ADGRL2

adhesion G protein-coupled receptor L2, the group of Adhesion G protein-coupled receptors, subfamily L

Basic information

Region (hg38): 1:81306147-81993932

Previous symbols: [ "LPHH1", "LPHN2" ]

Links

ENSG00000117114 ∙ NCBI:23266 ∙ OMIM:607018 ∙ HGNC:18582 ∙ Uniprot:O95490 ∙ 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 ADGRL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADGRL2 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				13	4	17
missense			58	5	8	71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				1		1
Total	0	0	58	19	12

Variants in ADGRL2

This is a list of pathogenic ClinVar variants found in the ADGRL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-81836976-G-A		ADGRL2-related disorder	Likely benign (Apr 02, 2019)
1-81836992-C-T		not specified	Uncertain significance (Jul 19, 2023)
1-81837010-G-A			Likely benign (Aug 01, 2022)
1-81837028-T-C		not specified	Uncertain significance (Sep 20, 2023)
1-81907037-C-G		not specified	Uncertain significance (Jun 24, 2022)
1-81907066-C-T			Likely benign (Feb 01, 2023)
1-81907088-C-G		not specified	Uncertain significance (Dec 16, 2022)
1-81907118-A-G		not specified	Uncertain significance (Aug 26, 2022)
1-81936728-G-T		not specified	Uncertain significance (Jun 24, 2022)
1-81936761-T-A		ADGRL2-related disorder	Likely benign (May 24, 2019)
1-81943130-G-T		not specified	Uncertain significance (Nov 17, 2022)
1-81943172-T-C		not specified	Uncertain significance (Jul 12, 2022)
1-81943464-T-A		not specified	Uncertain significance (Aug 08, 2023)
1-81943585-C-T		ADGRL2-related disorder	Likely benign (Aug 01, 2022)
1-81943664-A-G		not specified	Uncertain significance (Nov 20, 2023)
1-81943716-A-G		not specified	Uncertain significance (Jun 29, 2023)
1-81943736-T-C		not specified	Uncertain significance (Jul 15, 2021)
1-81943763-G-A		not specified	Uncertain significance (Jun 07, 2023)
1-81950227-C-G		not specified	Uncertain significance (Feb 07, 2023)
1-81950239-A-G		not specified	Uncertain significance (Apr 01, 2024)
1-81950246-C-T		not specified	Uncertain significance (Feb 06, 2023)
1-81950260-A-G		not specified	Uncertain significance (May 30, 2024)
1-81950266-C-G		not specified	Uncertain significance (Nov 01, 2022)
1-81950298-A-T		ADGRL2-related disorder	Benign (May 13, 2019)
1-81950339-T-C		not specified	Uncertain significance (Feb 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADGRL2	protein_coding	protein_coding	ENST00000319517	19	686276

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.88e-9	125728	0	17	125745	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	647	741	0.873	0.0000383	9215
Missense in Polyphen		261	349.46	0.74686		4363
Synonymous	-0.552	282	270	1.04	0.0000149	2692
Loss of Function	7.33	3	68.5	0.0438	0.00000420	775

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000127	0.000127
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000556	0.0000544
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.0000627	0.0000615
Middle Eastern	0.0000556	0.0000544
South Asian	0.0000399	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-independent receptor of low affinity for alpha- latrotoxin, an excitatory neurotoxin present in black widow spider venom which triggers massive exocytosis from neurons and neuroendocrine cells. Receptor probably implicated in the regulation of exocytosis. {ECO:0000250|UniProtKB:O88923}.
• Pathway: GPCRs, Other;GPCRs, Class B Secretin-like (Consensus)

Recessive Scores

• pRec: 0.262

Intolerance Scores

• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.31

Haploinsufficiency Scores

• pHI: 0.906
• hipred: Y
• hipred_score: 0.609
• ghis: 0.535

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Adgrl2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;brain development
• Cellular component: integral component of plasma membrane;integral component of membrane;neuron projection
• Molecular function: G protein-coupled receptor activity;latrotoxin receptor activity;carbohydrate binding