CTAG2 p.Ser157Pro
c.469T>C · rs143520716 · VCV2661856
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.302%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.052 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.67 | GERP -1.9 |
| Regional constraint | o/e 0.97 | unconstrained · MANE · 1,329 bp · p 0.74 · regional, not allelic |
| Overall | ||
| CADD | 17.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.302%
African / African-American · 173/57,210 alleles
Filtering AF
0.266%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.251%
Overall
0.0178%
215/1,208,042 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.302% | 331 |
| Middle Eastern | 0.0617% | 1,621 |
| Remaining individualsnot grpmax-eligible | 0.0316% | 3,166 |
| Admixed American | 0.0284% | 3,520 |
| European (non-Finnish) | 0.00134% | 74,556 |
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.Ser157Pro
- Coding
- c.469T>C
- MANE Select
- NM_172377
- dbSNP
- rs143520716
- Type
- single nucleotide variant
- Location
- chrX:154652203 (GRCh38)
- Structure
- AlphaFold pLDDT 47.90
- Residue 157
- 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-ser157pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown