Is CELSR1 p.Val2441= (c.7323C>T) pathogenic?

CELSR1 p.Val2441= (c.7323C>T) is classified Likely benign in CELSR1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-06-17). Very rare (popmax 0.00448%, eas); Associated with CELSR1-related disorder.

What condition is associated with CELSR1 p.Val2441= (c.7323C>T)?

CELSR1 p.Val2441= (c.7323C>T) is associated with CELSR1-related disorder (ClinVar).

How common is CELSR1 p.Val2441= (c.7323C>T) in the general population?

CELSR1 p.Val2441= (c.7323C>T) is very rare (popmax 0.00448%, eas) (gnomAD).

CELSR1 p.Val2441=

c.7323C>T · rs370573042 · VCV3029352

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00448%, eas)

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 -2.6	GERP -3
Overall
CADD	0.335	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00448% East Asian · 2/44,686 alleles

Filtering AF 0.000742% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000278%

Overall 0.00087% 14/1,608,286 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00448%	22,343
Admixed American	0.00168%	59,426
Remaining individualsnot grpmax-eligible	0.00161%	62,184
African / African-American	0.00134%	74,904
European (non-Finnish)	0.000764%	130,945

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.Val2441=
Coding: c.7323C>T
MANE Select: NM_001378328
dbSNP: rs370573042
Type: single nucleotide variant
Location: chr22:46378651 (GRCh38)
Gene constraint: LOEUF 0.564 · pLI <0.01 (gnomAD)
Residue 2441: a disulfide bond; a UniProt-annotated variant site (in lmphm9); the gain-b domain; the 'gps' region

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

Disease context

CELSR1-related disorder

Similar variants

CELSR1 p.Arg1643Gln Uncertain significance ★★ ⚠ same condition
CELSR1 p.Pro46His Uncertain significance ★★ ⚠ same condition
CELSR1 p.Ser2825Leu Uncertain significance ★★ same condition
CELSR1 p.Val2338Ile 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-val2441 (accessed [today's date]).

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