ConVarT

lpar1 (GeneID: 100124893) | Xenopus tropicalis

Description:	Xenopus tropicalis lysophosphatidic acid receptor 1 (lpar1), mRNA. [Source:RefSeq mRNA;Acc:NM_001102843]
Synonyms:	lpar1-b, lpa1, vzg-1, edg-2, lpa1r1, gpr26, par1-a, lpa1r, vzg1, edg2
Other ID(s):	XB-GENE-958415, ENSXETG00000002597
Protein Accession Numbers:	XP_012819232, XP_012819199, NP_001096313
Statistics:	ClinVar(70) gnomAD(702) COSMIC(1465) PTM(7)

ClinVar Pathogenicity of Variations

ClinVar Data

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Variation ID	Allele ID	RS Number	Variant Type	Record	Alteration	Clinicial Sig.	Last Update	Phenotypes	Cytogenetic	Review Status	RCV Acc.N.

gnomAD

Frameshift Variant

Inframe Deletion

Missense Variant

Splice Region Variant

Start Lost

Stop Gained

Synonymous Variant

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Variant ID	Transcript ID	Alteration	Annotation	Allele C.	Allele N.	Allele F.	rsNumber
9-113637705-A-G	ENST00000358883	p.Val364Ala	Missense Variant	0	0	0	rs752725919
9-113637705-A-G	ENST00000374430	p.Val364Ala	Missense Variant	0	0	0	rs752725919
9-113637705-A-G	ENST00000374431	p.Val364Ala	Missense Variant	0	0	0	rs752725919
9-113637712-A-G	ENST00000358883	p.Ser362Pro	Missense Variant	0	0	0	rs756095056
9-113637712-A-G	ENST00000374430	p.Ser362Pro	Missense Variant	0	0	0	rs756095056
9-113637712-A-G	ENST00000374431	p.Ser362Pro	Missense Variant	0	0	0	rs756095056
9-113637714-T-C	ENST00000358883	p.His361Arg	Missense Variant	0	0	0	rs777712568
9-113637714-T-C	ENST00000374430	p.His361Arg	Missense Variant	0	0	0	rs777712568
9-113637714-T-C	ENST00000374431	p.His361Arg	Missense Variant	0	0	0	rs777712568
9-113637720-T-C	ENST00000358883	p.Asn359Ser	Missense Variant	0	0	0	rs1048242692
9-113637720-T-C	ENST00000374430	p.Asn359Ser	Missense Variant	0	0	0	rs1048242692
9-113637720-T-C	ENST00000374431	p.Asn359Ser	Missense Variant	0	0	0	rs1048242692
9-113637724-T-C	ENST00000358883	p.Ser358Gly	Missense Variant	0	0	0	rs1170045607
9-113637724-T-C	ENST00000374430	p.Ser358Gly	Missense Variant	0	0	0	rs1170045607
9-113637724-T-C	ENST00000374431	p.Ser358Gly	Missense Variant	0	0	0	rs1170045607
9-113637741-A-G	ENST00000358883	p.Ile352Thr	Missense Variant	24	31394	0.000764	rs147367410
9-113637741-A-G	ENST00000374430	p.Ile352Thr	Missense Variant	24	31394	0.000764	rs147367410
9-113637741-A-G	ENST00000374431	p.Ile352Thr	Missense Variant	24	31394	0.000764	rs147367410
9-113637742-T-A	ENST00000358883	p.Ile352Phe	Missense Variant	0	0	0	rs147557148
9-113637742-T-A	ENST00000374430	p.Ile352Phe	Missense Variant	0	0	0	rs147557148

Showing 1 to 20 of 702 entries

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Post-translational Modifications (PTMs)

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Gene Name	ACC ID	PTM Type	Position	Mod-rsd	Site +/-7 Aa	Mw_kd	Site grpID
LPAR1	Q92633	Phosphorylation	236	T236-p	FGYVRQRtMRMsRHs	41.11	2764301
LPAR1	Q92633	Phosphorylation	240	S240-p	RQRtMRMsRHssGPR	41.11	22350325
LPAR1	Q92633	Phosphorylation	243	S243-p	tMRMsRHssGPRRNR	41.11	11136442
LPAR1	Q92633	Phosphorylation	244	S244-p	MRMsRHssGPRRNRD	41.11	11136446
LPAR1	Q92633	Phosphorylation	341	S341-p	PTGPTEGsDRsASSL	41.11	34502845
LPAR1	Q92633	Phosphorylation	344	S344-p	PTEGsDRsASSLNHT	41.11	4710491
LPAR1	Q92633	Phosphorylation	358	S358-p	TILAGVHsNDHSVV_	41.11	4710511

Showing 1 to 7 of 7 entries

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Catalogue of Somatic Mutations in Cancer (COSMIC)

Deletion - Frameshift

Nonstop Extension

Substitution - Coding Silent

Substitution - Missense

Substitution - Nonsense

Unknown

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Gene Name	Transcript ID	Sample name	Primary Site	Primary Histology	Mutation ID	Mutation CDS	Mutation Aa	Mutation Desc.	FATHMM Prediction	FATHMM Score	Mutation Somatic Status	PUBMED PMID	Tumor Origin	Position
LPAR1	ENST00000374431	TCGA-DA-A1HY-06	skin	malignant_melanoma	39078834	c.240C>T	p.F80=	Substitution - coding silent	PATHOGENIC	.94508	Confirmed somatic variant	PMID: N/A	NS	80
LPAR1	ENST00000374431	0213_CRUK_PC_0213_T1_DNA	prostate	carcinoma	39076858	c.793+24049A>G	p.?	Unknown	NEUTRAL	.04672	Confirmed somatic variant	PMID: N/A	primary	0
LPAR1	ENST00000374431	CPCG0237-F1	prostate	carcinoma	39075139	c.793+9776dup	p.?	Unknown			Confirmed somatic variant	PMID: N/A	primary	0
LPAR1	ENST00000374431	TCGA-DA-A1I5-06	skin	malignant_melanoma	39076209	c.528C>T	p.I176=	Substitution - coding silent	NEUTRAL	.14468	Confirmed somatic variant	PMID: N/A	NS	176
LPAR1	ENST00000374431	J32_T	lung	carcinoma	39078601	c.793+7279C>T	p.?	Unknown	NEUTRAL	.03671	Confirmed somatic variant	PMID: N/A	NS	0
LPAR1	ENST00000374431	RK107_C01	liver	carcinoma	39079435	c.-181-3922A>C	p.?	Unknown	NEUTRAL	.03803	Variant of unknown origin	PMID: N/A	primary	0
LPAR1	ENST00000374431	RK107_C01	liver	carcinoma	39079440	c.-181-10871T>A	p.?	Unknown	NEUTRAL	.00325	Variant of unknown origin	PMID: N/A	primary	0
LPAR1	ENST00000374431	EOPC-171_tumor_01	prostate	carcinoma	39079621	c.45+10745T>C	p.?	Unknown	NEUTRAL	.00256	Confirmed somatic variant	PMID: N/A	primary	0
LPAR1	ENST00000374431	RK144_C01	liver	carcinoma	39076894	c.-181-14453T>C	p.?	Unknown	NEUTRAL	.00616	Confirmed somatic variant	PMID: N/A	NS	0
LPAR1	ENST00000374431	tumor_4124432	haematopoietic_and_lymphoid_tissue	lymphoid_neoplasm	39079795	c.794-2826G>T	p.?	Unknown	NEUTRAL	.04773	Confirmed somatic variant	PMID: N/A	primary	0
LPAR1	ENST00000374431	AOCS-135-3-1	ovary	carcinoma	39076147	c.794-13842C>A	p.?	Unknown	NEUTRAL	.00147	Confirmed somatic variant	PMID: N/A	NS	0
LPAR1	ENST00000374431	tumor_4124432	haematopoietic_and_lymphoid_tissue	lymphoid_neoplasm	39079800	c.793+30370T>G	p.?	Unknown	NEUTRAL	.00549	Confirmed somatic variant	PMID: N/A	primary	0
LPAR1	ENST00000374431	PET134T	pancreas	carcinoid-endocrine_tumour	39077389	c.*1620C>T	p.?	Unknown	NEUTRAL	.0346	Confirmed somatic variant	PMID: N/A	primary	0
LPAR1	ENST00000374431	04-149J1	prostate	carcinoma	39077794	c.793+72C>G	p.?	Unknown	NEUTRAL	.04473	Confirmed somatic variant	PMID: 26928463	primary	0
LPAR1	ENST00000374431	5-VS018-T1	skin	carcinoma	39076406	c.748C>T	p.R250W	Substitution - Missense	PATHOGENIC	.95291	Confirmed somatic variant	PMID: 26950094	NS	250
LPAR1	ENST00000374431	5-VS018-T1	skin	carcinoma	39076461	c.96C>T	p.F32=	Substitution - coding silent	PATHOGENIC	.96079	Confirmed somatic variant	PMID: 26950094	NS	32
LPAR1	ENST00000374431	S02120_1	lung	carcinoma	39075242	c.619T>C	p.L207=	Substitution - coding silent	PATHOGENIC	.80891	Confirmed somatic variant	PMID: 26168399	primary	207
LPAR1	ENST00000374431	ccRCC-64	kidney	carcinoma	39076277	c.45+11475A>G	p.?	Unknown	NEUTRAL	.0032	Confirmed somatic variant	PMID: 23797736	NS	0
LPAR1	ENST00000374431	LP6005500-DNA_G02	oesophagus	carcinoma	39074621	c.-182+27192G>C	p.?	Unknown	NEUTRAL	.06559	Confirmed somatic variant	PMID: N/A	primary	0
LPAR1	ENST00000374431	ML_75_T_01	skin	carcinoma	39074934	c.46-14040T>C	p.?	Unknown	NEUTRAL	.00257	Confirmed somatic variant	PMID: N/A	primary	0

Showing 1 to 20 of 1,465 entries

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dbSNP

Gene ID	Transcript ID	Consequence	Position	HGVSp	Impact

Protein Domains (PFAM)

Pfam Domain	Domain Name	Description	Positions	Clan	Clan Name	Organism
NO RESULT FOUND
PF00001	7tm_1	7 transmembrane receptor (rhodopsin family)	66-311	CL0192	GPCR_A	Homo sapiens

List of the diseases from DisGeNET

Disease Name	Disease Category	DSI*	DPI**
Anosmia	Nervous System Diseases ; Pathological Conditions, Signs and Symptoms ;	0.586	0.552
Malignant neoplasm of breast	Neoplasms ; Skin and Connective Tissue Diseases ;	0.586	0.552
Fetal Death	Female Urogenital Diseases and Pregnancy Complications ; Pathological Conditions, Signs and Symptoms ;	0.586	0.552
Growth Disorders	Pathological Conditions, Signs and Symptoms ;	0.586	0.552
Leukemia, Myelocytic, Acute	Neoplasms ;	0.586	0.552
Acute Myeloid Leukemia, M1	Neoplasms ;	0.586	0.552
Prostatic Neoplasms	Neoplasms ; Male Urogenital Diseases ;	0.586	0.552
Schizophrenia	Mental Disorders ;	0.586	0.552
Malignant neoplasm of prostate	Neoplasms ; Male Urogenital Diseases ;	0.586	0.552
Craniofacial Abnormalities	Musculoskeletal Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ;	0.586	0.552
Olfaction Disorders	Nervous System Diseases ; Pathological Conditions, Signs and Symptoms ;	0.586	0.552
Breast Carcinoma	Neoplasms ; Skin and Connective Tissue Diseases ;	0.586	0.552
Mammary Neoplasms, Human	Neoplasms ; Skin and Connective Tissue Diseases ;	0.586	0.552
Mammary Neoplasms	Neoplasms ; Skin and Connective Tissue Diseases ;	0.586	0.552
Sense of smell altered	Nervous System Diseases ; Pathological Conditions, Signs and Symptoms ;	0.586	0.552
Acute Myeloid Leukemia (AML-M2)	Neoplasms ;	0.586	0.552
Cacosmia	Nervous System Diseases ; Pathological Conditions, Signs and Symptoms ;	0.586	0.552
NO RESULT FOUND

Classification of Clinicial Significance of ClinVar Data