Is CTNNA3 p.Arg327= (c.981G>T) pathogenic?

CTNNA3 p.Arg327= (c.981G>T) is classified Likely benign in CTNNA3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-27). Very rare (popmax 0.00446%, eas).

How common is CTNNA3 p.Arg327= (c.981G>T) in the general population?

CTNNA3 p.Arg327= (c.981G>T) is very rare (popmax 0.00446%, eas) (gnomAD).

CTNNA3 p.Arg327=

c.981G>T · VCV3837210

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00446%, eas)

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 -1.7	GERP -4.8
Overall
CADD	6.817	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00446% East Asian · 2/44,858 alleles

Filtering AF 0.000739% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000277%

Overall 0.000137% 2/1,461,594 alleles · very rare

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: CTNNA3
Protein: p.Arg327=
Coding: c.981G>T
MANE Select: NM_013266
Type: single nucleotide variant
Location: chr10:67180383 (GRCh38)
Gene constraint: LOEUF 0.875 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 81.65

Full CTNNA3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CTNNA3 p.Arg327Gln Uncertain significance ★★ ⚠ same residue
CTNNA3 p.Arg327Trp Uncertain significance ★★ same residue
CTNNA3 c.100-7A>G Uncertain significance ★★ same type
CTNNA3 c.843+1G>T Uncertain significance ★★ same type
CTNNA3 p.Ala124Thr Uncertain significance ★★ ⚠ same type
CTNNA3 p.Ala130Pro Uncertain significance ★★ ⚠ same type
CTNNA3 p.Ala131Val Uncertain significance ★★ same type
CTNNA3 p.Ala165Thr Uncertain significance ★★ ⚠ 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/ctnna3-p-arg327 (accessed [today's date]).

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