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): 1:109249539-109275751

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_specified (385 variants)
not_provided (294 variants)
CELSR2-related_disorder (53 variants)
Orofacial-digital_syndrome_III (1 variants)
Idiopathic_scoliosis (1 variants)
Esophageal_atresia/tracheoesophageal_fistula (1 variants)
Global_developmental_delay (1 variants)
Intellectual_disability (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. These statistics are base on transcript: NM_000001408.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	108 clinvar	28 clinvar	138
missense		2 clinvar	450 clinvar	31 clinvar	16 clinvar	499
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	2	456	139	44

Highest pathogenic variant AF is 0.0000409554

Loading clinvar variants...

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