GPR143

G protein-coupled receptor 143, the group of 7TM uncharacterized proteins

Basic information

Region (hg38): X:9725345-9786297

Previous symbols: [ "OA1" ]

Links

ENSG00000101850 ∙ NCBI:4935 ∙ OMIM:300808 ∙ HGNC:20145 ∙ Uniprot:P51810 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• X-linked recessive ocular albinism (Supportive), mode of inheritance: XL
• X-linked recessive ocular albinism (Strong), mode of inheritance: XL
• nystagmus 6, congenital, X-linked (Strong), mode of inheritance: XL
• inherited retinal dystrophy (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nystagmus 6, congenital, X-linked; Ocular albinism, type I	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic; Ophthalmologic	7915878; 7647783; 8634705; 9887374; 9529334; 11214907; 11520764; 11793467; 17516023; 18523664; 19123159; 19390656; 19604113; 19610097; 20301517; 20649618; 21274678; 21348135; 21423867; 22916221

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GPR143 gene.

• not provided (305 variants)
• Inborn genetic diseases (18 variants)
• not specified (13 variants)
• Ocular albinism, type I (12 variants)
• GPR143-related condition (8 variants)
• Nystagmus 6, congenital, X-linked (7 variants)
• Albinism (1 variants)
• Reduced eye contact;Ocular albinism;Nystagmus (1 variants)
• Ocular albinism, type I;Nystagmus 6, congenital, X-linked (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPR143 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				50	7	57
missense	4	8	110	5	9	136
nonsense	13					13
start loss	3	1				4
frameshift	19	2				21
inframe indel		1				1
splice donor/acceptor (+/-2bp)	9	9			1	19
splice region		2	3	6	1	12
non coding	1		1	21	14	37
Total	49	21	111	76	31

Highest pathogenic variant AF is 0.0000180

Variants in GPR143

This is a list of pathogenic ClinVar variants found in the GPR143 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-9725612-G-A			Benign (May 12, 2021)
X-9725758-A-C			Uncertain significance (Jun 05, 2022)
X-9725768-A-G			Benign (Jan 21, 2024)
X-9725769-G-A			Uncertain significance (Apr 04, 2022)
X-9725772-C-A			Uncertain significance (Jul 28, 2023)
X-9725779-A-G			Likely benign (Nov 27, 2023)
X-9725790-T-C			Uncertain significance (Mar 28, 2022)
X-9725804-C-T		Inborn genetic diseases	Uncertain significance (Jun 05, 2022)
X-9725805-T-C		GPR143-related disorder	Uncertain significance (Jul 07, 2023)
X-9725806-T-G			Benign (Jul 19, 2023)
X-9725810-G-A			Uncertain significance (Jan 28, 2021)
X-9725810-G-C			Uncertain significance (Oct 20, 2023)
X-9725816-A-T			Uncertain significance (Nov 07, 2023)
X-9725822-A-G			Uncertain significance (Mar 16, 2023)
X-9725828-C-T			Benign (Jan 02, 2024)
X-9725831-G-A			Uncertain significance (Jul 07, 2023)
X-9725844-G-C			Likely benign (Jul 15, 2022)
X-9739333-G-A			Benign (May 12, 2021)
X-9739465-T-C			Likely benign (Oct 21, 2021)
X-9739469-G-A		not specified	Benign (Jan 15, 2024)
X-9739470-C-A			Benign (Jan 12, 2024)
X-9739472-G-A			Likely benign (Dec 18, 2022)
X-9739474-CAG-C			Likely benign (Sep 03, 2022)
X-9739481-T-C		not specified	Benign (Jan 29, 2024)
X-9739492-C-G			Likely benign (Jul 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPR143	protein_coding	protein_coding	ENST00000467482	9	60952

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.925	0.0747	125686	6	10	125702	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.879	111	140	0.791	0.0000108	2562
Missense in Polyphen		26	51.408	0.50576		979
Synonymous	-0.161	64	62.4	1.03	0.00000541	853
Loss of Function	3.04	1	12.7	0.0788	8.78e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000952	0.000775
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000724	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000126	0.00000879
Middle Eastern	0.0000724	0.0000544
South Asian	0.0000528	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for tyrosine, L-DOPA and dopamine. After binding to L-DOPA, stimulates Ca(2+) influx into the cytoplasm, increases secretion of the neurotrophic factor SERPINF1 and relocalizes beta arrestin at the plasma membrane; this ligand- dependent signaling occurs through a G(q)-mediated pathway in melanocytic cells. Its activity is mediated by G proteins which activate the phosphoinositide signaling pathway. Plays also a role as an intracellular G protein-coupled receptor involved in melanosome biogenesis, organization and transport. {ECO:0000269|PubMed:10471510, ECO:0000269|PubMed:16524428, ECO:0000269|PubMed:18697795, ECO:0000269|PubMed:18828673, ECO:0000269|PubMed:19717472}.
• Disease: DISEASE: Albinism ocular 1 (OA1) [MIM:300500]: Form of albinism affecting only the eye. Pigment of the hair and skin is normal or only slightly diluted. Eyes may be severely affected with photophobia and reduced visual acuity. Nystagmus or strabismus are often associated. The irides and fundus are depigmented. {ECO:0000269|PubMed:11115845, ECO:0000269|PubMed:11214907, ECO:0000269|PubMed:16524428, ECO:0000269|PubMed:16621890, ECO:0000269|PubMed:16646960, ECO:0000269|PubMed:17822861, ECO:0000269|PubMed:17960122, ECO:0000269|PubMed:18697795, ECO:0000269|PubMed:18978956, ECO:0000269|PubMed:8634705, ECO:0000269|PubMed:9529334, ECO:0000269|PubMed:9887374}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Nystagmus congenital X-linked 6 (NYS6) [MIM:300814]: A condition defined as conjugated, spontaneous and involuntary ocular oscillations that appear at birth or during the first three months of life. Other associated features may include mildly decreased visual acuity, strabismus, astigmatism, and occasionally head nodding. {ECO:0000269|PubMed:17516023}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: GPCRs, Other;Signaling by GPCR;Signal Transduction;Amine ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.227

Intolerance Scores

• loftool: 0.0848
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.104
• hipred: Y
• hipred_score: 0.644
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Gpr143
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; pigmentation phenotype

Zebrafish Information Network

• Gene name: gpr143
• Affected structure: retinal pigmented epithelium
• Phenotype tag: abnormal
• Phenotype quality: decreased pigmentation

Gene ontology

• Biological process: eye pigment biosynthetic process;signal transduction;G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;visual perception;melanosome localization;melanosome transport;melanosome organization;calcium-mediated signaling using intracellular calcium source;phosphatidylinositol-mediated signaling;regulation of calcium-mediated signaling;regulation of melanosome transport;regulation of melanosome organization
• Cellular component: cytoplasm;lysosomal membrane;Golgi apparatus;plasma membrane;membrane;integral component of membrane;apical plasma membrane;melanosome membrane;melanosome
• Molecular function: G protein-coupled receptor activity;protein binding;dopamine binding;L-DOPA receptor activity;L-DOPA binding;tyrosine binding