ADGRL3

adhesion G protein-coupled receptor L3, the group of Adhesion G protein-coupled receptors, subfamily L

Basic information

Region (hg38): 4:61200325-62078335

Previous symbols: [ "LPHN3" ]

Links

ENSG00000150471 ∙ NCBI:23284 ∙ OMIM:616417 ∙ HGNC:20974 ∙ Uniprot:Q9HAR2 ∙ 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 ADGRL3 gene.

• Inborn genetic diseases (27 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADGRL3 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		1
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	0

Variants in ADGRL3

This is a list of pathogenic ClinVar variants found in the ADGRL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-61587263-G-A		not specified	Uncertain significance (May 16, 2023)
4-61587325-A-G		not specified	Uncertain significance (Apr 07, 2022)
4-61676882-C-T		not specified	Uncertain significance (Feb 27, 2024)
4-61732830-G-A			Likely benign (Mar 01, 2023)
4-61732883-C-G		not specified	Uncertain significance (Apr 25, 2023)
4-61732933-A-G		not specified	Uncertain significance (Jan 23, 2023)
4-61732948-A-G		not specified	Uncertain significance (Jan 16, 2024)
4-61733233-C-G		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
4-61733406-G-T		not specified	Uncertain significance (Oct 06, 2021)
4-61813880-T-C		not specified	Likely benign (Nov 08, 2022)
4-61892689-G-A		not specified	Uncertain significance (Feb 12, 2024)
4-61892712-C-T		not specified	Uncertain significance (Dec 01, 2022)
4-61892868-A-G		not specified	Uncertain significance (Apr 25, 2023)
4-61892914-G-A		not specified	Uncertain significance (Oct 12, 2021)
4-61892955-A-G		not specified	Uncertain significance (Jan 04, 2024)
4-61892956-T-C		not specified	Uncertain significance (Oct 05, 2021)
4-61895823-A-G		not specified	Uncertain significance (Nov 18, 2022)
4-61946945-C-A		not specified	Uncertain significance (Apr 22, 2022)
4-61946995-C-T		not specified	Uncertain significance (Jul 16, 2021)
4-61947039-G-A		not specified	Uncertain significance (Dec 16, 2023)
4-61948152-G-A		not specified	Uncertain significance (Sep 01, 2021)
4-61948188-G-A		not specified	Uncertain significance (Sep 29, 2023)
4-61948211-C-T		not specified	Uncertain significance (Mar 14, 2023)
4-61948217-A-G		not specified	Uncertain significance (Apr 19, 2023)
4-61979680-A-G		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADGRL3	protein_coding	protein_coding	ENST00000514591	23	877078

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000135	124788	0	9	124797	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.67	578	789	0.733	0.0000417	9609
Missense in Polyphen		223	385.83	0.57797		4853
Synonymous	-0.189	301	297	1.01	0.0000163	2869
Loss of Function	6.73	6	64.1	0.0935	0.00000344	797

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000882	0.0000882
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000458	0.0000441
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in cell-cell adhesion and neuron guidance via its interactions with FLRT2 and FLRT3 that are expressed at the surface of adjacent cells (PubMed:26235030). Plays a role in the development of glutamatergic synapses in the cortex. Important in determining the connectivity rates between the principal neurons in the cortex. {ECO:0000250|UniProtKB:Q80TS3, ECO:0000305|PubMed:26235030}.
• Pathway: GPCRs, Other;GPCRs, Class B Secretin-like (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.26

Haploinsufficiency Scores

• pHI: 0.168
• hipred: Y
• hipred_score: 0.626
• ghis: 0.518

Mouse Genome Informatics

• Gene name: Adgrl3
• Phenotype: homeostasis/metabolism 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: adgrl3.1
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: increased behavioural activity

Gene ontology

• Biological process: neuron migration;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;synapse assembly;brain development;locomotion involved in locomotory behavior;response to cocaine;positive regulation of synapse assembly;cell-cell adhesion via plasma-membrane adhesion molecules
• Cellular component: integral component of plasma membrane;cell-cell junction;integral component of membrane;axon;glutamatergic synapse
• Molecular function: G protein-coupled receptor activity;calcium ion binding;protein binding;carbohydrate binding