Is CELSR3 p.Arg3201Gln (c.9602G>A) pathogenic?

CELSR3 p.Arg3201Gln (c.9602G>A) is classified Benign in CELSR3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-12-31). AlphaMissense: likely benign (0.0844); Low-frequency (popmax 3.15%, afr).

How common is CELSR3 p.Arg3201Gln (c.9602G>A) in the general population?

CELSR3 p.Arg3201Gln (c.9602G>A) is low-frequency (popmax 3.15%, afr) (gnomAD).

What do computational predictors say about CELSR3 p.Arg3201Gln (c.9602G>A)?

AlphaMissense predicts likely benign (score 0.0844) — an in-silico prediction, not a clinical call.

CELSR3 p.Arg3201Gln

c.9602G>A · rs115648137 · VCV783379

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0844 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 3.15%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.0844	likely benign
REVEL	0.1	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.9	GERP 1.8, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 10 kb · p 0.0024 · regional, not allelic
Overall
CADD	23.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.15% African / African-American · 2,360/75,036 alleles

Filtering AF 3.04% ClinGen BA1/BS1 input FAF95, joint · FAF99 3%

Overall 0.171% 2,757/1,612,660 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.15%	32
Middle Eastern	0.248%	404
Admixed American	0.225%	445
Remaining individualsnot grpmax-eligible	0.213%	470
European (non-Finnish)	0.00949%	10,536
South Asian	0.0022%	45,543

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.Arg3201Gln
Coding: c.9602G>A
MANE Select: NM_001407
dbSNP: rs115648137
Type: single nucleotide variant
Location: chr3:48639983 (GRCh38)
Gene constraint: LOEUF 0.344 · pLI 1.00 (gnomAD)
Residue 3201: the 'disordered' region

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

Similar variants

CELSR3 p.Ala2862Val Uncertain significance ★★ ⚠ same type
CELSR3 p.Arg2345His Uncertain significance ★★ ⚠ same type
CELSR3 p.Gly2265Ser Uncertain significance ★★ ⚠ same type
CELSR3 p.Phe282Ser Uncertain significance ★★ ⚠ same type
CELSR3 p.Val1107Met Uncertain significance ★★ same type
CELSR3 p.Arg2886= Likely benign ★★ same type
CELSR3 p.Arg3189Gln Benign/Likely benign ★★ same type
CELSR3 p.Asn1770= Likely benign ★★ same type

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-arg3201gln (accessed [today's date]).

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