Is CTNNA3 p.Asp391= (c.1173T>C) pathogenic?

CTNNA3 p.Asp391= (c.1173T>C) is classified Likely benign in CTNNA3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-02-18). Very rare (popmax 0.00133%, afr).

How common is CTNNA3 p.Asp391= (c.1173T>C) in the general population?

CTNNA3 p.Asp391= (c.1173T>C) is very rare (popmax 0.00133%, afr) (gnomAD).

CTNNA3 p.Asp391=

c.1173T>C · rs1839856228 · VCV1740223

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

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 2.2	GERP -2.1, phastCons 1
Overall
CADD	7.169	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/74,916 alleles

Overall 0.000657% 1/152,166 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.Asp391=
Coding: c.1173T>C
MANE Select: NM_013266
dbSNP: rs1839856228
Type: single nucleotide variant
Location: chr10:66766372 (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.Asp391Val Uncertain significance ★★ ⚠ same residue
CTNNA3 p.Asp391Asn Uncertain significance ★ ⚠ same residue
CTNNA3 p.Asp391Gly Uncertain significance ★ ⚠ same residue
LRRTM3 p.Ser391Gly 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

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-asp391 (accessed [today's date]).

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