CTAG2 p.Ala3=
c.9C>T · rs1454700901 · VCV2661857
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0113%, sas)
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 -20 | GERP -2 |
| Overall | ||
| CADD | 4.127 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0113%
South Asian · 5/44,162 alleles
Filtering AF
0.0044%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0028%
Overall
0.00104%
10/963,696 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0113% | 8,832 |
| Remaining individualsnot grpmax-eligible | 0.00238% | 42,054 |
| European (non-Finnish) | 0.000496% | 201,466 |
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
- CTAG2
- Protein
- p.Ala3=
- Coding
- c.9C>T
- MANE Select
- NM_172377
- dbSNP
- rs1454700901
- Type
- single nucleotide variant
- Location
- chrX:154653507 (GRCh38)
- Structure
- AlphaFold pLDDT 47.90
- Residue 3
- the 'disordered' region
Similar variants
- CTAG2 c.405-28T>C Likely benign ★★ same type
- CTAG2 c.405-93G>C Benign ★★ same type
- CTAG2 p.Met94Val Benign ★★ same type
- CTAG2 p.Pro99Ala Benign ★★ same type
- CTAG2 c.404+107C>A Uncertain significance ★ ⚠ same type
- CTAG2 c.404+21G>C Uncertain significance ★ ⚠ same type
- CTAG2 c.404+35C>T Uncertain significance ★ ⚠ same type
- CTAG2 c.404+42G>A 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/ctag2-p-ala3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown