Is CELSR3 p.Arg312= (c.934C>A) pathogenic?

CELSR3 p.Arg312= (c.934C>A) is classified Benign in CELSR3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-01). Low-frequency (popmax 1.37%, afr); Associated with CELSR3-related disorder.

What condition is associated with CELSR3 p.Arg312= (c.934C>A)?

CELSR3 p.Arg312= (c.934C>A) is associated with CELSR3-related disorder (ClinVar).

How common is CELSR3 p.Arg312= (c.934C>A) in the general population?

CELSR3 p.Arg312= (c.934C>A) is low-frequency (popmax 1.37%, afr) (gnomAD).

CELSR3 p.Arg312=

c.934C>A · rs76423828 · VCV3037148

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.37%, afr)

Conditions

CELSR3-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Overall
CADD	7.588	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.37% African / African-American · 1,011/73,642 alleles

Filtering AF 1.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.27%

Overall 0.0757% 1,191/1,573,338 alleles · low-frequency exomes 553/1,420,984 · genomes 638/152,354 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.37%	73
Admixed American	0.152%	656
Remaining individualsnot grpmax-eligible	0.122%	818
South Asian	0.00466%	21,474
European (non-Finnish)	0.00164%	60,986

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: CELSR3
Protein: p.Arg312=
Coding: c.934C>A
MANE Select: NM_001407
dbSNP: rs76423828
Type: single nucleotide variant
Location: chr3:48661701 (GRCh38)
Gene constraint: LOEUF 0.344 · pLI 1.00 (gnomAD)

Full CELSR3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CELSR3-related disorder

Similar variants

CELSR3 p.Phe282Ser Uncertain significance ★★ ⚠ same condition
CELSR3 p.Cys1502Tyr Uncertain significance ★ ⚠ same condition
CELSR3 p.Ala3148Glu Uncertain significance ⚠ same condition
CELSR3 c.7464-9T>C Likely benign same condition
CELSR3 c.8086-5T>G Likely benign same condition
CELSR3 c.8165+7T>C Likely benign same condition
CELSR3 c.9912-8G>A Likely benign same condition
CELSR3 c.*9C>T Likely benign 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/celsr3-p-arg312 (accessed [today's date]).

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