ADGRL1

adhesion G protein-coupled receptor L1, the group of Adhesion G protein-coupled receptors, subfamily L

Basic information

Region (hg38): 19:14147742-14206187

Previous symbols: [ "LPHN1" ]

Links

ENSG00000072071 ∙ NCBI:22859 ∙ OMIM:616416 ∙ HGNC:20973 ∙ Uniprot:O94910 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental delay, behavioral abnormalities, and neuropsychiatric disorders (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental delay, behavioral abnormalities, and neuropsychiatric disorders6	AD	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	Craniofacial; Musculoskeletal; Neurologic	35907405

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADGRL1 gene.

• Inborn genetic diseases (68 variants)
• not provided (13 variants)
• Developmental delay, behavioral abnormalities, and neuropsychiatric disorders (9 variants)
• Seizure;Global developmental delay;Autistic behavior;Attention deficit hyperactivity disorder (2 variants)
• Intellectual disability;Global developmental delay;Autistic behavior;Attention deficit hyperactivity disorder (2 variants)
• Intellectual disability;Global developmental delay (2 variants)
• Global developmental delay (1 variants)
• not specified (1 variants)
• Specific learning disability;Global developmental delay (1 variants)
• Autistic behavior;Attention deficit hyperactivity disorder (1 variants)
• Neurodevelopmental disorder (1 variants)
• Specific learning disability;Intellectual disability;Global developmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADGRL1 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				3		3
missense	3	1	76		1	81
nonsense	3	2	1			6
start loss						0
frameshift	2	1				3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1		1
Total	8	4	77	4	1

Variants in ADGRL1

This is a list of pathogenic ClinVar variants found in the ADGRL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-14150892-T-G		Inborn genetic diseases	Uncertain significance (Oct 03, 2022)
19-14151030-T-A		Inborn genetic diseases	Uncertain significance (Feb 15, 2023)
19-14151035-T-G		Inborn genetic diseases	Uncertain significance (Nov 08, 2022)
19-14151055-C-T		Inborn genetic diseases	Uncertain significance (Nov 18, 2022)
19-14151082-T-C		Inborn genetic diseases	Uncertain significance (Aug 13, 2021)
19-14151085-G-C		Inborn genetic diseases	Uncertain significance (Jan 19, 2024)
19-14151099-C-T		Inborn genetic diseases	Uncertain significance (Feb 08, 2023)
19-14151103-C-T		Inborn genetic diseases	Uncertain significance (Jan 24, 2023)
19-14151105-G-C		Inborn genetic diseases	Uncertain significance (Aug 16, 2021)
19-14151144-T-C		Inborn genetic diseases	Uncertain significance (Apr 25, 2022)
19-14151147-A-C		Developmental delay, behavioral abnormalities, and neuropsychiatric disorders	Uncertain significance (Mar 26, 2024)
19-14151148-G-C		Inborn genetic diseases	Uncertain significance (May 27, 2022)
19-14151152-G-T			Uncertain significance (Nov 08, 2023)
19-14151157-G-C		Inborn genetic diseases	Uncertain significance (Jun 11, 2021)
19-14151193-C-T		Inborn genetic diseases	Uncertain significance (Jun 30, 2022)
19-14151199-C-G		Inborn genetic diseases	Uncertain significance (Nov 15, 2021)
19-14151207-C-T		Inborn genetic diseases	Uncertain significance (Nov 07, 2022)
19-14151229-C-T		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
19-14151309-C-T		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
19-14151318-C-A		Inborn genetic diseases	Uncertain significance (Jul 09, 2021)
19-14151322-C-T		Inborn genetic diseases	Uncertain significance (Dec 19, 2022)
19-14151349-C-T		Inborn genetic diseases	Uncertain significance (Sep 29, 2023)
19-14151361-C-T		Inborn genetic diseases	Uncertain significance (Jul 14, 2021)
19-14151432-A-G			Uncertain significance (Sep 01, 2023)
19-14151433-C-T		Inborn genetic diseases	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADGRL1	protein_coding	protein_coding	ENST00000340736	23	56250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.15e-7	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.43	640	935	0.685	0.0000651	9410
Missense in Polyphen		235	433.4	0.54222		4243
Synonymous	-1.72	470	425	1.11	0.0000323	3087
Loss of Function	6.99	7	70.3	0.0996	0.00000411	695

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000359	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000349	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-independent receptor of high affinity for alpha- latrotoxin, an excitatory neurotoxin present in black widow spider venom which triggers massive exocytosis from neurons and neuroendocrine cells. Receptor for TENM2 that mediates heterophilic synaptic cell-cell contact and postsynaptic specialization. Receptor probably implicated in the regulation of exocytosis (By similarity). {ECO:0000250}.
• Pathway: GPCRs, Class B Secretin-like (Consensus)

Recessive Scores

• pRec: 0.231

Intolerance Scores

• rvis_EVS: -2.63
• rvis_percentile_EVS: 0.8

Haploinsufficiency Scores

• pHI: 0.256
• hipred: Y
• hipred_score: 0.715
• ghis: 0.620

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Adgrl1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;calcium-mediated signaling using intracellular calcium source;positive regulation of synapse assembly;positive regulation of synapse maturation
• Cellular component: plasma membrane;integral component of plasma membrane;postsynaptic density;integral component of membrane;cell junction;axon;growth cone;presynaptic membrane;neuron projection;synapse
• Molecular function: G protein-coupled receptor activity;protein binding;latrotoxin receptor activity;carbohydrate binding;cell adhesion molecule binding