CELSR3

cadherin EGF LAG seven-pass G-type receptor 3, the group of Adhesion G protein-coupled receptors, subfamily C|MicroRNA protein coding host genes|CELSR cadherins

Basic information

Region (hg38): 3:48636463-48662886

Previous symbols: [ "EGFL1" ]

Links

ENSG00000008300 ∙ NCBI:1951 ∙ OMIM:604264 ∙ HGNC:3230 ∙ Uniprot:Q9NYQ7 ∙ 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 CELSR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CELSR3 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	23	5	29
missense			171	16	15	202
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1	1		2
splice region				3		3
non coding				1	1	2
Total	0	0	173	41	21

Variants in CELSR3

This is a list of pathogenic ClinVar variants found in the CELSR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-48638196-G-A		CELSR3-related disorder	Likely benign (Nov 25, 2019)
3-48638240-C-T		CELSR3-related disorder	Likely benign (Apr 05, 2019)
3-48639681-C-G			Benign (Dec 31, 2019)
3-48639703-G-A		not specified	Likely benign (Dec 08, 2017)
3-48639710-G-A			Likely benign (May 15, 2018)
3-48639717-A-G		not specified	Uncertain significance (Apr 10, 2023)
3-48639755-G-A		not specified	Uncertain significance (Sep 07, 2022)
3-48639758-G-A		CELSR3-related disorder	Benign (Apr 01, 2024)
3-48639861-G-C		not specified	Uncertain significance (Nov 22, 2023)
3-48639893-A-G		not specified	Likely benign (Apr 11, 2023)
3-48639896-G-A		not specified	Uncertain significance (Jan 19, 2022)
3-48639938-G-T		not specified	Uncertain significance (May 08, 2024)
3-48639951-G-T		not specified	Uncertain significance (Dec 18, 2023)
3-48639956-C-T		not specified	Uncertain significance (Apr 12, 2022)
3-48639983-C-T			Benign (Dec 31, 2019)
3-48640019-C-T		CELSR3-related disorder • Bladder exstrophy-epispadias-cloacal extrophy complex	Benign (-)
3-48640097-C-T		not specified	Uncertain significance (Jan 22, 2024)
3-48640103-C-T		not specified	Uncertain significance (Sep 15, 2021)
3-48640104-G-A		not specified	Likely benign (Apr 07, 2023)
3-48640107-G-A		CELSR3-related disorder	Likely benign (May 05, 2022)
3-48640136-C-T		CELSR3-related disorder	Likely benign (May 27, 2022)
3-48640142-G-T		CELSR3-related disorder	Uncertain significance (Jul 20, 2024)
3-48640184-A-T		not specified	Uncertain significance (Jan 16, 2024)
3-48640188-C-T		CELSR3-related disorder	Likely benign (May 16, 2023)
3-48640203-G-A		not specified	Uncertain significance (Sep 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CELSR3	protein_coding	protein_coding	ENST00000164024	35	26447

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000179	125676	1	71	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.08	1554	2.08e+3	0.748	0.000135	21145
Missense in Polyphen		530	903.29	0.58674		9468
Synonymous	2.01	810	886	0.914	0.0000573	7324
Loss of Function	8.54	21	123	0.170	0.00000693	1231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00215	0.00215
Ashkenazi Jewish	0.000203	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.000237	0.000231
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.000458	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor that may have an important role in cell/cell signaling during nervous system formation.
• Pathway: GPCRs, Other (Consensus)

Recessive Scores

• pRec: 0.245

Intolerance Scores

• loftool: 0.385
• rvis_EVS: -4.27
• rvis_percentile_EVS: 0.11

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.575
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.844

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Celsr3
• Phenotype: digestive/alimentary 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); respiratory system 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); homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: celsr3
• Affected structure: ON-bipolar cell
• Phenotype tag: abnormal
• Phenotype quality: functionality

Gene ontology

• Biological process: neuron migration;regulation of protein phosphorylation;homophilic cell adhesion via plasma membrane adhesion molecules;G protein-coupled receptor signaling pathway;axonal fasciculation;regulation of protein localization;dopaminergic neuron axon guidance;serotonergic neuron axon guidance;Wnt signaling pathway, planar cell polarity pathway;cilium assembly;planar cell polarity pathway involved in axon guidance
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: G protein-coupled receptor activity;calcium ion binding;protein binding