Is CELSR3 p.Arg3150Gln (c.9449G>A) pathogenic?

CELSR3 p.Arg3150Gln (c.9449G>A) is classified Likely benign in CELSR3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-05-27). AlphaMissense: likely benign (0.0748); Rare (popmax 0.168%, afr); Associated with CELSR3-related disorder.

What condition is associated with CELSR3 p.Arg3150Gln (c.9449G>A)?

CELSR3 p.Arg3150Gln (c.9449G>A) is associated with CELSR3-related disorder (ClinVar).

How common is CELSR3 p.Arg3150Gln (c.9449G>A) in the general population?

CELSR3 p.Arg3150Gln (c.9449G>A) is rare (popmax 0.168%, afr) (gnomAD).

What do computational predictors say about CELSR3 p.Arg3150Gln (c.9449G>A)?

AlphaMissense predicts likely benign (score 0.0748) — an in-silico prediction, not a clinical call.

CELSR3 p.Arg3150Gln

c.9449G>A · rs146659525 · VCV3057638

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0748 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.168%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

CELSR3-related disorder

Computational evidence

Protein change
AlphaMissense	0.0748	likely benign
REVEL	0.088	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 3.9	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 0.168% African / African-American · 126/75,052 alleles

Filtering AF 0.144% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.135%

Overall 0.0117% 188/1,612,354 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.168%	596
Admixed American	0.0283%	3,530
Middle Eastern	0.0165%	6,058
South Asian	0.00659%	15,180
Remaining individualsnot grpmax-eligible	0.0064%	15,621
European (non-Finnish)	0.00288%	34,704

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.Arg3150Gln
Coding: c.9449G>A
MANE Select: NM_001407
dbSNP: rs146659525
Type: single nucleotide variant
Location: chr3:48640136 (GRCh38)
Gene constraint: LOEUF 0.344 · pLI 1.00 (gnomAD)
Residue 3150: the 'disordered' region

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-arg3150gln (accessed [today's date]).

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