ADGRD1

adhesion G protein-coupled receptor D1, the group of Adhesion G protein-coupled receptors, subfamily D

Basic information

Region (hg38): 12:130953906-131141469

Previous symbols: [ "GPR133" ]

Links

ENSG00000111452 ∙ NCBI:283383 ∙ OMIM:613639 ∙ HGNC:19893 ∙ Uniprot:Q6QNK2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADGRD1 gene.

• Inborn genetic diseases (29 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADGRD1 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			1	2		3
missense			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	28	4	0

Variants in ADGRD1

This is a list of pathogenic ClinVar variants found in the ADGRD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-130966478-C-T		not specified	Uncertain significance (Jan 18, 2023)
12-130971529-G-A		not specified	Uncertain significance (Aug 04, 2023)
12-130971568-T-C		not specified	Uncertain significance (Nov 19, 2022)
12-130981944-C-T		not specified	Uncertain significance (Aug 09, 2021)
12-130981994-G-A		not specified	Uncertain significance (Mar 27, 2023)
12-130982041-G-T		not specified	Uncertain significance (May 31, 2023)
12-130987097-C-G		not specified	Uncertain significance (Jul 01, 2023)
12-130987198-T-G			Likely benign (Jan 01, 2023)
12-130987213-G-T		not specified	Uncertain significance (Sep 16, 2021)
12-130987245-A-G		not specified	Uncertain significance (Feb 15, 2023)
12-130992264-A-C		not specified	Uncertain significance (Sep 26, 2023)
12-130992264-A-G		not specified	Uncertain significance (Jun 02, 2023)
12-130992364-C-T		not specified	Uncertain significance (May 17, 2023)
12-131003188-A-G		not specified	Uncertain significance (May 27, 2022)
12-131003267-C-T		not specified	Uncertain significance (Aug 16, 2021)
12-131003278-G-A		not specified	Likely benign (Nov 08, 2021)
12-131004203-A-C		not specified	Likely benign (Sep 27, 2022)
12-131004237-G-A		not specified	Uncertain significance (Jan 26, 2022)
12-131005989-G-A		not specified	Uncertain significance (Jul 13, 2021)
12-131006026-A-G		not specified	Uncertain significance (Dec 16, 2023)
12-131076804-C-T		not specified	Uncertain significance (Jul 12, 2023)
12-131076818-T-G		not specified	Uncertain significance (Nov 10, 2022)
12-131076841-G-A		not specified	Uncertain significance (Dec 08, 2023)
12-131084581-C-T		not specified	Uncertain significance (May 17, 2023)
12-131084596-C-T		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADGRD1	protein_coding	protein_coding	ENST00000261654	25	187563

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.50e-14	0.990	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.326	512	533	0.960	0.0000325	5667
Missense in Polyphen		128	160.22	0.79888		1847
Synonymous	-0.658	252	239	1.05	0.0000171	1739
Loss of Function	2.63	30	50.1	0.599	0.00000233	560

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000523	0.000521
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000707	0.000707
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000371	0.000369
Middle Eastern	0.000707	0.000707
South Asian	0.000197	0.000196
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Orphan receptor. Signals via G(s)-alpha family of G- proteins (PubMed:22025619, PubMed:22575658). Has protumorigenic function especially in glioblastoma (PubMed:27775701). {ECO:0000269|PubMed:22025619, ECO:0000269|PubMed:22575658, ECO:0000269|PubMed:27775701}.
• Pathway: GPCRs, Other (Consensus)

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.34

Haploinsufficiency Scores

• pHI: 0.0835
• hipred: Y
• hipred_score: 0.540
• ghis: 0.522

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Adgrd1
• Phenotype: reproductive system phenotype; skeleton phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;integral component of membrane
• Molecular function: G protein-coupled receptor activity