Is CELSR1 p.Val2338= (c.7014C>T) pathogenic?

CELSR1 p.Val2338= (c.7014C>T) is classified Likely benign in CELSR1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-27). Low-frequency (popmax 4.84%, amr); Associated with CELSR1-related disorder.

What condition is associated with CELSR1 p.Val2338= (c.7014C>T)?

CELSR1 p.Val2338= (c.7014C>T) is associated with CELSR1-related disorder (ClinVar).

How common is CELSR1 p.Val2338= (c.7014C>T) in the general population?

CELSR1 p.Val2338= (c.7014C>T) is low-frequency (popmax 4.84%, amr) (gnomAD).

CELSR1 p.Val2338=

c.7014C>T · rs151055274 · VCV3059624

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 4.84%, amr)

Conditions

CELSR1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -14	GERP -3.1
Overall
CADD	0.168	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.84% Admixed American · 2,646/54,666 alleles

Filtering AF 4.69% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.62%

Overall 0.204% 3,214/1,573,268 alleles · low-frequency exomes 2,502/1,420,936 · genomes 712/152,332 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	4.84%	21
Finnishnot grpmax-eligible	0.322%	311
Remaining individualsnot grpmax-eligible	0.254%	394
African / African-American	0.0809%	1,237
East Asian	0.0656%	1,524
South Asian	0.0117%	8,576
European (non-Finnish)	0.0111%	9,003

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CELSR1
Protein: p.Val2338=
Coding: c.7014C>T
MANE Select: NM_001378328
dbSNP: rs151055274
Type: single nucleotide variant
Location: chr22:46381920 (GRCh38)
Gene constraint: LOEUF 0.564 · pLI <0.01 (gnomAD)
Residue 2338: a UniProt-annotated variant site (in lmphm9); the gain-b domain

Full CELSR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CELSR1-related disorder

Similar variants

CELSR1 p.Val2338Ile Uncertain significance ★★ ⚠ same residue
CELSR1 p.Arg1643Gln Uncertain significance ★★ ⚠ same condition
CELSR1 p.Pro46His Uncertain significance ★★ ⚠ same condition
CELSR1 p.Ser2825Leu Uncertain significance ★★ same condition
CELSR1 p.Leu979Phe Likely pathogenic ★ ⚠ same condition
CELSR1 p.Ala2486Pro Uncertain significance ★ same condition
CELSR1 p.Asp1201Asn Conflicting classifications of pathogenicity ★ same condition
CELSR1 p.Cys1934= Uncertain significance ★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/celsr1-p-val2338 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown