CleftGeneDB-Search

Gene: LHX6

Basic information

Tag	Content
Uniprot ID	Q9UPM6; A6PVQ1; A6PVQ2; A8K1B2; B7Z4D0; H0YN76; Q5T7S7; Q5T7S8; Q9NTK3; Q9UPM5;
Entrez ID	26468
Genbank protein ID	BAH12516.1; BAF82516.1; BAG36544.1; BAH13108.1; BAA83422.1; CAB66505.1; AAI03937.1; AAI03938.1; EAW87516.1; EAW87515.1; BAA83423.1;
Genbank nucleotide ID	NM_001242333.1; NM_014368.4; NM_199160.3; NM_001348190.1; NM_001242335.1; NM_001242334.1;
Ensembl protein ID	ENSP00000340137; ENSP00000362860; ENSP00000362859; ENSP00000475927; ENSP00000377854; ENSP00000441464;
Ensembl nucleotide ID	ENSG00000106852
Gene name	LIM/homeobox protein Lhx6
Gene symbol	LHX6
Organism	Homo sapiens
NCBI taxa ID	9606
Cleft type
Developmental stage
Data sources	Homology search
Reference
Functional description	Probable transcription factor required for the expression of a subset of genes involved in interneurons migration and development. Functions in the specification of cortical interneuron subtypes and in the migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex (By similarity).
Sequence	MAQPGSGCKA TTRCLEGTAP PAMAQSDAEA LAGALDKDEG QASPCTPSTP SVCSPPSAAS 60 SVPSAGKNIC SSCGLEILDR YLLKVNNLIW HVRCLECSVC RTSLRQQNSC YIKNKEIFCK 120 MDYFSRFGTK CARCGRQIYA SDWVRRARGN AYHLACFACF SCKRQLSTGE EFGLVEEKVL 180 CRIHYDTMIE NLKRAAENGN GLTLEGAVPS EQDSQPKPAK RARTSFTAEQ LQVMQAQFAQ 240 DNNPDAQTLQ KLADMTGLSR RVIQVWFQNC RARHKKHTPQ HPVPPSGAPP SRLPSALSDD 300 IHYTPFSSPE RARMVTLHGY IESQVQCGQV HCRLPYTAPP VHLKADMDGP LSNRGEKVIL 360 FQY 363

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	Developmental stage	Species	Evidence	Details
1:1 ortholog	LHX6	541261	E1B8I6			Bos taurus	Prediction	More>>
1:1 ortholog	LHX6		E2RA99			Canis lupus familiaris	Prediction	More>>
1:1 ortholog	LHX6		A0A452EBF4			Capra hircus	Prediction	More>>
1:1 ortholog	LHX6	26468	Q9UPM6			Homo sapiens	Prediction	More>>
1:1 ortholog	Lhx6	16874	Q9R1R0	CPO	E14.5	Mus musculus	Publication	More>>
1:1 ortholog	LHX6	735560	A0A2I3RGU2			Pan troglodytes	Prediction	More>>
1:1 ortholog	Lhx6		D3ZDG6			Rattus norvegicus	Prediction	More>>
1:1 ortholog	lhx6	445565	Q6BDC4			Danio rerio	Prediction	More>>

Other genetic variants/mutations

ID	Variant	Type	Disease	Chromosome\Coordinate	Evidence
rs1406935514	p.Ala2Pro	missense variant	-	NC_000009.12:g.122227474C>G	gnomAD
rs766793975	p.Gln3Glu	missense variant	-	NC_000009.12:g.122227471G>C	ExAC,TOPMed,gnomAD
rs1422760054	p.Gly5Val	missense variant	-	NC_000009.12:g.122227464C>A	TOPMed,gnomAD
rs1350004452	p.Ser6Ala	missense variant	-	NC_000009.12:g.122227462A>C	TOPMed
rs368987512	p.Gly7Arg	missense variant	-	NC_000009.12:g.122227459C>G	ESP,ExAC,TOPMed,gnomAD
rs368987512	p.Gly7Ser	missense variant	-	NC_000009.12:g.122227459C>T	ESP,ExAC,TOPMed,gnomAD
rs1191550373	p.Ala10Ser	missense variant	-	NC_000009.12:g.122227450C>A	gnomAD
rs753262130	p.Arg13Cys	missense variant	-	NC_000009.12:g.122227441G>A	ExAC,gnomAD
rs753262130	p.Arg13Gly	missense variant	-	NC_000009.12:g.122227441G>C	ExAC,gnomAD
rs1481335739	p.Ala19Ser	missense variant	-	NC_000009.12:g.122227423C>A	TOPMed
rs1206081225	p.Pro20Leu	missense variant	-	NC_000009.12:g.122227419G>A	gnomAD
rs763826373	p.Pro21Leu	missense variant	-	NC_000009.12:g.122227416G>A	ExAC,gnomAD
rs1362909237	p.Ala22Thr	missense variant	-	NC_000009.12:g.122227414C>T	TOPMed
rs1300995372	p.Met23Leu	missense variant	-	NC_000009.12:g.122227411T>A	gnomAD
rs924850315	p.Met23Thr	missense variant	-	NC_000009.12:g.122227410A>G	TOPMed
rs1292174061	p.Ala32Thr	missense variant	-	NC_000009.12:g.122227006C>T	gnomAD
rs1383639145	p.Gly33Glu	missense variant	-	NC_000009.12:g.122227002C>T	TOPMed
rs1156567799	p.Ala34Asp	missense variant	-	NC_000009.12:g.122226999G>T	gnomAD
rs1281159414	p.Asp36Asn	missense variant	-	NC_000009.12:g.122226994C>T	TOPMed
rs1371452441	p.Lys37Asn	missense variant	-	NC_000009.12:g.122226989C>G	gnomAD
rs930753919	p.Lys37Arg	missense variant	-	NC_000009.12:g.122226990T>C	TOPMed,gnomAD
rs770060170	p.Glu39Gln	missense variant	-	NC_000009.12:g.122226985C>G	ExAC,TOPMed,gnomAD
rs1421609364	p.Glu39Asp	missense variant	-	NC_000009.12:g.122226983C>A	gnomAD
rs1166293221	p.Glu39Ala	missense variant	-	NC_000009.12:g.122226984T>G	gnomAD
rs1254847391	p.Gly40Cys	missense variant	-	NC_000009.12:g.122226982C>A	gnomAD
rs1254847391	p.Gly40Ser	missense variant	-	NC_000009.12:g.122226982C>T	gnomAD
rs972481261	p.Gln41His	missense variant	-	NC_000009.12:g.122226977C>G	TOPMed
NCI-TCGA novel	p.Ala42Thr	missense variant	-	NC_000009.12:g.122226976C>T	NCI-TCGA
rs962039822	p.Ser43Cys	missense variant	-	NC_000009.12:g.122226972G>C	TOPMed,gnomAD
rs748326948	p.Cys45Arg	missense variant	-	NC_000009.12:g.122226967A>G	ExAC,TOPMed,gnomAD
rs748326948	p.Cys45Gly	missense variant	-	NC_000009.12:g.122226967A>C	ExAC,TOPMed,gnomAD
rs748326948	p.Cys45Ser	missense variant	-	NC_000009.12:g.122226967A>T	ExAC,TOPMed,gnomAD
rs1489535876	p.Thr46Met	missense variant	-	NC_000009.12:g.122226963G>A	gnomAD
rs781554821	p.Pro47Thr	missense variant	-	NC_000009.12:g.122226961G>T	ExAC,gnomAD
rs1216274158	p.Thr49Ser	missense variant	-	NC_000009.12:g.122226955T>A	gnomAD
rs1360445686	p.Pro50Leu	missense variant	-	NC_000009.12:g.122226951G>A	gnomAD
rs1188591238	p.Ser51Phe	missense variant	-	NC_000009.12:g.122226948G>A	TOPMed
NCI-TCGA novel	p.Val52Ala	missense variant	-	NC_000009.12:g.122226945A>G	NCI-TCGA
rs899943755	p.Pro55Leu	missense variant	-	NC_000009.12:g.122226936G>A	TOPMed
rs1242865793	p.Pro56Ser	missense variant	-	NC_000009.12:g.122226934G>A	gnomAD
COSM6182444	p.Ser57Phe	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000009.12:g.122226930G>A	NCI-TCGA Cosmic
rs1321247028	p.Ala58Thr	missense variant	-	NC_000009.12:g.122226928C>T	gnomAD
rs780658108	p.Ala58Val	missense variant	-	NC_000009.12:g.122226927G>A	ExAC,gnomAD
rs1342239564	p.Ala59Thr	missense variant	-	NC_000009.12:g.122226925C>T	TOPMed,gnomAD
rs1431783110	p.Ser61Tyr	missense variant	-	NC_000009.12:g.122226918G>T	TOPMed
rs753416011	p.Val62Leu	missense variant	-	NC_000009.12:g.122226916C>A	ExAC,gnomAD
rs865857751	p.Pro63Gln	missense variant	-	NC_000009.12:g.122226912G>T	TOPMed
rs368544328	p.Ser64Pro	missense variant	-	NC_000009.12:g.122226910A>G	ESP,ExAC,TOPMed,gnomAD
rs1367417547	p.Ile69Asn	missense variant	-	NC_000009.12:g.122226894A>T	gnomAD
rs185007094	p.Asp79Glu	missense variant	-	NC_000009.12:g.122226863G>T	1000Genomes,gnomAD
rs774057122	p.Asn87Lys	missense variant	-	NC_000009.12:g.122226489G>T	ExAC,gnomAD
rs762036833	p.Val92Met	missense variant	-	NC_000009.12:g.122226476C>T	ExAC,gnomAD
rs762036833	p.Val92Leu	missense variant	-	NC_000009.12:g.122226476C>A	ExAC,gnomAD
rs1237674513	p.Arg93Gln	missense variant	-	NC_000009.12:g.122226472C>T	gnomAD
rs1442941361	p.Glu96Gln	missense variant	-	NC_000009.12:g.122226464C>G	gnomAD
rs1258262409	p.Ser98Phe	missense variant	-	NC_000009.12:g.122226457G>A	gnomAD
rs1344100877	p.Val99Met	missense variant	-	NC_000009.12:g.122226455C>T	gnomAD
NCI-TCGA novel	p.Arg101Pro	missense variant	-	NC_000009.12:g.122226448C>G	NCI-TCGA
rs903795376	p.Thr102Met	missense variant	-	NC_000009.12:g.122226445G>A	TOPMed,gnomAD
rs903795376	p.Thr102Lys	missense variant	-	NC_000009.12:g.122226445G>T	TOPMed,gnomAD
rs772377957	p.Arg105Lys	missense variant	-	NC_000009.12:g.122226436C>T	ExAC,gnomAD
rs889378022	p.Asn108Ser	missense variant	-	NC_000009.12:g.122226427T>C	TOPMed,gnomAD
NCI-TCGA novel	p.Tyr111Cys	missense variant	-	NC_000009.12:g.122226418T>C	NCI-TCGA
rs1341735721	p.Ile112Leu	missense variant	-	NC_000009.12:g.122226416T>G	gnomAD
NCI-TCGA novel	p.Asn114Asp	missense variant	-	NC_000009.12:g.122226410T>C	NCI-TCGA
COSM1104813	p.Glu116Asp	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000009.12:g.122226402C>A	NCI-TCGA Cosmic
NCI-TCGA novel	p.Glu116Gln	missense variant	-	NC_000009.12:g.122226404C>G	NCI-TCGA
rs114142278	p.Met121Thr	missense variant	-	NC_000009.12:g.122226388A>G	1000Genomes,ExAC
NCI-TCGA novel	p.Phe124Leu	missense variant	-	NC_000009.12:g.122226378G>T	NCI-TCGA
NCI-TCGA novel	p.Arg126Gln	missense variant	-	NC_000009.12:g.122217286C>T	NCI-TCGA
NCI-TCGA novel	p.Gly128Arg	missense variant	-	NC_000009.12:g.122217281C>T	NCI-TCGA
rs1280715232	p.Gly128Arg	missense variant	-	NC_000009.12:g.122217281C>G	gnomAD
rs1340343102	p.Ala132Val	missense variant	-	NC_000009.12:g.122217268G>A	gnomAD
rs756354677	p.Arg133Trp	missense variant	-	NC_000009.12:g.122217266G>A	TOPMed,gnomAD
rs1348298532	p.Arg133Gln	missense variant	-	NC_000009.12:g.122217265C>T	gnomAD
rs1322977789	p.Arg136Ter	stop gained	-	NC_000009.12:g.122217257G>A	gnomAD
rs565893915	p.Gln137His	missense variant	-	NC_000009.12:g.122217252C>A	TOPMed,gnomAD
COSM1459803	p.Ser141Asn	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000009.12:g.122217241C>T	NCI-TCGA Cosmic
COSM1242462	p.Asp142Asn	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000009.12:g.122217239C>T	NCI-TCGA Cosmic
NCI-TCGA novel	p.Asp142Tyr	missense variant	-	NC_000009.12:g.122217239C>A	NCI-TCGA
rs1052901227	p.Asp142Glu	missense variant	-	NC_000009.12:g.122217237G>T	TOPMed,gnomAD
NCI-TCGA novel	p.Trp143Leu	missense variant	-	NC_000009.12:g.122217235C>A	NCI-TCGA
COSM1213331	p.Arg145Trp	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000009.12:g.122217230G>A	NCI-TCGA Cosmic
NCI-TCGA novel	p.Cys156Ter	stop gained	-	NC_000009.12:g.122217195G>T	NCI-TCGA
NCI-TCGA novel	p.Ser161Leu	missense variant	-	NC_000009.12:g.122217181G>A	NCI-TCGA
rs1259396465	p.Lys163Arg	missense variant	-	NC_000009.12:g.122217175T>C	gnomAD
NCI-TCGA novel	p.Ser167Ala	missense variant	-	NC_000009.12:g.122217164A>C	NCI-TCGA
COSM4828827	p.Glu170Ter	stop gained	Variant assessed as Somatic; HIGH impact.	NC_000009.12:g.122217155C>A	NCI-TCGA Cosmic
NCI-TCGA novel	p.Glu176Ter	stop gained	-	NC_000009.12:g.122217137C>A	NCI-TCGA
NCI-TCGA novel	p.Glu177Gln	missense variant	-	NC_000009.12:g.122217134C>G	NCI-TCGA
NCI-TCGA novel	p.Glu177Lys	missense variant	-	NC_000009.12:g.122217134C>T	NCI-TCGA
rs771625399	p.Ile183Met	missense variant	-	NC_000009.12:g.122217114G>C	ExAC,TOPMed,gnomAD
rs1253921056	p.His184Gln	missense variant	-	NC_000009.12:g.122217111G>T	TOPMed
COSM1459799	p.Asp186Asn	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000009.12:g.122217107C>T	NCI-TCGA Cosmic
rs1329346796	p.Met188Val	missense variant	-	NC_000009.12:g.122217101T>C	gnomAD
COSM3653859	p.Met188Ile	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000009.12:g.122217099C>T	NCI-TCGA Cosmic
rs201011938	p.Ile189Val	missense variant	-	NC_000009.12:g.122217098T>C	TOPMed,gnomAD
rs749060535	p.Arg194Lys	missense variant	-	NC_000009.12:g.122217082C>T	ExAC,gnomAD
NCI-TCGA novel	p.Gly199Arg	missense variant	-	NC_000009.12:g.122217068C>T	NCI-TCGA
rs756959110	p.Thr203Ala	missense variant	-	NC_000009.12:g.122214372T>C	ExAC,gnomAD
rs748176324	p.Gly206Glu	missense variant	-	NC_000009.12:g.122214362C>T	ExAC,gnomAD
NCI-TCGA novel	p.Ser210Trp	missense variant	-	NC_000009.12:g.122214350G>C	NCI-TCGA
rs200081104	p.Gln212Arg	missense variant	-	NC_000009.12:g.122214344T>C	TOPMed,gnomAD
COSM3323236	p.Ala219Val	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000009.12:g.122214323G>A	NCI-TCGA Cosmic
rs1324004468	p.Ala219Thr	missense variant	-	NC_000009.12:g.122214324C>T	TOPMed
rs751619203	p.Arg221Gly	missense variant	-	NC_000009.12:g.122214318G>C	ExAC,gnomAD
NCI-TCGA novel	p.Thr227Ser	missense variant	-	NC_000009.12:g.122214299G>C	NCI-TCGA
rs141012050	p.Ala228Thr	missense variant	-	NC_000009.12:g.122214297C>T	1000Genomes,ESP,ExAC,TOPMed,gnomAD
NCI-TCGA novel	p.Gln232Ter	stop gained	-	NC_000009.12:g.122214285G>A	NCI-TCGA
rs1250236296	p.Val233Leu	missense variant	-	NC_000009.12:g.122214069C>G	gnomAD
COSM3847559	p.Met234Ile	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000009.12:g.122214064C>T	NCI-TCGA Cosmic
rs778214950	p.Met234Thr	missense variant	-	NC_000009.12:g.122214065A>G	ExAC,gnomAD
rs753322621	p.Ala239Thr	missense variant	-	NC_000009.12:g.122214051C>T	ExAC,TOPMed,gnomAD
NCI-TCGA novel	p.Asp241His	missense variant	-	NC_000009.12:g.122214045C>G	NCI-TCGA
rs1453959910	p.Asp245Val	missense variant	-	NC_000009.12:g.122214032T>A	gnomAD
NCI-TCGA novel	p.Ala246Thr	missense variant	-	NC_000009.12:g.122214030C>T	NCI-TCGA
rs1464492837	p.Gln247His	missense variant	-	NC_000009.12:g.122214025C>A	TOPMed
rs1195136440	p.Ala253Glu	missense variant	-	NC_000009.12:g.122214008G>T	gnomAD
rs776502085	p.Met255Arg	missense variant	-	NC_000009.12:g.122214002A>C	ExAC,gnomAD
rs761309017	p.Met255Val	missense variant	-	NC_000009.12:g.122214003T>C	ExAC,TOPMed,gnomAD
rs776502085	p.Met255Lys	missense variant	-	NC_000009.12:g.122214002A>T	ExAC,gnomAD
rs761309017	p.Met255Leu	missense variant	-	NC_000009.12:g.122214003T>A	ExAC,TOPMed,gnomAD
rs761309017	p.Met255Leu	missense variant	-	NC_000009.12:g.122214003T>G	ExAC,TOPMed,gnomAD
rs763932135	p.Thr256Met	missense variant	-	NC_000009.12:g.122213999G>A	ExAC
rs760455304	p.Gly257Cys	missense variant	-	NC_000009.12:g.122213997C>A	ExAC,gnomAD
rs1478925023	p.Ser259Arg	missense variant	-	NC_000009.12:g.122213991T>G	TOPMed
rs1404837187	p.Gln264Arg	missense variant	-	NC_000009.12:g.122213975T>C	gnomAD
rs1397091334	p.Gln264Glu	missense variant	-	NC_000009.12:g.122213976G>C	gnomAD
NCI-TCGA novel	p.Trp266Arg	missense variant	-	NC_000009.12:g.122213777A>G	NCI-TCGA
NCI-TCGA novel	p.Gln268Ter	stop gained	-	NC_000009.12:g.122213771G>A	NCI-TCGA
NCI-TCGA novel	p.Gln280Ter	stop gained	-	NC_000009.12:g.122213735G>A	NCI-TCGA
rs755776987	p.Pro282Ser	missense variant	-	NC_000009.12:g.122213729G>A	ExAC,TOPMed,gnomAD
rs142314211	p.Pro284Leu	missense variant	-	NC_000009.12:g.122213722G>A	ESP,ExAC,TOPMed,gnomAD
rs142314211	p.Pro284Gln	missense variant	-	NC_000009.12:g.122213722G>T	ESP,ExAC,TOPMed,gnomAD
rs1379186056	p.Pro285Ser	missense variant	-	NC_000009.12:g.122213720G>A	gnomAD
rs1353732780	p.Ala288Thr	missense variant	-	NC_000009.12:g.122213711C>T	gnomAD
rs1353732780	p.Ala288Ser	missense variant	-	NC_000009.12:g.122213711C>A	gnomAD
rs1334502985	p.Pro289Thr	missense variant	-	NC_000009.12:g.122213708G>T	TOPMed,gnomAD
rs1334502985	p.Pro289Ser	missense variant	-	NC_000009.12:g.122213708G>A	TOPMed,gnomAD
rs1172612099	p.Pro290Leu	missense variant	-	NC_000009.12:g.122213704G>A	gnomAD
rs983219818	p.Pro290Thr	missense variant	-	NC_000009.12:g.122213705G>T	TOPMed,gnomAD
rs983219818	p.Pro290Ala	missense variant	-	NC_000009.12:g.122213705G>C	TOPMed,gnomAD
rs1176015977	p.Pro294Leu	missense variant	-	NC_000009.12:g.122213692G>A	gnomAD
rs1238423445	p.Ser295Pro	missense variant	-	NC_000009.12:g.122213690A>G	TOPMed,gnomAD
rs758346959	p.Ala296Val	missense variant	-	NC_000009.12:g.122213686G>A	ExAC,gnomAD
COSM1104809	p.Leu297Met	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000009.12:g.122213684G>T	NCI-TCGA Cosmic
rs765474854	p.Leu297Val	missense variant	-	NC_000009.12:g.122213684G>C	ExAC,gnomAD
rs761983883	p.Asp299Gly	missense variant	-	NC_000009.12:g.122213677T>C	ExAC,gnomAD
rs1465713836	p.Asp299Asn	missense variant	-	NC_000009.12:g.122213678C>T	TOPMed
rs776753440	p.Asp299Glu	missense variant	-	NC_000009.12:g.122213676G>C	ExAC,TOPMed,gnomAD
rs764350949	p.Asp300Ala	missense variant	-	NC_000009.12:g.122213674T>G	ExAC
rs775881165	p.Ile301Ser	missense variant	-	NC_000009.12:g.122213671A>C	ExAC,gnomAD
rs775881165	p.Ile301Asn	missense variant	-	NC_000009.12:g.122213671A>T	ExAC,gnomAD
rs1378520379	p.His302Gln	missense variant	-	NC_000009.12:g.122213667G>C	gnomAD
rs746314669	p.His302Arg	missense variant	-	NC_000009.12:g.122213668T>C	ExAC,TOPMed,gnomAD
rs1319744562	p.Thr304Asn	missense variant	-	NC_000009.12:g.122213662G>T	TOPMed
rs774825314	p.Pro305Arg	missense variant	-	NC_000009.12:g.122213659G>C	ExAC,TOPMed,gnomAD
rs1373371597	p.Ser307Arg	missense variant	-	NC_000009.12:g.122213652G>C	gnomAD
rs1230274664	p.Ser307Gly	missense variant	-	NC_000009.12:g.122213654T>C	TOPMed
rs1298888313	p.Ser308Asn	missense variant	-	NC_000009.12:g.122213650C>T	TOPMed
rs769359783	p.Pro309Ala	missense variant	-	NC_000009.12:g.122213648G>C	ExAC,TOPMed,gnomAD
rs769359783	p.Pro309Ser	missense variant	-	NC_000009.12:g.122213648G>A	ExAC,TOPMed,gnomAD
rs1156240673	p.Glu310Lys	missense variant	-	NC_000009.12:g.122213645C>T	gnomAD
COSM487006	p.Ala312Val	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000009.12:g.122213638G>A	NCI-TCGA Cosmic
rs1257450478	p.Ala312Thr	missense variant	-	NC_000009.12:g.122213639C>T	TOPMed
rs1463111102	p.Arg313His	missense variant	-	NC_000009.12:g.122213635C>T	TOPMed
rs375958601	p.Met314Thr	missense variant	-	NC_000009.12:g.122213632A>G	1000Genomes,ESP,ExAC,TOPMed,gnomAD
rs780731428	p.Met314Val	missense variant	-	NC_000009.12:g.122213633T>C	ExAC,TOPMed,gnomAD
rs1465769702	p.His318Arg	missense variant	-	NC_000009.12:g.122213620T>C	TOPMed
rs1474458901	p.Gly319Arg	missense variant	-	NC_000009.12:g.122213618C>G	TOPMed,gnomAD
rs1474458901	p.Gly319Ser	missense variant	-	NC_000009.12:g.122213618C>T	TOPMed,gnomAD
COSM4877404	p.Tyr320Cys	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000009.12:g.122213614T>C	NCI-TCGA Cosmic
rs779843806	p.Tyr320His	missense variant	-	NC_000009.12:g.122213615A>G	ExAC,gnomAD
NCI-TCGA novel	p.Ile321Asn	missense variant	-	NC_000009.12:g.122213611A>T	NCI-TCGA
rs745505125	p.Val325Leu	missense variant	-	NC_000009.12:g.122209712C>G	ExAC,TOPMed,gnomAD
rs745505125	p.Val325Leu	missense variant	-	NC_000009.12:g.122209712C>A	ExAC,TOPMed,gnomAD
rs1039247770	p.Gln326Arg	missense variant	-	NC_000009.12:g.122209708T>C	gnomAD
rs1394481320	p.Cys327Tyr	missense variant	-	NC_000009.12:g.122209705C>T	gnomAD
COSM1701655	p.Gly328Glu	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000009.12:g.122209702C>T	NCI-TCGA Cosmic
rs373915153	p.Gly328Arg	missense variant	-	NC_000009.12:g.122209703C>T	ESP,ExAC,TOPMed,gnomAD
rs1403608419	p.Val330Met	missense variant	-	NC_000009.12:g.122209697C>T	TOPMed,gnomAD
rs547463991	p.His331Gln	missense variant	-	NC_000009.12:g.122209692G>C	1000Genomes,ExAC,gnomAD
rs1174667644	p.Cys332Arg	missense variant	-	NC_000009.12:g.122209691A>G	gnomAD
rs371503306	p.Arg333Gln	missense variant	-	NC_000009.12:g.122209687C>T	ESP,ExAC,TOPMed,gnomAD
rs1396979515	p.Tyr336Cys	missense variant	-	NC_000009.12:g.122209678T>C	gnomAD
rs367663922	p.Ala338Val	missense variant	-	NC_000009.12:g.122209672G>A	ESP,ExAC,TOPMed,gnomAD
rs766877341	p.Ala338Thr	missense variant	-	NC_000009.12:g.122209673C>T	ExAC,gnomAD
rs773582289	p.Pro339Ala	missense variant	-	NC_000009.12:g.122209670G>C	ExAC,TOPMed,gnomAD
rs773582289	p.Pro339Thr	missense variant	-	NC_000009.12:g.122209670G>T	ExAC,TOPMed,gnomAD
rs41273919	p.Pro340Thr	missense variant	-	NC_000009.12:g.122209667G>T	1000Genomes,ESP,ExAC,TOPMed,gnomAD
rs41273919	p.Pro340Ser	missense variant	-	NC_000009.12:g.122209667G>A	1000Genomes,ESP,ExAC,TOPMed,gnomAD
rs771797999	p.Pro340Leu	missense variant	-	NC_000009.12:g.122209666G>A	ExAC,gnomAD
rs41273919	p.Pro340Ala	missense variant	-	NC_000009.12:g.122209667G>C	1000Genomes,ESP,ExAC,TOPMed,gnomAD
COSM5347908	p.Val341SerPheSerTerUnkUnkUnk	frameshift	Variant assessed as Somatic; HIGH impact.	NC_000009.12:g.122209665G>-	NCI-TCGA Cosmic
rs771003127	p.Val341Ile	missense variant	-	NC_000009.12:g.122209664C>T	ExAC,TOPMed
rs749304681	p.His342Pro	missense variant	-	NC_000009.12:g.122209660T>G	ExAC,gnomAD
rs756257207	p.Leu343His	missense variant	-	NC_000009.12:g.122209657A>T	ExAC,gnomAD
rs1181230340	p.Ala345Val	missense variant	-	NC_000009.12:g.122209651G>A	gnomAD
rs781424815	p.Asp346Asn	missense variant	-	NC_000009.12:g.122209649C>T	ExAC,gnomAD
rs200077245	p.Asp346Gly	missense variant	-	NC_000009.12:g.122209648T>C	1000Genomes,ExAC,gnomAD
rs1297908688	p.Met347Thr	missense variant	-	NC_000009.12:g.122209645A>G	gnomAD
rs549579918	p.Met347Val	missense variant	-	NC_000009.12:g.122209646T>C	1000Genomes,ExAC,gnomAD
rs531957865	p.Met347Ile	missense variant	-	NC_000009.12:g.122209644C>T	1000Genomes,ExAC,gnomAD
rs758688851	p.Gly349Arg	missense variant	-	NC_000009.12:g.122209640C>T	ExAC,TOPMed,gnomAD
rs561275677	p.Pro350Leu	missense variant	-	NC_000009.12:g.122209636G>A	1000Genomes,ExAC,TOPMed,gnomAD
rs146076339	p.Leu351Ile	missense variant	-	NC_000009.12:g.122209634G>T	1000Genomes,ExAC,gnomAD
rs774135453	p.Arg354Pro	missense variant	-	NC_000009.12:g.122209624C>G	ExAC,TOPMed,gnomAD
rs767286367	p.Arg354Trp	missense variant	-	NC_000009.12:g.122209625G>A	ExAC,TOPMed,gnomAD
rs774135453	p.Arg354Gln	missense variant	-	NC_000009.12:g.122209624C>T	ExAC,TOPMed,gnomAD
rs774135453	p.Arg354Leu	missense variant	-	NC_000009.12:g.122209624C>A	ExAC,TOPMed,gnomAD
rs1306790045	p.Gly355Arg	missense variant	-	NC_000009.12:g.122209622C>G	TOPMed
rs1306790045	p.Gly355Ser	missense variant	-	NC_000009.12:g.122209622C>T	TOPMed
NCI-TCGA novel	p.Gln362SerPheSerTerUnkUnk	frameshift	-	NC_000009.12:g.122204768_122204769insA	NCI-TCGA

Disease or phenotype associated information

Disease ID	Disease Name	Disease Type	Source
C0036341	Schizophrenia	disease	BEFREE;PSYGENET
C0040517	Gilles de la Tourette syndrome	disease	BEFREE
C0242379	Malignant neoplasm of lung	disease	BEFREE
C0684249	Carcinoma of lung	disease	BEFREE
C1306460	Primary malignant neoplasm of lung	disease	BEFREE

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:0003700	DNA-binding transcription factor activity	NAS
GO:0005515	protein binding	IPI
GO:0046872	metal ion binding	IEA

GO:Biological Process

GO ID	GO Term	Evidence
GO:0021799	cerebral cortex radially oriented cell migration	ISS
GO:0021800	cerebral cortex tangential migration	ISS
GO:0021853	cerebral cortex GABAergic interneuron migration	ISS
GO:0021884	forebrain neuron development	IBA
GO:0030182	neuron differentiation	IBA
GO:0045944	positive regulation of transcription by RNA polymerase II	IBA
GO:0048469	cell maturation	ISS

GO:Cellular Component

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

Reactome Pathway

Reactome ID	Reactome Term	Evidence

Drugs and compounds information

ID	Drug Name	Action	PubMed
C009505	4,4'-diaminodiphenylmethane	4,4'-diaminodiphenylmethane affects the expression of LHX6 mRNA	18648102
D000082	Acetaminophen	Acetaminophen affects the expression of LHX6 mRNA	17562736
D016604	Aflatoxin B1	Aflatoxin B1 results in increased expression of LHX6 mRNA	21641981
D016604	Aflatoxin B1	Aflatoxin B1 results in decreased expression of LHX6 mRNA	19770486
C029753	aflatoxin B2	aflatoxin B2 results in increased methylation of LHX6 intron	30157460
D000447	Aldehydes	Aldehydes results in increased expression of LHX6 mRNA	25014914
D000077237	Arsenic Trioxide	Arsenic Trioxide results in decreased expression of LHX6 mRNA	15761015
C015001	arsenite	arsenite results in increased methylation of LHX6 promoter	23974009
D001280	Atrazine	Atrazine results in increased expression of LHX6 mRNA	22378314
C547126	AZM551248	AZM551248 results in decreased expression of LHX6 mRNA	22323515
D001564	Benzo(a)pyrene	Benzo(a)pyrene affects the methylation of LHX6 intron	30157460
D001564	Benzo(a)pyrene	Benzo(a)pyrene results in decreased expression of LHX6 mRNA	19770486
C026487	benzo(e)pyrene	benzo(e)pyrene results in increased methylation of LHX6 intron	30157460
C006780	bisphenol A	bisphenol A affects the methylation of LHX6 promoter	27334623
C006780	bisphenol A	bisphenol A affects the expression of LHX6 mRNA	21786754
C006780	bisphenol A	bisphenol A affects the expression of LHX6 mRNA	25181051
C006780	bisphenol A	[bisphenol A co-treated with Diethylhexyl Phthalate co-treated with Dibutyl Phthalate] affects the methylation of LHX6 promoter	23359474
C018475	butyraldehyde	butyraldehyde results in increased expression of LHX6 mRNA	26079696
D002251	Carbon Tetrachloride	Carbon Tetrachloride results in decreased expression of LHX6 mRNA	31150632
D002794	Choline	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in decreased expression of LHX6 mRNA	20938992
D002794	Choline	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in increased methylation of and results in decreased expression of LHX6	20938992
D002794	Choline	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in increased methylation of LHX6 gene	20938992
D002945	Cisplatin	Cisplatin results in increased expression of LHX6 mRNA	27392435
D019327	Copper Sulfate	Copper Sulfate results in increased expression of LHX6 mRNA	19549813
D003471	Cuprizone	Cuprizone results in decreased expression of LHX6 mRNA	26577399
D016572	Cyclosporine	Cyclosporine results in decreased expression of LHX6 mRNA	19770486
D000077209	Decitabine	Decitabine results in decreased expression of LHX6 mRNA	27915011
D003907	Dexamethasone	Dexamethasone inhibits the reaction [RX3 gene mutant form affects the expression of LHX6 mRNA]	27941970
D003993	Dibutyl Phthalate	[bisphenol A co-treated with Diethylhexyl Phthalate co-treated with Dibutyl Phthalate] affects the methylation of LHX6 promoter	23359474
D004051	Diethylhexyl Phthalate	[bisphenol A co-treated with Diethylhexyl Phthalate co-treated with Dibutyl Phthalate] affects the methylation of LHX6 promoter	23359474
D013759	Dronabinol	Dronabinol affects the methylation of LHX6 gene	26044905
D004958	Estradiol	[Estradiol co-treated with TGFB1 protein] results in increased expression of LHX6 mRNA	30165855
D000431	Ethanol	Ethanol affects the expression of and affects the splicing of LHX6 mRNA	30319688
D017313	Fenretinide	Fenretinide results in increased expression of LHX6 mRNA	28973697
D005492	Folic Acid	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in decreased expression of LHX6 mRNA	20938992
D005492	Folic Acid	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in increased methylation of and results in decreased expression of LHX6	20938992
D005492	Folic Acid	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in increased methylation of LHX6 gene	20938992
C039281	furan	furan results in decreased expression of LHX6 mRNA	25539665
D006861	Hydrogen Peroxide	Hydrogen Peroxide affects the expression of LHX6 mRNA	20044591
D008701	Methapyrilene	Methapyrilene results in increased methylation of LHX6 intron	30157460
D008715	Methionine	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in decreased expression of LHX6 mRNA	20938992
D008715	Methionine	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in increased methylation of and results in decreased expression of LHX6	20938992
D008715	Methionine	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in increased methylation of LHX6 gene	20938992
D008741	Methyl Methanesulfonate	Methyl Methanesulfonate results in increased expression of LHX6 mRNA	26011545
C583365	N-(2-(1,1'-bicyclopropyl)-2-ylphenyl)-3-(difluoromethyl)-1-methyl-1H-pyrazole-4-carboxamide	N-(2-(1,1'-bicyclopropyl)-2-ylphenyl)-3-(difluoromethyl)-1-methyl-1H-pyrazole-4-carboxamide results in decreased expression of LHX6 mRNA	29244179
D018817	N-Methyl-3,4-methylenedioxyamphetamine	N-Methyl-3,4-methylenedioxyamphetamine results in increased expression of LHX6 mRNA	26251327
C046012	pentanal	pentanal results in increased expression of LHX6 mRNA	26079696
D010634	Phenobarbital	NR1I3 protein affects the reaction [Phenobarbital results in increased expression of LHX6 mRNA]	19482888
D010634	Phenobarbital	Phenobarbital results in increased expression of LHX6 mRNA	19482888
C006253	pirinixic acid	pirinixic acid results in increased expression of LHX6 mRNA	23811191
D010936	Plant Extracts	Plant Extracts results in decreased expression of LHX6 mRNA	23557933
D011192	Potassium Dichromate	Potassium Dichromate results in decreased expression of LHX6 mRNA	23608068
C005556	propionaldehyde	propionaldehyde results in increased expression of LHX6 mRNA	26079696
D011441	Propylthiouracil	Propylthiouracil results in increased expression of LHX6 mRNA	24780913; 25825206;
C017947	sodium arsenite	sodium arsenite affects the methylation of LHX6 gene	28589171
C105686	SU 5402	SU 5402 results in decreased expression of LHX6 mRNA	15355794
D013629	Tamoxifen	Tamoxifen results in decreased expression of LHX6 mRNA	25123088
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin affects the expression of LHX6 mRNA	21570461; 24058054;
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin results in decreased expression of LHX6 mRNA	19770486; 28922406;
C009495	titanium dioxide	titanium dioxide results in increased expression of LHX6 mRNA	29264374
D014212	Tretinoin	Tretinoin results in decreased expression of LHX6 mRNA	16000160
D014241	Trichloroethylene	Trichloroethylene results in increased expression of LHX6 mRNA	25549359
C016805	tris(1,3-dichloro-2-propyl)phosphate	tris(1,3-dichloro-2-propyl)phosphate results in decreased expression of LHX6 mRNA	26179874
D014635	Valproic Acid	Valproic Acid results in decreased methylation of LHX6 gene	29154799
D001335	Vehicle Emissions	Vehicle Emissions results in decreased methylation of LHX6 gene	25560391
D024483	Vitamin K 3	Vitamin K 3 affects the expression of LHX6 mRNA	20044591

Functional annotations

Keywords

Keyword ID	Keyword Term
KW-0025	Alternative splicing
KW-0217	Developmental protein
KW-0221	Differentiation
KW-0238	DNA-binding
KW-0371	Homeobox
KW-0440	LIM domain
KW-0479	Metal-binding
KW-0524	Neurogenesis
KW-0539	Nucleus
KW-1185	Reference proteome
KW-0677	Repeat
KW-0804	Transcription
KW-0805	Transcription regulation
KW-0862	Zinc

Interpro

InterPro ID	InterPro Term
IPR009057	Homeobox-like_sf
IPR017970	Homeobox_CS
IPR001356	Homeobox_dom
IPR001781	Znf_LIM

PROSITE

PROSITE ID	PROSITE Term
PS00027	HOMEOBOX_1
PS50071	HOMEOBOX_2
PS00478	LIM_DOMAIN_1
PS50023	LIM_DOMAIN_2

Pfam

Pfam ID	Pfam Term
PF00046	Homeodomain
PF00412	LIM

Gene: LHX6

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

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