CleftGeneDB-Search

Gene: PCYT1A

Basic information

Tag	Content
Uniprot ID	P49585; A9LYK9; D3DXB1; Q86Y88;
Entrez ID	5130
Genbank protein ID	ABX44666.1; AAA72127.1; EAW53655.1; EAW53662.1; AAH46355.1;
Genbank nucleotide ID	NM_005017.3; NM_001312673.1;
Ensembl protein ID	ENSP00000394617; ENSP00000292823;
Ensembl nucleotide ID	ENSG00000161217
Gene name	Choline-phosphate cytidylyltransferase A
Gene symbol	PCYT1A
Organism	Homo sapiens
NCBI taxa ID	9606
Cleft type
Developmental stage
Data sources	Manually collected
Reference	20662904
Functional description	Controls phosphatidylcholine synthesis.
Sequence	MDAQCSAKVN ARKRRKEAPG PNGATEEDGV PSKVQRCAVG LRQPAPFSDE IEVDFSKPYV 60 RVTMEEASRG TPCERPVRVY ADGIFDLFHS GHARALMQAK NLFPNTYLIV GVCSDELTHN 120 FKGFTVMNEN ERYDAVQHCR YVDEVVRNAP WTLTPEFLAE HRIDFVAHDD IPYSSAGSDD 180 VYKHIKEAGM FAPTQRTEGI STSDIITRIV RDYDVYARRN LQRGYTAKEL NVSFINEKKY 240 HLQERVDKVK KKVKDVEEKS KEFVQKVEEK SIDLIQKWEE KSREFIGSFL EMFGPEGALK 300 HMLKEGKGRM LQAISPKQSP SSSPTRERSP SPSFRWPFSG KTSPPCSPAN LSRHKAAAYD 360 ISEDEED 367

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

There is no orthologous record for this gene !

Identified variants/mutations related to cleft phenotype

Gene symbol	Significant Variants/SNPS	Methods	PubMed ID
PCYT1A	rs712012T>C	PCR-RFLP	20662904

Other genetic variants/mutations

ID	Variant	Type	Disease	Chromosome\Coordinate	Evidence
rs1289492978	p.Asp2Ala	missense variant	-	NC_000003.12:g.196270527T>G	TOPMed
rs765878411	p.Ala3Glu	missense variant	-	NC_000003.12:g.196270524G>T	ExAC,TOPMed,gnomAD
rs772648306	p.Gln4Arg	missense variant	-	NC_000003.12:g.196270521T>C	ExAC,gnomAD
rs374200334	p.Cys5Phe	missense variant	-	NC_000003.12:g.196270518C>A	ESP,ExAC,TOPMed,gnomAD
rs149559427	p.Cys5Arg	missense variant	-	NC_000003.12:g.196270519A>G	TOPMed,gnomAD
rs374200334	p.Cys5Tyr	missense variant	-	NC_000003.12:g.196270518C>T	ESP,ExAC,TOPMed,gnomAD
rs1292608628	p.Ala11Ser	missense variant	-	NC_000003.12:g.196270501C>A	gnomAD
NCI-TCGA novel	p.Arg12Lys	missense variant	-	NC_000003.12:g.196270497C>T	NCI-TCGA
rs781198337	p.Arg15Thr	missense variant	-	NC_000003.12:g.196270488C>G	ExAC,gnomAD
rs768525820	p.Lys16Arg	missense variant	-	NC_000003.12:g.196270485T>C	ExAC,gnomAD
rs1315588404	p.Lys16Glu	missense variant	-	NC_000003.12:g.196270486T>C	gnomAD
rs1338129212	p.Glu17Gly	missense variant	-	NC_000003.12:g.196270482T>C	gnomAD
rs746866627	p.Ala18Val	missense variant	-	NC_000003.12:g.196270479G>A	ExAC,TOPMed,gnomAD
rs1041304990	p.Pro19Leu	missense variant	-	NC_000003.12:g.196270476G>A	TOPMed
rs142952629	p.Gly20Arg	missense variant	-	NC_000003.12:g.196270474C>G	1000Genomes,ExAC,TOPMed,gnomAD
rs142952629	p.Gly20Arg	missense variant	-	NC_000003.12:g.196270474C>T	1000Genomes,ExAC,TOPMed,gnomAD
rs150416628	p.Pro21Thr	missense variant	-	NC_000003.12:g.196270471G>T	1000Genomes,ESP,ExAC,TOPMed
RCV000521748	p.Pro21Ter	frameshift	-	NC_000003.12:g.196270472dup	ClinVar
rs150416628	p.Pro21Ser	missense variant	-	NC_000003.12:g.196270471G>A	1000Genomes,ESP,ExAC,TOPMed
rs753801861	p.Asn22Ser	missense variant	-	NC_000003.12:g.196270467T>C	ExAC,gnomAD
rs756683597	p.Gly23Arg	missense variant	-	NC_000003.12:g.196270465C>T	ExAC,gnomAD
rs1309199348	p.Gly23Glu	missense variant	-	NC_000003.12:g.196270464C>T	TOPMed
rs200752223	p.Thr25Ala	missense variant	-	NC_000003.12:g.196270459T>C	gnomAD
rs371965700	p.Gly29Arg	missense variant	-	NC_000003.12:g.196270447C>T	ESP,ExAC,TOPMed,gnomAD
rs749118491	p.Val30Phe	missense variant	-	NC_000003.12:g.196270444C>A	TOPMed
rs749118491	p.Val30Ile	missense variant	-	NC_000003.12:g.196270444C>T	TOPMed
rs866650732	p.Pro31Ser	missense variant	-	NC_000003.12:g.196270441G>A	-
NCI-TCGA novel	p.Pro31Leu	missense variant	-	NC_000003.12:g.196270440G>A	NCI-TCGA
rs897503443	p.Lys33Arg	missense variant	-	NC_000003.12:g.196270434T>C	TOPMed,gnomAD
rs1036001219	p.Val34Met	missense variant	-	NC_000003.12:g.196270432C>T	TOPMed
rs772948955	p.Arg36Leu	missense variant	-	NC_000003.12:g.196270425C>A	ExAC,TOPMed,gnomAD
rs772948955	p.Arg36His	missense variant	-	NC_000003.12:g.196270425C>T	ExAC,TOPMed,gnomAD
rs181492393	p.Arg36Cys	missense variant	-	NC_000003.12:g.196270426G>A	1000Genomes,ExAC,TOPMed,gnomAD
rs556753084	p.Cys37Tyr	missense variant	-	NC_000003.12:g.196270422C>T	1000Genomes,ExAC,TOPMed,gnomAD
COSM256204	p.Cys37Gly	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196270423A>C	NCI-TCGA Cosmic
rs761404113	p.Ala38Thr	missense variant	-	NC_000003.12:g.196270420C>T	ExAC,gnomAD
rs1227619597	p.Val39Leu	missense variant	-	NC_000003.12:g.196270417C>G	gnomAD
rs1274235817	p.Gly40Asp	missense variant	-	NC_000003.12:g.196257886C>T	gnomAD
rs142165028	p.Arg42Trp	missense variant	-	NC_000003.12:g.196257881G>A	1000Genomes,ESP,ExAC,TOPMed,gnomAD
rs771223117	p.Arg42Gln	missense variant	-	NC_000003.12:g.196257880C>T	ExAC,TOPMed,gnomAD
rs373774305	p.Pro44Gln	missense variant	-	NC_000003.12:g.196257874G>T	ESP,ExAC,TOPMed,gnomAD
rs373774305	p.Pro44Arg	missense variant	-	NC_000003.12:g.196257874G>C	ESP,ExAC,TOPMed,gnomAD
rs770025140	p.Ala45Ser	missense variant	-	NC_000003.12:g.196257872C>A	ExAC
rs748171719	p.Pro46Ser	missense variant	-	NC_000003.12:g.196257869G>A	ExAC,gnomAD
rs781768969	p.Pro46Leu	missense variant	-	NC_000003.12:g.196257868G>A	ExAC,TOPMed,gnomAD
rs1038475192	p.Phe47Leu	missense variant	-	NC_000003.12:g.196257864A>T	TOPMed
rs777509855	p.Ser48Cys	missense variant	-	NC_000003.12:g.196257862G>C	ExAC,gnomAD
rs1355304743	p.Asp49Gly	missense variant	-	NC_000003.12:g.196257859T>C	gnomAD
COSM3591856	p.Asp49Asn	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196257860C>T	NCI-TCGA Cosmic
rs752031936	p.Glu50Lys	missense variant	-	NC_000003.12:g.196257857C>T	ExAC,gnomAD
rs780253017	p.Ile51Thr	missense variant	-	NC_000003.12:g.196257853A>G	ExAC,gnomAD
rs1466833415	p.Asp54Gly	missense variant	-	NC_000003.12:g.196257844T>C	gnomAD
rs1388282947	p.Lys57Asn	missense variant	-	NC_000003.12:g.196257834C>A	gnomAD
rs561949003	p.Tyr59Ser	missense variant	-	NC_000003.12:g.196257829T>G	1000Genomes,ExAC,TOPMed,gnomAD
rs370657415	p.Tyr59Ter	stop gained	-	NC_000003.12:g.196257828A>T	ESP,ExAC,gnomAD
rs561949003	p.Tyr59Cys	missense variant	-	NC_000003.12:g.196257829T>C	1000Genomes,ExAC,TOPMed,gnomAD
rs760187621	p.Arg61Gly	missense variant	-	NC_000003.12:g.196257824T>C	ExAC,TOPMed,gnomAD
rs1481436343	p.Thr63Ser	missense variant	-	NC_000003.12:g.196257818T>A	gnomAD
rs752190012	p.Met64Val	missense variant	-	NC_000003.12:g.196257815T>C	ExAC,gnomAD
rs1482237707	p.Glu65Gly	missense variant	-	NC_000003.12:g.196257811T>C	gnomAD
rs1210245046	p.Glu65Lys	missense variant	-	NC_000003.12:g.196257812C>T	TOPMed
rs767556887	p.Glu66Asp	missense variant	-	NC_000003.12:g.196257807T>A	ExAC,gnomAD
rs759359405	p.Ala67Asp	missense variant	-	NC_000003.12:g.196257805G>T	ExAC,TOPMed,gnomAD
rs759359405	p.Ala67Gly	missense variant	-	NC_000003.12:g.196257805G>C	ExAC,TOPMed,gnomAD
COSM4116381	p.Ser68Asn	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196257802C>T	NCI-TCGA Cosmic
rs770656499	p.Thr71Ser	missense variant	-	NC_000003.12:g.196257794T>A	ExAC,TOPMed,gnomAD
rs199961207	p.Pro72Thr	missense variant	-	NC_000003.12:g.196257791G>T	ESP,ExAC,TOPMed,gnomAD
rs773573877	p.Cys73Gly	missense variant	-	NC_000003.12:g.196257788A>C	ExAC,gnomAD
rs1285004802	p.Arg75Ter	stop gained	-	NC_000003.12:g.196248318G>A	gnomAD
rs369594442	p.Arg75Gln	missense variant	-	NC_000003.12:g.196248317C>T	ESP,ExAC,TOPMed,gnomAD
rs1237888354	p.Arg78Thr	missense variant	-	NC_000003.12:g.196248308C>G	TOPMed
rs759039449	p.Val79Ile	missense variant	-	NC_000003.12:g.196248306C>T	ExAC,TOPMed,gnomAD
rs759039449	p.Val79Leu	missense variant	-	NC_000003.12:g.196248306C>G	ExAC,TOPMed,gnomAD
rs1454902800	p.Asp82Tyr	missense variant	-	NC_000003.12:g.196248297C>A	gnomAD
COSM4116380	p.Asp82Asn	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196248297C>T	NCI-TCGA Cosmic
rs1162073603	p.Leu87Ter	stop gained	-	NC_000003.12:g.196248281A>T	TOPMed
rs1157763363	p.Leu87Phe	missense variant	-	NC_000003.12:g.196248280T>A	gnomAD
rs1455352648	p.His89Tyr	missense variant	-	NC_000003.12:g.196248276G>A	gnomAD
rs1160679788	p.Ser90Pro	missense variant	-	NC_000003.12:g.196248273A>G	gnomAD
rs1003483302	p.Gly91Asp	missense variant	-	NC_000003.12:g.196248269C>T	TOPMed,gnomAD
rs938675798	p.Ala93Thr	missense variant	-	NC_000003.12:g.196248264C>T	TOPMed,gnomAD
rs938675798	p.Ala93Ser	missense variant	-	NC_000003.12:g.196248264C>A	TOPMed,gnomAD
rs773131861	p.Arg94Gly	missense variant	-	NC_000003.12:g.196248261G>C	ExAC,gnomAD
rs773131861	p.Arg94Ter	stop gained	-	NC_000003.12:g.196248261G>A	ExAC,gnomAD
rs566752063	p.Ala95Gly	missense variant	-	NC_000003.12:g.196248257G>C	1000Genomes
rs587777191	p.Ala99Thr	missense variant	-	NC_000003.12:g.196248246C>T	-
rs587777191	p.Ala99Thr	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)	NC_000003.12:g.196248246C>T	UniProt,dbSNP
VAR_071083	p.Ala99Thr	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)	NC_000003.12:g.196248246C>T	UniProt
rs587777189	p.Ala99Val	missense variant	-	NC_000003.12:g.196248245G>A	ExAC,TOPMed,gnomAD
rs587777189	p.Ala99Val	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)	NC_000003.12:g.196248245G>A	UniProt,dbSNP
VAR_071084	p.Ala99Val	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)	NC_000003.12:g.196248245G>A	UniProt
RCV000087314	p.Ala99Val	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMD-CRD)	NC_000003.12:g.196248245G>A	ClinVar
RCV000087316	p.Ala99Thr	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMD-CRD)	NC_000003.12:g.196248246C>T	ClinVar
RCV000622339	p.Ala99Val	missense variant	Inborn genetic diseases	NC_000003.12:g.196248245G>A	ClinVar
rs776823706	p.Asn101Lys	missense variant	-	NC_000003.12:g.196248238G>C	ExAC,gnomAD
COSM4116378	p.Asn101Ser	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196248239T>C	NCI-TCGA Cosmic
rs939839175	p.Thr106Met	missense variant	-	NC_000003.12:g.196248224G>A	TOPMed
rs375791987	p.Ile109Val	missense variant	-	NC_000003.12:g.196248216T>C	ESP,ExAC,TOPMed,gnomAD
rs1433265727	p.Ser114Arg	missense variant	-	NC_000003.12:g.196247513T>G	gnomAD
rs1442385114	p.Ser114Ile	missense variant	-	NC_000003.12:g.196247512C>A	TOPMed
rs758461951	p.His119Tyr	missense variant	-	NC_000003.12:g.196247498G>A	ExAC,gnomAD
rs1365763649	p.Phe121Leu	missense variant	-	NC_000003.12:g.196247490G>C	gnomAD
rs1235010313	p.Lys122Arg	missense variant	-	NC_000003.12:g.196247488T>C	TOPMed
rs765196598	p.Thr125Met	missense variant	-	NC_000003.12:g.196247479G>A	ExAC,gnomAD
RCV000412999	p.Thr125Met	missense variant	-	NC_000003.12:g.196247479G>A	ClinVar
rs1271221173	p.Met127Ile	missense variant	-	NC_000003.12:g.196247472C>G	TOPMed
NCI-TCGA novel	p.Asn128Thr	missense variant	-	NC_000003.12:g.196247470T>G	NCI-TCGA
rs587777194	p.Glu129Lys	missense variant	-	NC_000003.12:g.196247468C>T	-
rs587777194	p.Glu129Lys	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)	NC_000003.12:g.196247468C>T	UniProt,dbSNP
VAR_071085	p.Glu129Lys	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)	NC_000003.12:g.196247468C>T	UniProt
RCV000087320	p.Glu129Lys	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMD-CRD)	NC_000003.12:g.196247468C>T	ClinVar
rs760919068	p.Asn130Ser	missense variant	-	NC_000003.12:g.196247464T>C	ExAC,gnomAD
rs1205319354	p.Arg132His	missense variant	-	NC_000003.12:g.196247458C>T	TOPMed
rs772473697	p.Arg132Cys	missense variant	-	NC_000003.12:g.196247459G>A	ExAC,gnomAD
COSM1043015	p.Arg132Ser	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196247459G>T	NCI-TCGA Cosmic
rs767604749	p.Tyr133Cys	missense variant	-	NC_000003.12:g.196247455T>C	ExAC,gnomAD
rs759570486	p.Ala135Val	missense variant	-	NC_000003.12:g.196247449G>A	ExAC,TOPMed,gnomAD
rs771371499	p.Arg140Cys	missense variant	-	NC_000003.12:g.196247435G>A	ExAC,TOPMed,gnomAD
NCI-TCGA novel	p.Arg140His	missense variant	-	NC_000003.12:g.196247434C>T	NCI-TCGA
rs1398190721	p.Val142Met	missense variant	-	NC_000003.12:g.196247429C>T	TOPMed
COSM2947261	p.Ala149Val	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196247407G>A	NCI-TCGA Cosmic
rs587777190	p.Pro150Ala	missense variant	-	NC_000003.12:g.196247405G>C	gnomAD
rs587777190	p.Pro150Ala	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)	NC_000003.12:g.196247405G>C	UniProt,dbSNP
VAR_071086	p.Pro150Ala	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)	NC_000003.12:g.196247405G>C	UniProt
RCV000087315	p.Pro150Ala	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMD-CRD)	NC_000003.12:g.196247405G>C	ClinVar
rs746655391	p.Thr152Met	missense variant	-	NC_000003.12:g.196247398G>A	ExAC,TOPMed,gnomAD
rs746655391	p.Thr152Lys	missense variant	-	NC_000003.12:g.196247398G>T	ExAC,TOPMed,gnomAD
rs1243780999	p.Leu153Arg	missense variant	-	NC_000003.12:g.196247395A>C	gnomAD
COSM276683	p.Thr154Ile	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196247392G>A	NCI-TCGA Cosmic
rs771742784	p.Pro155Ser	missense variant	-	NC_000003.12:g.196247390G>A	ExAC,gnomAD
rs1293887137	p.Pro155Leu	missense variant	-	NC_000003.12:g.196247389G>A	TOPMed
rs779048770	p.Glu156Lys	missense variant	-	NC_000003.12:g.196247387C>T	ExAC,gnomAD
NCI-TCGA novel	p.Leu158AspPheSerTerUnkUnk	frameshift	-	NC_000003.12:g.196247381_196247382insGAACTCGGGTGTCAGCGTC	NCI-TCGA
rs1271650484	p.Ala159Val	missense variant	-	NC_000003.12:g.196247377G>A	TOPMed
rs757210925	p.Ala159Ser	missense variant	-	NC_000003.12:g.196247378C>A	ExAC,TOPMed,gnomAD
rs755814954	p.Glu160Gly	missense variant	-	NC_000003.12:g.196247374T>C	ExAC
rs140290837	p.Glu160Lys	missense variant	-	NC_000003.12:g.196247375C>T	1000Genomes,ExAC,TOPMed,gnomAD
rs1279839195	p.His161Leu	missense variant	-	NC_000003.12:g.196247371T>A	TOPMed
rs200813228	p.Arg162Gln	missense variant	-	NC_000003.12:g.196247368C>T	1000Genomes,ExAC,TOPMed,gnomAD
rs375663930	p.Arg162Trp	missense variant	-	NC_000003.12:g.196247369G>A	1000Genomes,ESP,ExAC,TOPMed,gnomAD
rs750339641	p.Phe165LeuPheSerTerUnk	frameshift	-	NC_000003.12:g.196242632A>-	NCI-TCGA
NCI-TCGA novel	p.Phe165Val	missense variant	-	NC_000003.12:g.196242634A>C	NCI-TCGA
rs888459030	p.Val166Ile	missense variant	-	NC_000003.12:g.196242631C>T	TOPMed
NCI-TCGA novel	p.Asp170Gly	missense variant	-	NC_000003.12:g.196242618T>C	NCI-TCGA
COSM3408548	p.Tyr173Ter	stop gained	Variant assessed as Somatic; HIGH impact.	NC_000003.12:g.196242608A>C	NCI-TCGA Cosmic
COSM460823	p.Ser174Leu	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196242606G>A	NCI-TCGA Cosmic
rs778531532	p.Ser175Thr	missense variant	-	NC_000003.12:g.196242604A>T	ExAC,gnomAD
rs770821991	p.Ala176Val	missense variant	-	NC_000003.12:g.196242600G>A	ExAC,TOPMed,gnomAD
rs1391986278	p.Gly177Ser	missense variant	-	NC_000003.12:g.196242598C>T	gnomAD
rs749270094	p.Ser178Thr	missense variant	-	NC_000003.12:g.196242594C>G	ExAC,TOPMed,gnomAD
rs777529998	p.Asp179Val	missense variant	-	NC_000003.12:g.196242591T>A	ExAC,TOPMed,gnomAD
rs773571578	p.Lys186Glu	missense variant	-	NC_000003.12:g.196242571T>C	TOPMed,gnomAD
rs587777195	p.Phe191Leu	missense variant	-	NC_000003.12:g.196242085A>G	-
rs587777195	p.Phe191Leu	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)	NC_000003.12:g.196242085A>G	UniProt,dbSNP
VAR_071087	p.Phe191Leu	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)	NC_000003.12:g.196242085A>G	UniProt
RCV000087321	p.Phe191Leu	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMD-CRD)	NC_000003.12:g.196242085A>G	ClinVar
COSM3591853	p.Thr194Ile	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196242075G>A	NCI-TCGA Cosmic
rs187437949	p.Gln195Arg	missense variant	-	NC_000003.12:g.196242072T>C	1000Genomes,ExAC,TOPMed,gnomAD
rs1408929771	p.Gln195Ter	stop gained	-	NC_000003.12:g.196242073G>A	TOPMed,gnomAD
rs1295174913	p.Gly199Asp	missense variant	-	NC_000003.12:g.196242060C>T	gnomAD
rs1189822613	p.Ile200Met	missense variant	-	NC_000003.12:g.196242056G>C	gnomAD
rs367857863	p.Ser201Phe	missense variant	-	NC_000003.12:g.196242054G>A	ESP,ExAC,TOPMed,gnomAD
rs1365448084	p.Thr202Ala	missense variant	-	NC_000003.12:g.196242052T>C	TOPMed
rs1162129680	p.Ile205Val	missense variant	-	NC_000003.12:g.196242043T>C	gnomAD
rs747258330	p.Arg208Ter	stop gained	-	NC_000003.12:g.196242034G>A	ExAC,TOPMed,gnomAD
rs867290911	p.Arg208Gln	missense variant	-	NC_000003.12:g.196242033C>T	-
COSM1485042	p.Ile209Ser	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196242030A>C	NCI-TCGA Cosmic
rs758512237	p.Arg211Trp	missense variant	-	NC_000003.12:g.196242025G>A	ExAC,gnomAD
COSM3774841	p.Arg211Gln	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196242024C>T	NCI-TCGA Cosmic
NCI-TCGA novel	p.Asp212Glu	missense variant	-	NC_000003.12:g.196242020A>C	NCI-TCGA
rs375261933	p.Ala217Val	missense variant	-	NC_000003.12:g.196242006G>A	ESP,ExAC,gnomAD
COSM446258	p.Arg218Ser	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196242002C>A	NCI-TCGA Cosmic
rs1330097122	p.Arg219Trp	missense variant	-	NC_000003.12:g.196242001G>A	gnomAD
rs1227589548	p.Gln222Ter	stop gained	-	NC_000003.12:g.196241992G>A	gnomAD
rs540053239	p.Arg223Ser	missense variant	-	NC_000003.12:g.196241987C>G	-
rs540053239	p.Arg223Ser	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)	NC_000003.12:g.196241987C>G	UniProt,dbSNP
VAR_071088	p.Arg223Ser	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)	NC_000003.12:g.196241987C>G	UniProt
RCV000087319	p.Arg223Ser	missense variant	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMD-CRD)	NC_000003.12:g.196241987C>G	ClinVar
rs201929666	p.Asn236Ser	missense variant	-	NC_000003.12:g.196241949T>C	1000Genomes,ExAC,gnomAD
rs778480685	p.Glu237Lys	missense variant	-	NC_000003.12:g.196239735C>T	ExAC,gnomAD
NCI-TCGA novel	p.Leu242Phe	missense variant	-	NC_000003.12:g.196239718C>A	NCI-TCGA
rs1339129542	p.Arg245Ser	missense variant	-	NC_000003.12:g.196239709C>A	TOPMed
rs781390558	p.Lys250Arg	missense variant	-	NC_000003.12:g.196239695T>C	ExAC,TOPMed,gnomAD
rs200025823	p.Lys254Glu	missense variant	-	NC_000003.12:g.196239684T>C	1000Genomes
COSM1043013	p.Glu262Ter	stop gained	Variant assessed as Somatic; HIGH impact.	NC_000003.12:g.196239660C>A	NCI-TCGA Cosmic
NCI-TCGA novel	p.Phe263Cys	missense variant	-	NC_000003.12:g.196239656A>C	NCI-TCGA
rs750077469	p.Val267Met	missense variant	-	NC_000003.12:g.196239645C>T	ExAC,TOPMed,gnomAD
NCI-TCGA novel	p.Ser271AlaPheSerTerUnkUnk	frameshift	-	NC_000003.12:g.196239633T>-	NCI-TCGA
rs1156587499	p.Ile272Val	missense variant	-	NC_000003.12:g.196239630T>C	gnomAD
rs753337043	p.Leu274Phe	missense variant	-	NC_000003.12:g.196239624G>A	ExAC,TOPMed,gnomAD
NCI-TCGA novel	p.Gln276Arg	missense variant	-	NC_000003.12:g.196239617T>C	NCI-TCGA
rs377634842	p.Lys277Arg	missense variant	-	NC_000003.12:g.196239614T>C	ESP,ExAC,TOPMed,gnomAD
rs1439542974	p.Trp278Arg	missense variant	-	NC_000003.12:g.196239612A>T	gnomAD
COSM1421985	p.Lys281SerPheSerTerUnkUnk	frameshift	Variant assessed as Somatic; HIGH impact.	NC_000003.12:g.196239602T>-	NCI-TCGA Cosmic
rs587777192	p.Arg283Ter	stop gained	-	NC_000003.12:g.196239597G>A	TOPMed,gnomAD
rs1282668916	p.Arg283Gln	missense variant	-	NC_000003.12:g.196239596C>T	gnomAD
RCV000087317	p.Arg283Ter	nonsense	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMD-CRD)	NC_000003.12:g.196239597G>A	ClinVar
rs775447503	p.Glu284Asp	missense variant	-	NC_000003.12:g.196239592T>A	ExAC
NCI-TCGA novel	p.Glu284Ter	stop gained	-	NC_000003.12:g.196239594C>A	NCI-TCGA
rs771791109	p.Ile286Val	missense variant	-	NC_000003.12:g.196239588T>C	ExAC,gnomAD
rs759307632	p.Ile286Thr	missense variant	-	NC_000003.12:g.196239587A>G	ExAC,gnomAD
rs1173104415	p.Ile286Met	missense variant	-	NC_000003.12:g.196239586A>C	TOPMed
rs1303263775	p.Phe289Ser	missense variant	-	NC_000003.12:g.196239578A>G	gnomAD
rs1232207713	p.Glu291Gln	missense variant	-	NC_000003.12:g.196239573C>G	gnomAD
rs1367500129	p.Gly294Arg	missense variant	-	NC_000003.12:g.196239564C>G	gnomAD
rs774447329	p.Pro295Leu	missense variant	-	NC_000003.12:g.196239560G>A	ExAC,TOPMed,gnomAD
rs1376024004	p.Leu299Pro	missense variant	-	NC_000003.12:g.196239548A>G	gnomAD
rs539292115	p.Gly306Arg	missense variant	-	NC_000003.12:g.196238876C>T	1000Genomes,TOPMed
COSM270718	p.Gly306Val	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196238875C>A	NCI-TCGA Cosmic
NCI-TCGA novel	p.Lys307ArgPheSerTerUnkUnkUnk	frameshift	-	NC_000003.12:g.196238874C>-	NCI-TCGA
rs1183286028	p.Gly308Asp	missense variant	-	NC_000003.12:g.196238869C>T	gnomAD
rs963356951	p.Arg309Trp	missense variant	-	NC_000003.12:g.196238867G>A	-
rs973487210	p.Arg309Gln	missense variant	-	NC_000003.12:g.196238866C>T	TOPMed,gnomAD
rs1240246373	p.Gln312Ter	stop gained	-	NC_000003.12:g.196238858G>A	gnomAD
NCI-TCGA novel	p.Gln312Arg	missense variant	-	NC_000003.12:g.196238857T>C	NCI-TCGA
rs773520771	p.Ala313Thr	missense variant	-	NC_000003.12:g.196238855C>T	ExAC,TOPMed,gnomAD
rs571188438	p.Ala313Asp	missense variant	-	NC_000003.12:g.196238854G>T	1000Genomes,ExAC,TOPMed,gnomAD
rs571188438	p.Ala313Val	missense variant	-	NC_000003.12:g.196238854G>A	1000Genomes,ExAC,TOPMed,gnomAD
rs1367107619	p.Ile314Leu	missense variant	-	NC_000003.12:g.196238852T>G	TOPMed
rs1217573932	p.Ser315Gly	missense variant	-	NC_000003.12:g.196238849T>C	TOPMed
rs1305786964	p.Ser315Asn	missense variant	-	NC_000003.12:g.196238848C>T	TOPMed,gnomAD
rs1305786964	p.Ser315Thr	missense variant	-	NC_000003.12:g.196238848C>G	TOPMed,gnomAD
rs1229173418	p.Pro316Ser	missense variant	-	NC_000003.12:g.196238846G>A	gnomAD
rs747402568	p.Pro316Leu	missense variant	-	NC_000003.12:g.196238845G>A	ExAC,TOPMed,gnomAD
rs751722689	p.Ser319Asn	missense variant	-	NC_000003.12:g.196238836C>T	gnomAD
RCV000414367	p.Ser319Ter	frameshift	-	NC_000003.12:g.196238836_196238837CT[3]	ClinVar
rs183054905	p.Pro320Leu	missense variant	-	NC_000003.12:g.196238833G>A	1000Genomes,ExAC,gnomAD
rs748967839	p.Pro320Ser	missense variant	-	NC_000003.12:g.196238834G>A	ExAC,TOPMed,gnomAD
rs1166285887	p.Ser322Gly	missense variant	-	NC_000003.12:g.196238828T>C	gnomAD
RCV000087322	p.Ser323Ter	frameshift	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMD-CRD)	NC_000003.12:g.196238824dup	ClinVar
rs372957517	p.Thr325Ala	missense variant	-	NC_000003.12:g.196238819T>C	ESP,ExAC,TOPMed,gnomAD
rs549056100	p.Arg326His	missense variant	-	NC_000003.12:g.196238815C>T	1000Genomes,TOPMed,gnomAD
rs766301243	p.Arg326Gly	missense variant	-	NC_000003.12:g.196238816G>C	ExAC,TOPMed,gnomAD
rs549056100	p.Arg326Pro	missense variant	-	NC_000003.12:g.196238815C>G	1000Genomes,TOPMed,gnomAD
rs766301243	p.Arg326Cys	missense variant	-	NC_000003.12:g.196238816G>A	ExAC,TOPMed,gnomAD
rs144403921	p.Glu327Gln	missense variant	-	NC_000003.12:g.196238813C>G	1000Genomes,ESP,ExAC,TOPMed,gnomAD
rs144403921	p.Glu327Lys	missense variant	-	NC_000003.12:g.196238813C>T	1000Genomes,ESP,ExAC,TOPMed,gnomAD
rs61737437	p.Arg328Cys	missense variant	-	NC_000003.12:g.196238810G>A	ExAC,TOPMed,gnomAD
rs61737437	p.Arg328Gly	missense variant	-	NC_000003.12:g.196238810G>C	ExAC,TOPMed,gnomAD
rs199831548	p.Arg328His	missense variant	-	NC_000003.12:g.196238809C>T	1000Genomes,ESP,ExAC,TOPMed,gnomAD
NCI-TCGA novel	p.Arg328Leu	missense variant	-	NC_000003.12:g.196238809C>A	NCI-TCGA
rs1479942890	p.Ser329Pro	missense variant	-	NC_000003.12:g.196238807A>G	gnomAD
rs551412906	p.Pro330Ser	missense variant	-	NC_000003.12:g.196238804G>A	1000Genomes,ExAC,TOPMed,gnomAD
rs1222327977	p.Pro330Leu	missense variant	-	NC_000003.12:g.196238803G>A	gnomAD
rs374831064	p.Ser331Ala	missense variant	-	NC_000003.12:g.196238801A>C	ESP,ExAC
RCV000087318	p.Ser331Ter	frameshift	Spondylometaphyseal dysplasia with cone-rod dystrophy (SMD-CRD)	NC_000003.12:g.196238806del	ClinVar
rs200703149	p.Pro332Ser	missense variant	-	NC_000003.12:g.196238798G>A	ExAC,TOPMed,gnomAD
rs754397679	p.Arg335Gln	missense variant	-	NC_000003.12:g.196238788C>T	ExAC,TOPMed,gnomAD
rs551199725	p.Arg335Ter	stop gained	-	NC_000003.12:g.196238789G>A	gnomAD
rs751579909	p.Trp336Ter	stop gained	-	NC_000003.12:g.196238784C>T	ExAC,TOPMed,gnomAD
rs142799242	p.Pro337Ser	missense variant	-	NC_000003.12:g.196238783G>A	ESP,ExAC,TOPMed,gnomAD
rs148500335	p.Pro337His	missense variant	-	NC_000003.12:g.196238782G>T	1000Genomes,ESP,ExAC,TOPMed,gnomAD
rs148500335	p.Pro337Leu	missense variant	-	NC_000003.12:g.196238782G>A	1000Genomes,ESP,ExAC,TOPMed,gnomAD
rs146337013	p.Gly340Cys	missense variant	-	NC_000003.12:g.196238774C>A	ESP,ExAC,TOPMed,gnomAD
rs146337013	p.Gly340Ser	missense variant	-	NC_000003.12:g.196238774C>T	ESP,ExAC,TOPMed,gnomAD
rs775986884	p.Pro344Leu	missense variant	-	NC_000003.12:g.196238761G>A	ExAC,gnomAD
rs1468052548	p.Cys346Tyr	missense variant	-	NC_000003.12:g.196238755C>T	gnomAD
rs772551986	p.Cys346Arg	missense variant	-	NC_000003.12:g.196238756A>G	ExAC,gnomAD
rs759958810	p.Ser347Ala	missense variant	-	NC_000003.12:g.196238753A>C	ExAC,TOPMed,gnomAD
rs759958810	p.Ser347Pro	missense variant	-	NC_000003.12:g.196238753A>G	ExAC,TOPMed,gnomAD
NCI-TCGA novel	p.Ser347Phe	missense variant	-	NC_000003.12:g.196238752G>A	NCI-TCGA
rs369326424	p.Pro348Ser	missense variant	-	NC_000003.12:g.196238750G>A	ESP,ExAC,TOPMed,gnomAD
rs369326424	p.Pro348Ala	missense variant	-	NC_000003.12:g.196238750G>C	ESP,ExAC,TOPMed,gnomAD
NCI-TCGA novel	p.Ala349Val	missense variant	-	NC_000003.12:g.196238746G>A	NCI-TCGA
COSM4116375	p.Ala349Gly	missense variant	Variant assessed as Somatic; MODERATE impact.	NC_000003.12:g.196238746G>C	NCI-TCGA Cosmic
rs200512211	p.Asn350Ser	missense variant	-	NC_000003.12:g.196238743T>C	1000Genomes,TOPMed,gnomAD
rs747858848	p.Leu351Phe	missense variant	-	NC_000003.12:g.196238741G>A	ExAC,gnomAD
rs1234408601	p.Arg353Lys	missense variant	-	NC_000003.12:g.196238734C>T	gnomAD
rs746462763	p.His354Arg	missense variant	-	NC_000003.12:g.196238731T>C	ExAC,gnomAD
rs780201072	p.His354Gln	missense variant	-	NC_000003.12:g.196238730G>C	ExAC,gnomAD
rs774160718	p.His354Tyr	missense variant	-	NC_000003.12:g.196238732G>A	ExAC,TOPMed,gnomAD
rs758409027	p.Ala356Gly	missense variant	-	NC_000003.12:g.196238725G>C	ExAC,gnomAD
rs376383380	p.Ala357Thr	missense variant	-	NC_000003.12:g.196238723C>T	ESP,ExAC,TOPMed,gnomAD
rs754092372	p.Asp360Gly	missense variant	-	NC_000003.12:g.196238713T>C	ExAC,TOPMed,gnomAD
rs764163062	p.Ser362Asn	missense variant	-	NC_000003.12:g.196238707C>T	ExAC,gnomAD
rs1393418641	p.Ser362Gly	missense variant	-	NC_000003.12:g.196238708T>C	gnomAD
rs146135588	p.Glu363Asp	missense variant	-	NC_000003.12:g.196238703C>G	ESP,ExAC,gnomAD
rs752768453	p.Glu365Lys	missense variant	-	NC_000003.12:g.196238699C>T	ExAC
NCI-TCGA novel	p.Glu366Lys	missense variant	-	NC_000003.12:g.196238696C>T	NCI-TCGA

Disease or phenotype associated information

Disease ID	Disease Name	Disease Type	Source
C0003873	Rheumatoid Arthritis	disease	BEFREE
C0004106	Astigmatism	disease	HPO
C0004134	Ataxia	phenotype	BEFREE
C0007137	Squamous cell carcinoma	disease	BEFREE
C0007758	Cerebellar Ataxia	phenotype	BEFREE
C0009398	Color vision defect	phenotype	HPO
C0010068	Coronary heart disease	disease	BEFREE
C0011847	Diabetes	disease	BEFREE
C0011849	Diabetes Mellitus	group	BEFREE
C0013336	Dwarfism	disease	HPO
C0014065	Congenital cerebral hernia	disease	HPO
C0014544	Epilepsy	disease	HPO
C0014859	Esophageal Neoplasms	group	BEFREE
C0016053	Fibromyalgia	disease	BEFREE
C0017636	Glioblastoma	disease	BEFREE
C0018790	Cardiac Arrest	disease	BEFREE
C0019193	Hepatitis, Toxic	disease	CTD_human
C0022578	Keratoconus	disease	HPO
C0023467	Leukemia, Myelocytic, Acute	disease	BEFREE
C0023470	Myeloid Leukemia	disease	BEFREE
C0024003	Lordosis	phenotype	HPO
C0024636	Malocclusion	phenotype	HPO
C0026764	Multiple Myeloma	disease	BEFREE
C0026827	Muscle hypotonia	phenotype	HPO
C0027092	Myopia	disease	HPO
C0027765	nervous system disorder	group	BEFREE
C0028077	Night Blindness	disease	HPO
C0028738	Nystagmus	disease	HPO
C0029463	Osteosarcoma	disease	BEFREE
C0030193	Pain	phenotype	BEFREE
C0030567	Parkinson Disease	disease	BEFREE
C0036572	Seizures	phenotype	HPO
C0037932	Curvature of spine	phenotype	HPO
C0038219	Status Dysraphicus	disease	CTD_human
C0080178	Spina Bifida	disease	BEFREE;CTD_human
C0085636	Photophobia	phenotype	HPO
C0086543	Cataract	disease	HPO
C0152018	Esophageal carcinoma	disease	BEFREE
C0153594	Malignant neoplasm of testis	disease	BEFREE
C0154920	Pigmentary iris degeneration	phenotype	HPO
C0162298	Joint stiffness	phenotype	HPO
C0205851	Germ cell tumor	group	BEFREE
C0220641	Lip and Oral Cavity Carcinoma	disease	BEFREE
C0221032	Familial generalized lipodystrophy	disease	BEFREE
C0221357	Brachydactyly	disease	HPO
C0234629	Abnormal color vision	phenotype	HPO
C0239138	Hip joint varus deformity - observation	phenotype	HPO
C0239594	Short finger	phenotype	HPO
C0241688	Peripheral visual field loss	phenotype	HPO
C0266508	Rachischisis	disease	CTD_human
C0266929	Chronic Periodontitis	disease	BEFREE
C0338591	Amnesia, Transient Global	disease	BEFREE
C0339527	Leber Congenital Amaurosis	disease	ORPHANET
C0345905	Intrahepatic Cholangiocarcinoma	disease	BEFREE
C0375206	Hemiplegia/hemiparesis	disease	HPO
C0409959	Osteoarthritis, Knee	disease	BEFREE
C0426826	Flared ribs	phenotype	HPO
C0476397	Electroretinogram abnormal	phenotype	HPO
C0543822	Atherosclerotic occlusive disease	disease	BEFREE
C0546837	Malignant neoplasm of esophagus	disease	BEFREE
C0566888	Narrow sacrosciatic notch	phenotype	HPO
C0585442	Osteosarcoma of bone	disease	BEFREE
C0596263	Carcinogenesis	phenotype	BEFREE
C0600139	Prostate carcinoma	disease	BEFREE
C0678222	Breast Carcinoma	disease	BEFREE
C0700208	Acquired scoliosis	phenotype	HPO
C0700635	Strudwick syndrome	disease	BEFREE;HPO
C0730290	Cone dystrophy	disease	HPO
C0747085	Recurrent otitis media	disease	HPO
C0854723	Retinal Dystrophies	group	BEFREE
C0860207	Drug-Induced Liver Disease	disease	CTD_human
C0950123	Genetic Diseases, Inborn	group	CLINVAR
C1140680	Malignant neoplasm of ovary	disease	BEFREE
C1262760	Hepatitis, Drug-Induced	disease	CTD_human
C1301509	Severe visual impairment	disease	HPO
C1332986	Childhood Osteosarcoma	disease	BEFREE
C1510497	Lens Opacities	phenotype	HPO
C1707444	Columnar Cell Change of the Breast	phenotype	BEFREE
C1720508	Retinal pigment epithelial abnormality	phenotype	HPO
C1836589	Decreased hip abduction	phenotype	HPO
C1837073	Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy	disease	BEFREE;CLINVAR;CTD_human;ORPHANET;UNIPROT
C1837078	Hypoplastic inferior ilia	phenotype	HPO
C1837081	Tibial bowing	phenotype	HPO
C1837082	Metaphyseal cupping	phenotype	HPO
C1837084	Short metacarpal	phenotype	HPO
C1837087	Macular pigmentary changes	phenotype	HPO
C1837249	Malformations of Cortical Development, Group II	disease	HPO
C1837454	SPINOCEREBELLAR ATAXIA 8	disease	BEFREE
C1838662	Metaphyseal irregularity	phenotype	HPO
C1839364	Progressive visual loss	phenotype	HPO
C1842083	Abnormality of the ribs	phenotype	HPO
C1842937	AURAL ATRESIA, CONGENITAL	disease	BEFREE
C1844548	Hypoplastic finger	phenotype	HPO
C1844704	Platyspondyly	phenotype	HPO
C1849039	Metaphyseal widening	phenotype	HPO
C1850293	Severe platyspondyly	phenotype	HPO
C1855340	Bowing of the long bones	phenotype	HPO
C1855665	Ovoid vertebral bodies	phenotype	HPO
C1855676	Aplasia/Hypoplasia of the cerebellar vermis	phenotype	HPO
C1859461	Femoral bowing	phenotype	HPO
C1859778	Postnatal growth retardation	phenotype	HPO
C1862475	Abnormality of retinal pigmentation	phenotype	HPO
C1865039	Cupped ribs	phenotype	HPO
C1866730	Rhizomelia	disease	HPO
C2239176	Liver carcinoma	disease	BEFREE
C2937228	Tunnel visual field constriction	phenotype	HPO
C3277697	Decreased visual acuity, progressive	phenotype	HPO
C3280770	Cerebellar vermis aplasia or hypoplasia	phenotype	HPO
C3552853	Color vision defect, severe	phenotype	HPO
C3658290	Drug-Induced Acute Liver Injury	disease	CTD_human
C3665386	Abnormal vision	phenotype	HPO
C3714756	Intellectual Disability	group	GENOMICS_ENGLAND
C3808249	Abnormality of the optic disc	phenotype	HPO
C3840049	Dysexecutive syndrome	disease	BEFREE
C4020844	Bullet vertebral body	phenotype	HPO
C4020885	Difficulties with night vision	phenotype	HPO
C4020887	Photodysphoria	phenotype	HPO
C4024665	High-grade hypermetropia	phenotype	HPO
C4024756	Abnormality of macular pigmentation	phenotype	HPO
C4025800	Large central visual field defect	phenotype	HPO
C4085590	Cone-Rod Dystrophies	disease	HPO
C4229565	Loss in color vision	phenotype	HPO
C4275024	Spinocerebellar ataxia type 8	disease	BEFREE
C4277682	Chemical and Drug Induced Liver Injury	disease	CTD_human
C4279912	Chemically-Induced Liver Toxicity	disease	CTD_human
C4280613	Angle class 3 malocclusion	phenotype	HPO
C4280614	Angle class 2 malocclusion	disease	HPO

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID	GO Term	Evidence
GO:0004105	choline-phosphate cytidylyltransferase activity	ISS
GO:0004105	choline-phosphate cytidylyltransferase activity	IBA
GO:0005516	calmodulin binding	IEA
GO:0031210	phosphatidylcholine binding	IBA
GO:0042803	protein homodimerization activity	IEA

GO:Biological Process

GO ID	GO Term	Evidence
GO:0006656	phosphatidylcholine biosynthetic process	ISS
GO:0006656	phosphatidylcholine biosynthetic process	TAS
GO:0006657	CDP-choline pathway	ISS

GO:Cellular Component

GO ID	GO Term	Evidence
GO:0005635	nuclear envelope	IEA
GO:0005737	cytoplasm	IBA
GO:0005783	endoplasmic reticulum	IBA
GO:0005789	endoplasmic reticulum membrane	ISS
GO:0005789	endoplasmic reticulum membrane	TAS
GO:0005829	cytosol	IEA
GO:0005886	plasma membrane	IEA
GO:0042587	glycogen granule	ISS

Reactome Pathway

Reactome ID	Reactome Term	Evidence
R-HSA-1430728	Metabolism	TAS
R-HSA-1483191	Synthesis of PC	TAS
R-HSA-1483206	Glycerophospholipid biosynthesis	TAS
R-HSA-1483257	Phospholipid metabolism	TAS
R-HSA-556833	Metabolism of lipids	TAS

Drugs and compounds information

ID	Drug Name	Action	PubMed
C517943	1-(4-(6-bromobenzo(1,3)dioxol-5-yl)-3a,4,5,9b-tetrahydro-3H-cyclopenta(c)quinolin-8-yl)ethanone	1-(4-(6-bromobenzo(1,3)dioxol-5-yl)-3a,4,5,9b-tetrahydro-3H-cyclopenta(c)quinolin-8-yl)ethanone results in decreased phosphorylation of PCYT1A protein	27026707
D015655	1-Methyl-4-phenylpyridinium	U 0126 affects the reaction [1-Methyl-4-phenylpyridinium affects the expression of PCYT1A mRNA]	12710931
C029790	2,2',3',4,4',5-hexachlorobiphenyl	2,2',3',4,4',5-hexachlorobiphenyl results in decreased expression of PCYT1A mRNA	23829299
C016403	2,4-dinitrotoluene	2,4-dinitrotoluene affects the expression of PCYT1A mRNA	21346803
C572491	3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-ol	3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-ol results in increased expression of PCYT1A protein	26194647
D016604	Aflatoxin B1	Aflatoxin B1 results in increased expression of PCYT1A mRNA	19770486
D000643	Ammonium Chloride	Ammonium Chloride affects the expression of PCYT1A mRNA	16483693
D000069059	Atorvastatin	Atorvastatin results in decreased activity of PCYT1A protein	9653895
D000069059	Atorvastatin	Atorvastatin results in increased activity of PCYT1A protein	12056585
D001564	Benzo(a)pyrene	Benzo(a)pyrene results in increased expression of PCYT1A mRNA	21632981
D001629	Bezafibrate	Bezafibrate results in decreased activity of PCYT1A protein	9653895
C006780	bisphenol A	bisphenol A results in increased expression of PCYT1A mRNA	21932408
C006780	bisphenol A	bisphenol A results in decreased expression of PCYT1A mRNA	25181051
C006780	bisphenol A	bisphenol A results in increased expression of PCYT1A mRNA	30816183
D000069286	Bortezomib	Bortezomib results in increased expression of PCYT1A mRNA	20977926
D000069286	Bortezomib	[BRCA1 mutant form results in increased susceptibility to Bortezomib] which results in increased expression of PCYT1A mRNA	25522274
D002065	Buspirone	Buspirone results in increased expression of PCYT1A mRNA	24136188
D002104	Cadmium	Cadmium results in increased expression of PCYT1A mRNA	17066326
D019256	Cadmium Chloride	Cadmium Chloride results in increased expression of PCYT1A mRNA	17066326
D002330	Carmustine	Carmustine results in decreased expression of PCYT1A mRNA	15980968
C018021	cobaltous chloride	cobaltous chloride results in increased expression of PCYT1A mRNA	19320972
D019327	Copper Sulfate	Copper Sulfate results in increased expression of PCYT1A mRNA	19549813
D016572	Cyclosporine	Cyclosporine results in increased expression of PCYT1A mRNA	20106945; 27989131;
D004041	Dietary Fats	Dietary Fats results in decreased expression of PCYT1A mRNA	25016146
D004041	Dietary Fats	Dietary Fats results in increased expression of PCYT1A mRNA	19030233
D004317	Doxorubicin	Doxorubicin results in decreased expression of PCYT1A mRNA	29803840
D004791	Enzyme Inhibitors	[Enzyme Inhibitors results in decreased activity of OGA protein] which results in increased O-linked glycosylation of PCYT1A protein	23301498
D004958	Estradiol	Estradiol affects the phosphorylation of PCYT1A protein	27026707
D000431	Ethanol	Ethanol affects the splicing of PCYT1A mRNA	30319688
D004997	Ethinyl Estradiol	Ethinyl Estradiol results in increased expression of PCYT1A mRNA	17942748
D004997	Ethinyl Estradiol	[Tetrachlorodibenzodioxin co-treated with Ethinyl Estradiol] results in increased expression of PCYT1A mRNA	17942748
D004997	Ethinyl Estradiol	Ethinyl Estradiol results in increased expression of PCYT1A mRNA	23129252
D005419	Flavonoids	Flavonoids results in decreased expression of PCYT1A mRNA	18035473
D005485	Flutamide	Flutamide results in increased expression of PCYT1A mRNA	24136188
C039281	furan	furan results in increased expression of PCYT1A mRNA	26194646
D008694	Methamphetamine	Methamphetamine results in decreased expression of PCYT1A mRNA	29802913
D008727	Methotrexate	Methotrexate results in increased expression of PCYT1A mRNA	15120968
C004925	methylmercuric chloride	methylmercuric chloride results in decreased expression of PCYT1A mRNA	23103053
D008798	Mevalonic Acid	Mevalonic Acid results in increased activity of PCYT1A protein	12056585
D008798	Mevalonic Acid	Mevalonic Acid results in increased expression of PCYT1A mRNA	12056585
C000622638	MLN7243	MLN7243 results in increased sumoylation of PCYT1A protein	31285264
C016599	mono-(2-ethylhexyl)phthalate	mono-(2-ethylhexyl)phthalate results in decreased expression of PCYT1A mRNA	22401849
C523799	MRK 003	PCYT1A results in increased susceptibility to MRK 003	19903844
D009532	Nickel	Nickel results in increased expression of PCYT1A mRNA	24768652; 25583101;
D018817	N-Methyl-3,4-methylenedioxyamphetamine	N-Methyl-3,4-methylenedioxyamphetamine results in decreased expression of PCYT1A mRNA	26251327
D018817	N-Methyl-3,4-methylenedioxyamphetamine	N-Methyl-3,4-methylenedioxyamphetamine results in increased expression of PCYT1A mRNA	20188158
D018817	N-Methyl-3,4-methylenedioxyamphetamine	N-Methyl-3,4-methylenedioxyamphetamine results in increased methylation of PCYT1A promoter	26251327
D000077150	Oxaliplatin	[Oxaliplatin co-treated with Topotecan] results in decreased expression of PCYT1A mRNA	25729387
C410127	PCB 180	PCB 180 results in increased expression of PCYT1A mRNA	23829299
C023036	perfluorooctanoic acid	perfluorooctanoic acid results in decreased expression of PCYT1A protein	26879310
D010634	Phenobarbital	Phenobarbital affects the expression of PCYT1A mRNA	23091169
D010713	Phosphatidylcholines	PCYT1A protein promotes the reaction [PLPP6 protein results in increased chemical synthesis of Phosphatidylcholines]	18930839
C006253	pirinixic acid	pirinixic acid results in decreased expression of PCYT1A mRNA	17426115
C006253	pirinixic acid	pirinixic acid results in increased expression of PCYT1A mRNA	18301758
D010936	Plant Extracts	Plant Extracts results in increased expression of PCYT1A mRNA	23557933
D012822	Silicon Dioxide	Silicon Dioxide results in increased expression of PCYT1A mRNA	29203145
C017947	sodium arsenite	sodium arsenite results in decreased expression of PCYT1A mRNA	19822182
D012999	Soman	Soman results in increased expression of PCYT1A mRNA	19281266
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin results in increased expression of PCYT1A mRNA	17555868
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin affects the expression of PCYT1A mRNA	21570461; 26377647;
D013749	Tetrachlorodibenzodioxin	[Tetrachlorodibenzodioxin co-treated with Ethinyl Estradiol] results in increased expression of PCYT1A mRNA	17942748
D014028	Tobacco Smoke Pollution	Tobacco Smoke Pollution results in increased expression of PCYT1A mRNA	28065790
D000077867	Tolcapone	Tolcapone binds to PCYT1A protein	19783845
D019772	Topotecan	[Oxaliplatin co-treated with Topotecan] results in decreased expression of PCYT1A mRNA	25729387
C483909	torcetrapib	torcetrapib results in increased expression of PCYT1A mRNA	23228038
D014280	Triglycerides	PCYT1A protein inhibits the reaction [PLPP6 protein results in increased abundance of Triglycerides]	18930839
C113580	U 0126	U 0126 affects the reaction [1-Methyl-4-phenylpyridinium affects the expression of PCYT1A mRNA]	12710931
D014635	Valproic Acid	Valproic Acid results in increased expression of PCYT1A mRNA	23179753; 28001369;
D015032	Zinc	Zinc affects the expression of PCYT1A mRNA	17181878

Functional annotations

Keywords

Keyword ID	Keyword Term
KW-0007	Acetylation
KW-0182	Cone-rod dystrophy
KW-0963	Cytoplasm
KW-0225	Disease mutation
KW-0242	Dwarfism
KW-0444	Lipid biosynthesis
KW-0443	Lipid metabolism
KW-0472	Membrane
KW-0548	Nucleotidyltransferase
KW-0594	Phospholipid biosynthesis
KW-1208	Phospholipid metabolism
KW-0597	Phosphoprotein
KW-1185	Reference proteome
KW-0677	Repeat
KW-0808	Transferase
KW-0832	Ubl conjugation

Interpro

InterPro ID	InterPro Term
IPR041723	CCT
IPR004821	Cyt_trans-like
IPR014729	Rossmann-like_a/b/a_fold

PROSITE

PROSITE ID	PROSITE Term

Pfam

Pfam ID	Pfam Term
PF01467	CTP_transf_like

Gene: PCYT1A

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

There is no orthologous record for this gene !

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