NCI-TCGA novel	p.Asp72Tyr	missense variant	-	NC_000010.11:g.117137843C>A	NCI-TCGA
rs1422260776	p.Asp72Glu	missense variant	-	NC_000010.11:g.117137841A>T	gnomAD
rs143954756	p.Asp72Asn	missense variant	-	NC_000010.11:g.117137843C>T	ESP,ExAC,TOPMed,gnomAD
rs1164914533	p.Asp72Ala	missense variant	-	NC_000010.11:g.117137842T>G	gnomAD
rs1372402560	p.Arg75Cys	missense variant	-	NC_000010.11:g.117137834G>A	TOPMed
rs1420816659	p.Arg76Gln	missense variant	-	NC_000010.11:g.117137830C>T	TOPMed,gnomAD
rs762901857	p.Arg76Gly	missense variant	-	NC_000010.11:g.117137831G>C	ExAC,gnomAD
rs1420816659	p.Arg76Leu	missense variant	-	NC_000010.11:g.117137830C>A	TOPMed,gnomAD
NCI-TCGA novel	p.Leu78Met	missense variant	-	NC_000010.11:g.117137825G>T	NCI-TCGA
rs536410336	p.Val79Ala	missense variant	-	NC_000010.11:g.117137821A>G	1000Genomes,ExAC,gnomAD
rs536410336	p.Val79Gly	missense variant	-	NC_000010.11:g.117137821A>C	1000Genomes,ExAC,gnomAD
rs1176473736	p.Arg80Gln	missense variant	-	NC_000010.11:g.117137818C>T	TOPMed,gnomAD
rs1176473736	p.Arg80Leu	missense variant	-	NC_000010.11:g.117137818C>A	TOPMed,gnomAD
rs1482844157	p.Asp81Asn	missense variant	-	NC_000010.11:g.117137816C>T	gnomAD
NCI-TCGA novel	p.Gly84Val	missense variant	-	NC_000010.11:g.117136650C>A	NCI-TCGA
NCI-TCGA novel	p.Gly84Arg	missense variant	-	NC_000010.11:g.117136651C>T	NCI-TCGA
COSM4011980	p.Gly84Trp	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117136651C>A	NCI-TCGA Cosmic
NCI-TCGA novel	p.Ser85ValPheSerTerUnkUnk	frameshift	-	NC_000010.11:g.117136648_117136649insC	NCI-TCGA
rs765279998	p.Ser85Phe	missense variant	-	NC_000010.11:g.117136647G>A	ExAC,TOPMed,gnomAD
rs1259528166	p.Ile86Thr	missense variant	-	NC_000010.11:g.117136644A>G	gnomAD
rs776532808	p.Arg87Gln	missense variant	-	NC_000010.11:g.117136641C>T	ExAC,gnomAD
rs759249350	p.Arg87Ter	stop gained	-	NC_000010.11:g.117136642G>A	ExAC,gnomAD
rs1285594976	p.Ile89Leu	missense variant	-	NC_000010.11:g.117136636T>G	gnomAD
rs1330216367	p.Lys93Asn	missense variant	-	NC_000010.11:g.117136622C>G	gnomAD
NCI-TCGA novel	p.Gly94Ser	missense variant	-	NC_000010.11:g.117136621C>T	NCI-TCGA
COSM4011978	p.Leu95Met	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117136618G>T	NCI-TCGA Cosmic
COSM1139334	p.Arg99Leu	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117136605C>A	NCI-TCGA Cosmic
COSM1584778	p.Arg99Gln	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117136605C>T	NCI-TCGA Cosmic
COSM6065001	p.Arg99Trp	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117136606G>A	NCI-TCGA Cosmic
NCI-TCGA novel	p.Lys101Thr	missense variant	-	NC_000010.11:g.117136599T>G	NCI-TCGA
rs1431071024	p.Lys101Arg	missense variant	-	NC_000010.11:g.117136599T>C	gnomAD
rs371683596	p.Thr103Met	missense variant	-	NC_000010.11:g.117136593G>A	NCI-TCGA,NCI-TCGA Cosmic
rs371683596	p.Thr103Met	missense variant	-	NC_000010.11:g.117136593G>A	ESP,ExAC,TOPMed,gnomAD
rs371683596	p.Thr103Lys	missense variant	-	NC_000010.11:g.117136593G>T	ESP,ExAC,TOPMed,gnomAD
rs749442766	p.Arg104Pro	missense variant	-	NC_000010.11:g.117136590C>G	ExAC,gnomAD
COSM2054986	p.Arg104His	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117136590C>T	NCI-TCGA Cosmic
rs1233582980	p.Thr105Met	missense variant	-	NC_000010.11:g.117136587G>A	gnomAD
RCV000551421	p.Thr105Ter	frameshift	Microphthalmia, syndromic 11 (MCOPS11)	NC_000010.11:g.117136589dup	ClinVar
rs1377337113	p.Ala109Val	missense variant	-	NC_000010.11:g.117136575G>A	gnomAD
NCI-TCGA novel	p.Glu110Ter	stop gained	-	NC_000010.11:g.117136573C>A	NCI-TCGA
COSM4917957	p.Gln111His	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117136568C>G	NCI-TCGA Cosmic
rs746198450	p.Leu112Phe	missense variant	-	NC_000010.11:g.117136567G>A	ExAC,gnomAD
rs202102160	p.Glu116Gly	missense variant	-	NC_000010.11:g.117136554T>C	ExAC,gnomAD
rs763540517	p.Met117Arg	missense variant	-	NC_000010.11:g.117136551A>C	ExAC,gnomAD
rs751218017	p.Met117Leu	missense variant	-	NC_000010.11:g.117136552T>A	ExAC,gnomAD
rs1202233356	p.Met117Ile	missense variant	-	NC_000010.11:g.117136550C>T	gnomAD
rs763540517	p.Met117Thr	missense variant	-	NC_000010.11:g.117136551A>G	ExAC,gnomAD
rs1343825025	p.Glu118Val	missense variant	-	NC_000010.11:g.117136548T>A	gnomAD
rs752322155	p.Arg121His	missense variant	-	NC_000010.11:g.117136539C>T	ExAC,gnomAD
rs547581837	p.Arg121Cys	missense variant	-	NC_000010.11:g.117136540G>A	1000Genomes,ExAC,gnomAD
rs752322155	p.Arg121Pro	missense variant	-	NC_000010.11:g.117136539C>G	ExAC,gnomAD
rs547581837	p.Arg121Cys	missense variant	-	NC_000010.11:g.117136540G>A	NCI-TCGA,NCI-TCGA Cosmic
rs1296235144	p.Cys122Arg	missense variant	-	NC_000010.11:g.117136537A>G	gnomAD
rs1421106668	p.Cys122Phe	missense variant	-	NC_000010.11:g.117136536C>A	TOPMed
rs765056555	p.Tyr124Ter	stop gained	-	NC_000010.11:g.117136529G>T	ExAC,gnomAD
COSM3414726	p.Val125Met	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117136528C>T	NCI-TCGA Cosmic
rs766278617	p.Val126Ala	missense variant	-	NC_000010.11:g.117136524A>G	ExAC,TOPMed,gnomAD
COSM6128386	p.Arg128Leu	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117136518C>A	NCI-TCGA Cosmic
COSM3686521	p.Arg128His	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117136518C>T	NCI-TCGA Cosmic
rs1325502393	p.Thr131Ser	missense variant	-	NC_000010.11:g.117136509G>C	TOPMed
rs762065524	p.Glu132Gln	missense variant	-	NC_000010.11:g.117136507C>G	ExAC,gnomAD
rs762065524	p.Glu132Lys	missense variant	-	NC_000010.11:g.117136507C>T	ExAC,gnomAD
rs1282134900	p.Leu133Ile	missense variant	-	NC_000010.11:g.117136504G>T	gnomAD
COSM4740214	p.Ala134Thr	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117136501C>T	NCI-TCGA Cosmic
rs143950742	p.Arg135Trp	missense variant	-	NC_000010.11:g.117136498G>A	ESP,TOPMed
rs143950742	p.Arg135Trp	missense variant	-	NC_000010.11:g.117136498G>A	NCI-TCGA,NCI-TCGA Cosmic
rs906191563	p.Arg135Gln	missense variant	-	NC_000010.11:g.117136497C>T	TOPMed,gnomAD
NCI-TCGA novel	p.Leu137Ile	missense variant	-	NC_000010.11:g.117136492G>T	NCI-TCGA
rs762909313	p.Ser140Pro	missense variant	-	NC_000010.11:g.117136483A>G	ExAC,gnomAD
NCI-TCGA novel	p.Glu141Lys	missense variant	-	NC_000010.11:g.117136480C>T	NCI-TCGA
rs1185828769	p.Glu141Asp	missense variant	-	NC_000010.11:g.117136478C>G	TOPMed,gnomAD
rs770153633	p.Thr142Ile	missense variant	-	NC_000010.11:g.117136476G>A	ExAC,gnomAD
rs387907252	p.Arg152Ser	missense variant	Microphthalmia, syndromic 11 (mcops11)	NC_000010.11:g.117134559G>T	-
rs387907252	p.Arg152Ser	missense variant	Microphthalmia, syndromic, 11 (MCOPS11)	NC_000010.11:g.117134559G>T	UniProt,dbSNP
VAR_067307	p.Arg152Ser	missense variant	Microphthalmia, syndromic, 11 (MCOPS11)	NC_000010.11:g.117134559G>T	UniProt
RCV000030635	p.Arg152Ser	missense variant	Microphthalmia, syndromic 11 (MCOPS11)	NC_000010.11:g.117134559G>T	ClinVar
rs759903028	p.Lys157Arg	missense variant	-	NC_000010.11:g.117134543T>C	ExAC,gnomAD
rs777113215	p.Gly160Asp	missense variant	-	NC_000010.11:g.117134534C>T	ExAC,gnomAD
rs1314934842	p.Asp162Asn	missense variant	-	NC_000010.11:g.117134529C>T	TOPMed
rs771498158	p.Ser163Leu	missense variant	-	NC_000010.11:g.117134525G>A	ExAC,TOPMed,gnomAD
rs1220259234	p.Glu164Lys	missense variant	-	NC_000010.11:g.117134523C>T	gnomAD
rs1214575426	p.Glu171Gln	missense variant	-	NC_000010.11:g.117134502C>G	TOPMed
rs1465836213	p.Leu179Pro	missense variant	-	NC_000010.11:g.117134477A>G	TOPMed
rs1370078092	p.Arg180Trp	missense variant	-	NC_000010.11:g.117134475G>A	TOPMed,gnomAD
rs377184623	p.Leu181Met	missense variant	-	NC_000010.11:g.117134472G>T	TOPMed,gnomAD
rs373002811	p.Glu183Ala	missense variant	-	NC_000010.11:g.117134465T>G	TOPMed
rs200538721	p.Gly185Asp	missense variant	-	NC_000010.11:g.117134459C>T	TOPMed
rs778224173	p.Arg186Cys	missense variant	-	NC_000010.11:g.117134457G>A	ExAC,gnomAD
rs754493198	p.Leu188Phe	missense variant	-	NC_000010.11:g.117134449C>A	ExAC,gnomAD
rs1177682517	p.Ser189Leu	missense variant	-	NC_000010.11:g.117134447G>A	gnomAD
rs1481203437	p.Pro190Ser	missense variant	-	NC_000010.11:g.117134445G>A	gnomAD
rs1190088030	p.Gly192Ser	missense variant	-	NC_000010.11:g.117134439C>T	gnomAD
rs1482796493	p.Ala195Glu	missense variant	-	NC_000010.11:g.117134429G>T	gnomAD
rs993656136	p.Pro199Leu	missense variant	-	NC_000010.11:g.117134417G>A	TOPMed
rs200933454	p.Ala201Thr	missense variant	-	NC_000010.11:g.117134412C>T	TOPMed,gnomAD
rs1263514983	p.Thr202Arg	missense variant	-	NC_000010.11:g.117134408G>C	TOPMed,gnomAD
rs1263514983	p.Thr202Met	missense variant	-	NC_000010.11:g.117134408G>A	TOPMed,gnomAD
rs1314135592	p.Gly203Asp	missense variant	-	NC_000010.11:g.117134405C>T	TOPMed,gnomAD
rs1205383057	p.Gly203Arg	missense variant	-	NC_000010.11:g.117134406C>G	TOPMed,gnomAD
rs1205383057	p.Gly203Ser	missense variant	-	NC_000010.11:g.117134406C>T	TOPMed,gnomAD
rs1314135592	p.Gly203Ala	missense variant	-	NC_000010.11:g.117134405C>G	TOPMed,gnomAD
rs1040112444	p.Leu205Val	missense variant	-	NC_000010.11:g.117134400G>C	TOPMed,gnomAD
rs1362686438	p.Leu205Pro	missense variant	-	NC_000010.11:g.117134399A>G	gnomAD
rs1299927974	p.Gly206Asp	missense variant	-	NC_000010.11:g.117134396C>T	gnomAD
rs1281672094	p.Gly206Arg	missense variant	-	NC_000010.11:g.117134397C>G	TOPMed
rs1433517337	p.Ser207Pro	missense variant	-	NC_000010.11:g.117134394A>G	gnomAD
rs1337775304	p.Ala208Ser	missense variant	-	NC_000010.11:g.117134391C>A	gnomAD
rs1241921077	p.Leu209Gln	missense variant	-	NC_000010.11:g.117134387A>T	TOPMed
rs1237879004	p.Gly211Arg	missense variant	-	NC_000010.11:g.117134382C>G	TOPMed
rs780107711	p.Pro212Ser	missense variant	-	NC_000010.11:g.117134379G>A	ExAC,TOPMed,gnomAD
rs780107711	p.Pro212Thr	missense variant	-	NC_000010.11:g.117134379G>T	ExAC,TOPMed,gnomAD
rs1157104990	p.Ser213Thr	missense variant	-	NC_000010.11:g.117134375C>G	TOPMed
rs1420943430	p.Pro215Gln	missense variant	-	NC_000010.11:g.117134369G>T	TOPMed,gnomAD
rs977663663	p.Ser225Leu	missense variant	-	NC_000010.11:g.117134339G>A	TOPMed
rs1390036718	p.Ala227Val	missense variant	-	NC_000010.11:g.117134333G>A	TOPMed,gnomAD
rs1261998507	p.Ala228Ser	missense variant	-	NC_000010.11:g.117134331C>A	TOPMed
rs1261998507	p.Ala228Thr	missense variant	-	NC_000010.11:g.117134331C>T	TOPMed
rs571879048	p.Ala230Thr	missense variant	-	NC_000010.11:g.117134325C>T	1000Genomes,ExAC,TOPMed,gnomAD
rs1253636317	p.Ala231Thr	missense variant	-	NC_000010.11:g.117134322C>T	TOPMed
rs1253636317	p.Ala231Ser	missense variant	-	NC_000010.11:g.117134322C>A	TOPMed
rs1467628874	p.Ala232Val	missense variant	-	NC_000010.11:g.117134318G>A	TOPMed
rs1427337241	p.Ala232Ser	missense variant	-	NC_000010.11:g.117134319C>A	TOPMed
RCV000732163	p.Ala232Ser	missense variant	-	NC_000010.11:g.117134319C>A	ClinVar
rs1173735611	p.Ala233Ser	missense variant	-	NC_000010.11:g.117134316C>A	TOPMed
rs1165722579	p.Pro234Arg	missense variant	-	NC_000010.11:g.117134312G>C	TOPMed,gnomAD
rs1165722579	p.Pro234Leu	missense variant	-	NC_000010.11:g.117134312G>A	TOPMed,gnomAD
RCV000177118	p.Ala239Ser	missense variant	-	NC_000010.11:g.117134298C>A	ClinVar
rs794727490	p.Ala239Ser	missense variant	-	NC_000010.11:g.117134298C>A	TOPMed,gnomAD
rs794727490	p.Ala239Thr	missense variant	-	NC_000010.11:g.117134298C>T	TOPMed,gnomAD
rs994080192	p.Pro242Arg	missense variant	-	NC_000010.11:g.117134288G>C	TOPMed
rs1483245112	p.Pro245Leu	missense variant	-	NC_000010.11:g.117134279G>A	TOPMed
rs1267022885	p.Ala246Val	missense variant	-	NC_000010.11:g.117134276G>A	TOPMed
rs1199681849	p.Ala250Gly	missense variant	-	NC_000010.11:g.117134264G>C	TOPMed
rs1482127577	p.Pro251Leu	missense variant	-	NC_000010.11:g.117134261G>A	gnomAD
rs897985454	p.Gly252Arg	missense variant	-	NC_000010.11:g.117134259C>G	TOPMed,gnomAD
rs897985454	p.Gly252Cys	missense variant	-	NC_000010.11:g.117134259C>A	TOPMed,gnomAD
rs1206822958	p.Pro253Ala	missense variant	-	NC_000010.11:g.117134256G>C	gnomAD
rs1469409574	p.Gly254Glu	missense variant	-	NC_000010.11:g.117134252C>T	gnomAD
rs1209604989	p.Gly254Arg	missense variant	-	NC_000010.11:g.117134253C>T	gnomAD
rs1371607210	p.Pro255Leu	missense variant	-	NC_000010.11:g.117134249G>A	TOPMed
rs1308374977	p.Ala256Thr	missense variant	-	NC_000010.11:g.117134247C>T	gnomAD
rs1276844540	p.Ala256Asp	missense variant	-	NC_000010.11:g.117134246G>T	gnomAD
rs1008630883	p.Gly260Glu	missense variant	-	NC_000010.11:g.117134234C>T	TOPMed,gnomAD
rs1008630883	p.Gly260Val	missense variant	-	NC_000010.11:g.117134234C>A	TOPMed,gnomAD
rs1226333548	p.Gly260Arg	missense variant	-	NC_000010.11:g.117134235C>T	gnomAD
rs1050099504	p.Leu261Ser	missense variant	-	NC_000010.11:g.117134231A>G	TOPMed
rs1365060185	p.His262Asp	missense variant	-	NC_000010.11:g.117134229G>C	TOPMed,gnomAD
rs1365060185	p.His262Tyr	missense variant	-	NC_000010.11:g.117134229G>A	TOPMed,gnomAD
rs1243574513	p.Ala263Val	missense variant	-	NC_000010.11:g.117134225G>A	TOPMed,gnomAD
rs1316294546	p.Ala263Thr	missense variant	-	NC_000010.11:g.117134226C>T	TOPMed,gnomAD
rs1377353359	p.Gly264Ser	missense variant	-	NC_000010.11:g.117134223C>T	TOPMed,gnomAD
rs758484978	p.Ala265Thr	missense variant	-	NC_000010.11:g.117134220C>T	ExAC,gnomAD
rs1372077016	p.Pro266Ser	missense variant	-	NC_000010.11:g.117134217G>A	TOPMed,gnomAD
rs1372077016	p.Pro266Ala	missense variant	-	NC_000010.11:g.117134217G>C	TOPMed,gnomAD
rs935643016	p.Pro266Arg	missense variant	-	NC_000010.11:g.117134216G>C	TOPMed,gnomAD
rs1445331705	p.Ala268Val	missense variant	-	NC_000010.11:g.117134210G>A	TOPMed
rs1385340882	p.Gly269Ser	missense variant	-	NC_000010.11:g.117134208C>T	gnomAD
rs1255216202	p.Ser274Thr	missense variant	-	NC_000010.11:g.117134192C>G	gnomAD
rs1177625367	p.Ser274Arg	missense variant	-	NC_000010.11:g.117134191G>T	gnomAD
rs1320456609	p.Pro276Ser	missense variant	-	NC_000010.11:g.117134187G>A	TOPMed,gnomAD
rs1254291057	p.Val277Met	missense variant	-	NC_000010.11:g.117134184C>T	TOPMed,gnomAD
rs1203315887	p.Pro278Leu	missense variant	-	NC_000010.11:g.117134180G>A	TOPMed,gnomAD
rs1203315887	p.Pro278His	missense variant	-	NC_000010.11:g.117134180G>T	TOPMed,gnomAD
rs1292605878	p.Ser279Leu	missense variant	-	NC_000010.11:g.117134177G>A	gnomAD
rs752978368	p.Gly282Arg	missense variant	-	NC_000010.11:g.117134169C>G	ExAC,TOPMed,gnomAD
rs1352750213	p.Ser283Tyr	missense variant	-	NC_000010.11:g.117134165G>T	gnomAD
rs1352750213	p.Ser283Cys	missense variant	-	NC_000010.11:g.117134165G>C	gnomAD
rs765435813	p.Ser283Pro	missense variant	-	NC_000010.11:g.117134166A>G	ExAC,TOPMed,gnomAD
rs1312685600	p.Ala285Gly	missense variant	-	NC_000010.11:g.117134159G>C	TOPMed
rs1305745454	p.Ser286Gly	missense variant	-	NC_000010.11:g.117134157T>C	gnomAD
NCI-TCGA novel	p.Arg287Ser	missense variant	-	NC_000010.11:g.117134154G>T	NCI-TCGA
rs1408856424	p.Arg287Leu	missense variant	-	NC_000010.11:g.117134153C>A	gnomAD
NCI-TCGA novel	p.Ala291Thr	missense variant	-	NC_000010.11:g.117134142C>T	NCI-TCGA
rs1456321270	p.Pro292Ser	missense variant	-	NC_000010.11:g.117134139G>A	gnomAD
rs917061935	p.Pro292Arg	missense variant	-	NC_000010.11:g.117134138G>C	TOPMed,gnomAD
rs1159520457	p.Thr294Ala	missense variant	-	NC_000010.11:g.117134133T>C	gnomAD
RCV000177117	p.Met295Val	missense variant	-	NC_000010.11:g.117134130T>C	ClinVar
rs1348710977	p.Met295Thr	missense variant	-	NC_000010.11:g.117134129A>G	TOPMed
rs794727489	p.Met295Val	missense variant	-	NC_000010.11:g.117134130T>C	TOPMed,gnomAD
rs1210672677	p.Ala296Thr	missense variant	-	NC_000010.11:g.117134127C>T	TOPMed
rs939451478	p.Gly297Ala	missense variant	-	NC_000010.11:g.117134123C>G	TOPMed
rs1180211093	p.Ala300Val	missense variant	-	NC_000010.11:g.117134114G>A	gnomAD
rs1482853490	p.Gly301Glu	missense variant	-	NC_000010.11:g.117134111C>T	gnomAD
rs1172184635	p.Gly301Arg	missense variant	-	NC_000010.11:g.117134112C>T	gnomAD
COSM1584780	p.Glu305Ter	stop gained	Variant assessed as Somatic; HIGH impact.	NC_000010.11:g.117134100C>A	NCI-TCGA Cosmic
rs1424742433	p.Leu306Phe	missense variant	-	NC_000010.11:g.117134097G>A	TOPMed
rs1006865637	p.Ser307Ala	missense variant	-	NC_000010.11:g.117134094A>C	TOPMed,gnomAD
rs1487773914	p.Ala308Pro	missense variant	-	NC_000010.11:g.117134091C>G	gnomAD
rs1028355406	p.Arg309Gln	missense variant	-	NC_000010.11:g.117134087C>T	TOPMed,gnomAD
rs1451874313	p.Ser314Leu	missense variant	-	NC_000010.11:g.117134072G>A	TOPMed
rs1286856217	p.Tyr319Ter	stop gained	-	NC_000010.11:g.117134056G>C	gnomAD
rs1345819807	p.Thr322Ser	missense variant	-	NC_000010.11:g.117134048G>C	gnomAD
rs773495703	p.Glu326Asp	missense variant	-	NC_000010.11:g.117134035T>G	ExAC,TOPMed,gnomAD
NCI-TCGA novel	p.Glu329Lys	missense variant	-	NC_000010.11:g.117134028C>T	NCI-TCGA
rs1268886309	p.Lys330Glu	missense variant	-	NC_000010.11:g.117134025T>C	TOPMed
RCV000535598	p.Ala332Ter	frameshift	Microphthalmia, syndromic 11 (MCOPS11)	NC_000010.11:g.117134025dup	ClinVar
COSM915229	p.Ala332Val	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000010.11:g.117134018G>A	NCI-TCGA Cosmic
rs1384605148	p.Leu333Met	missense variant	-	NC_000010.11:g.117134016G>T	gnomAD
rs1389423932	p.Ter335Trp	stop lost	-	NC_000010.11:g.117134008T>C	gnomAD

Disease or phenotype associated information

Disease ID	Disease Name	Disease Type	Source
C0001418	Adenocarcinoma	group	BEFREE
C0003119	Anophthalmos	disease	BEFREE
C0005684	Malignant neoplasm of urinary bladder	disease	BEFREE
C0005695	Bladder Neoplasm	group	BEFREE
C0007137	Squamous cell carcinoma	disease	BEFREE
C0008924	Cleft upper lip	disease	GWASCAT;HPO
C0026010	Microphthalmos	disease	BEFREE;HPO
C0175754	Agenesis of corpus callosum	disease	BEFREE;HPO
C0338503	Septo-Optic Dysplasia	disease	BEFREE
C0557874	Global developmental delay	disease	HPO
C0699885	Carcinoma of bladder	disease	BEFREE
C0810364	Cleft Lip with or without Cleft Palate	disease	BEFREE
C1864897	Cognitive delay	phenotype	HPO
C2981150	Uranostaphyloschisis	disease	HPO
C3553077	MICROPHTHALMIA, SYNDROMIC 11	disease	CLINVAR;CTD_human;UNIPROT
C3553078	Agenesis of pineal gland	phenotype	HPO
C4020875	Mental and motor retardation	phenotype	HPO
C4280625	Decreased size of eyeball	phenotype	HPO
C4280808	Abnormally small eyeball	phenotype	HPO

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID	GO Term	Evidence
GO:0000978	RNA polymerase II cis-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:0001162	RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding	IBA
GO:0001227	DNA-binding transcription repressor activity, RNA polymerase II-specific	IBA
GO:0031490	chromatin DNA binding	IEA

GO:Biological Process

GO ID	GO Term	Evidence
GO:0000122	negative regulation of transcription by RNA polymerase II	IEA
GO:0001764	neuron migration	IEA
GO:0006357	regulation of transcription by RNA polymerase II	IBA
GO:0007406	negative regulation of neuroblast proliferation	IEA
GO:0007411	axon guidance	IEA
GO:0007417	central nervous system development	IBA
GO:0007420	brain development	IEA
GO:0030182	neuron differentiation	IBA
GO:0035914	skeletal muscle cell differentiation	IEA
GO:0043010	camera-type eye development	IEA
GO:0060021	roof of mouth development	IEA

GO:Cellular Component

GO ID	GO Term	Evidence
GO:0000790	nuclear chromatin	ISA
GO:0005634	nucleus	IBA

Reactome Pathway

Reactome ID	Reactome Term	Evidence

Drugs and compounds information

ID	Drug Name	Action	PubMed
D000643	Ammonium Chloride	Ammonium Chloride affects the expression of VAX1 mRNA	16483693
C006780	bisphenol A	bisphenol A affects the methylation of VAX1 promoter	27334623
C006780	bisphenol A	bisphenol A results in decreased expression of VAX1 mRNA	25181051
C018475	butyraldehyde	butyraldehyde results in increased expression of VAX1 mRNA	26079696
D002794	Choline	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in increased methylation of VAX1 gene	20938992
D003300	Copper	Copper deficiency results in increased expression of VAX1 mRNA	26033743
D000077209	Decitabine	Decitabine results in decreased expression of VAX1 mRNA	27915011
D019422	Dietary Sucrose	Dietary Sucrose results in increased expression of VAX1 mRNA	26033743
D017313	Fenretinide	Fenretinide results in decreased expression of VAX1 mRNA	28973697
D005419	Flavonoids	Flavonoids results in increased expression of VAX1 mRNA	18035473
D005492	Folic Acid	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in increased methylation of VAX1 gene	20938992
C561695	(+)-JQ1 compound	(+)-JQ1 compound results in decreased expression of VAX1 mRNA	24796395
D008694	Methamphetamine	Methamphetamine results in increased expression of VAX1 mRNA	29802913
D008715	Methionine	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in increased methylation of VAX1 gene	20938992
D010936	Plant Extracts	Plant Extracts results in decreased expression of VAX1 mRNA	23557933
D011192	Potassium Dichromate	Potassium Dichromate results in decreased expression of VAX1 mRNA	23608068
D011441	Propylthiouracil	Propylthiouracil results in decreased expression of VAX1 mRNA	24780913
C020806	tetrabromobisphenol A	tetrabromobisphenol A results in increased expression of VAX1 mRNA	31326446
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin affects the expression of VAX1 mRNA	24058054

Functional annotations

Keywords

Keyword ID	Keyword Term
KW-0025	Alternative splicing
KW-0217	Developmental protein
KW-0225	Disease mutation
KW-0238	DNA-binding
KW-0371	Homeobox
KW-1013	Microphthalmia
KW-0539	Nucleus
KW-1185	Reference proteome
KW-0804	Transcription
KW-0805	Transcription regulation

Interpro

InterPro ID	InterPro Term
IPR009057	Homeobox-like_sf
IPR017970	Homeobox_CS
IPR001356	Homeobox_dom
IPR000047	HTH_motif
IPR033020	Vax1

PROSITE

PROSITE ID	PROSITE Term
PS00027	HOMEOBOX_1
PS50071	HOMEOBOX_2

Pfam

Pfam ID	Pfam Term
PF00046	Homeodomain

Gene: VAX1

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-miRNA interaction