Is CTNNB1 p.Arg486Ser (c.1456C>A) pathogenic?

CTNNB1 p.Arg486Ser (c.1456C>A) is classified Uncertain significance in CTNNB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-07). AlphaMissense: likely pathogenic (0.9903); Very rare (popmax 0.00133%, afr).

How common is CTNNB1 p.Arg486Ser (c.1456C>A) in the general population?

CTNNB1 p.Arg486Ser (c.1456C>A) is very rare (popmax 0.00133%, afr) (gnomAD).

What do computational predictors say about CTNNB1 p.Arg486Ser (c.1456C>A)?

AlphaMissense predicts likely pathogenic (score 0.9903) — an in-silico prediction, not a clinical call.

CTNNB1 p.Arg486Ser

c.1456C>A · VCV3644894

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9903 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9903	likely pathogenic
REVEL	0.436	indeterminate
SaProt	LLR -13.70	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 2.1, phastCons 1
Regional constraint	o/e 0.53	unconstrained · MANE · 12 kb · p 2.8e-39 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/74,970 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000205% 3/1,460,864 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00133%	74,970
European (non-Finnish)	0.00017%	589,595

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: CTNNB1
Protein: p.Arg486Ser
Coding: c.1456C>A
MANE Select: NM_001904
Type: single nucleotide variant
Location: chr3:41233799 (GRCh38)
Gene constraint: LOEUF 0.139 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 81.02 · 50 PDB
Residue 486: an α-helix

Full CTNNB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CTNNB1 p.Arg486His Uncertain significance ★★ ⚠ same residue
CTNNB1 p.Arg486Cys Uncertain significance ★ ⚠ same residue
CTNNB1 c.1081+1G>T Pathogenic/Likely pathogenic ★★ same type
CTNNB1 c.1082-1G>C Pathogenic ★★ same type
CTNNB1 c.735-1G>C Pathogenic ★★ same type
CTNNB1 p.Arg474Ter Pathogenic ★★ same type
CTNNB1 p.Arg515Ter Pathogenic ★★ same type
CTNNB1 p.Arg535Ter Pathogenic ★★ 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/ctnnb1-p-arg486ser (accessed [today's date]).

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