Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 77.2%, eas) — too common for a highly-penetrant pathogenic allele
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 -5.6 | GERP -2.3 |
| Overall | ||
| CADD | 3.045 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
77.2%
East Asian · 25,920/33,580 alleles
Filtering AF
76.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 76.1%
Overall
59.2%
714,190/1,207,035 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 77.2% | 1 |
| Amishnot grpmax-eligible | 68.3% | 1 |
| Finnishnot grpmax-eligible | 63.7% | 2 |
| European (non-Finnish) | 62.6% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 59.9% | 2 |
| Remaining individualsnot grpmax-eligible | 57.5% | 2 |
| Middle Eastern | 57.4% | 2 |
| Admixed American | 53.2% | 2 |
| South Asian | 45.8% | 2 |
| African / African-American | 10.8% | 9 |
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.Pro115=
- Coding
- c.345G>T
- MANE Select
- NM_172377
- dbSNP
- rs4326559
- Type
- single nucleotide variant
- Location
- chrX:154652556 (GRCh38)
- Structure
- AlphaFold pLDDT 47.90
Similar variants
- CTAG2 p.Pro115Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown