CTNNA2 p.Ser321=
c.963C>A · rs373147177 · VCV3042960
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.128%, afr)
Conditions
1
CTNNA2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.1 | GERP -5.4 |
| Overall | ||
| CADD | 7.197 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.128%
African / African-American · 96/75,066 alleles
Filtering AF
0.107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0995%
Overall
0.00719%
116/1,614,026 alleles · rare
exomes 60/1,461,658 · genomes 56/152,368 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.128% | 782 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,682 |
| Admixed American | 0.0117% | 8,574 |
| South Asian | 0.0022% | 45,527 |
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
- CTNNA2
- Protein
- p.Ser321=
- Coding
- c.963C>A
- MANE Select
- NM_001282597
- dbSNP
- rs373147177
- Type
- single nucleotide variant
- Location
- chr2:79909704 (GRCh38)
- Gene constraint
- LOEUF 0.491 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 80.78 · 1 PDB
Disease context
CTNNA2-related disorder
Similar variants
- CTNNA2 p.Val877Ile Uncertain significance ★★ ⚠ same condition
- CTNNA2 c.-5-6C>T Likely benign same condition
- CTNNA2 c.*3C>T Likely benign same condition
- CTNNA2 p.Ala234= Likely benign same condition
- CTNNA2 p.Arg120= Likely benign same condition
- CTNNA2 p.Asp638= Likely benign same condition
- CTNNA2 p.Asp705= Likely benign same condition
- CTNNA2 p.Gly804= 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/ctnna2-p-ser321 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown