CELSR2

cadherin EGF LAG seven-pass G-type receptor 2, the group of CELSR cadherins|Adhesion G protein-coupled receptors, subfamily C

Basic information

Region (hg38): 1:109249538-109275751

Previous symbols: [ "EGFL2" ]

Links

ENSG00000143126 ∙ NCBI:1952 ∙ OMIM:604265 ∙ HGNC:3231 ∙ Uniprot:Q9HCU4 ∙ 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 CELSR2 gene.

• not provided (236 variants)
• Inborn genetic diseases (123 variants)
• Global developmental delay;Intellectual disability (1 variants)
• Idiopathic scoliosis (1 variants)
• Orofacial-digital syndrome III (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CELSR2 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				74	34	108
missense		1	179	20	16	216
nonsense						0
start loss						0
frameshift			1			1
inframe indel			2		1	3
splice donor/acceptor (+/-2bp)						0
splice region			1	4	3	8
non coding			1	7	6	14
Total	0	1	183	101	57

Highest pathogenic variant AF is 0.0000328

Variants in CELSR2

This is a list of pathogenic ClinVar variants found in the CELSR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-109250083-C-T		not specified	Uncertain significance (Mar 14, 2023)
1-109250113-A-ACGC			Benign (Jan 29, 2024)
1-109250113-A-ACGCCGC			Uncertain significance (Nov 14, 2022)
1-109250129-T-C			Likely benign (May 08, 2023)
1-109250150-T-A		not specified	Uncertain significance (Oct 27, 2022)
1-109250154-G-A			Likely benign (Jun 08, 2023)
1-109250162-C-T			Likely benign (Jun 26, 2023)
1-109250179-G-A		not specified	Uncertain significance (Mar 21, 2023)
1-109250187-C-T			Likely benign (Jul 30, 2021)
1-109250204-C-A		not specified	Uncertain significance (Apr 25, 2023)
1-109250243-G-T		not specified	Uncertain significance (May 26, 2022)
1-109250278-C-T		not specified	Uncertain significance (Apr 07, 2023)
1-109250351-G-A			Benign (Dec 12, 2023)
1-109250412-C-T			Benign (Jan 18, 2024)
1-109250455-C-A		CELSR2-related disorder	Likely benign (Feb 01, 2024)
1-109250474-C-T		not specified	Uncertain significance (Jun 22, 2021)
1-109250506-C-T			Benign (May 15, 2023)
1-109250541-C-T			Likely benign (Jan 29, 2024)
1-109250554-G-A		not specified	Uncertain significance (Oct 25, 2022)
1-109250557-GAAAG-AAAA			Uncertain significance (Dec 19, 2017)
1-109250560-A-C			Benign (Jan 12, 2024)
1-109250569-G-C		not specified	Uncertain significance (Aug 20, 2023)
1-109250578-C-G		not specified	Uncertain significance (Sep 14, 2023)
1-109250613-C-T			Likely benign (Mar 30, 2023)
1-109250651-C-T		not specified	Uncertain significance (Sep 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CELSR2	protein_coding	protein_coding	ENST00000271332	34	25732

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000612	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.18	1555	1.82e+3	0.856	0.000121	18738
Missense in Polyphen		505	711.23	0.71004		7405
Synonymous	-1.74	847	785	1.08	0.0000533	6273
Loss of Function	8.24	20	116	0.173	0.00000676	1168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000153
Ashkenazi Jewish	0.000106	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000161	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000668	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.150

Intolerance Scores

• loftool: 0.228
• rvis_EVS: -1.81
• rvis_percentile_EVS: 2.18

Haploinsufficiency Scores

• pHI: 0.217
• hipred: Y
• hipred_score: 0.614
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.605

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Celsr2
• 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)

Zebrafish Information Network

• Gene name: celsr2
• Affected structure: facial nerve motor nucleus
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: regulation of transcription, DNA-templated;homophilic cell adhesion via plasma membrane adhesion molecules;G protein-coupled receptor signaling pathway;Wnt signaling pathway;neural plate anterior/posterior regionalization;regulation of cell-cell adhesion;dendrite morphogenesis;Wnt signaling pathway, planar cell polarity pathway
• Cellular component: cytoplasm;plasma membrane;integral component of membrane
• Molecular function: G protein-coupled receptor activity;calcium ion binding