CTF1 p.Ala25=
c.75C>A · rs759831407 · VCV2177898
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0048%, eas)
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 4.7 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 14.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0048%
East Asian · 2/41,668 alleles
Filtering AF
0.000795%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000298%
Overall
0.000191%
3/1,569,818 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0048% | 20,834 |
| Remaining individualsnot grpmax-eligible | 0.00168% | 59,584 |
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
- CTF1
- Protein
- p.Ala25=
- Coding
- c.75C>A
- MANE Select
- NM_001330
- dbSNP
- rs759831407
- Type
- single nucleotide variant
- Location
- chr16:30899464 (GRCh38)
- Gene constraint
- LOEUF 1.959 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.94
Similar variants
- CTF1 c.*5C>A Uncertain significance ★★ same type
- CTF1 p.Ala156Thr Uncertain significance ★★ ⚠ same type
- CTF1 p.Ala34Val Uncertain significance ★★ same type
- CTF1 p.Arg107Ser Uncertain significance ★★ ⚠ same type
- CTF1 p.Arg176His Uncertain significance ★★ ⚠ same type
- CTF1 p.Arg65Gln Uncertain significance ★★ ⚠ same type
- CTF1 p.Asp191Glu Uncertain significance ★★ ⚠ same type
- CTF1 p.Asp54Glu 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/ctf1-p-ala25 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown