CTF1 p.Thr38=
c.114C>A · VCV3730087
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00442%, afr)
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 2.2 | GERP 0.12, phastCons 1 |
| Overall | ||
| CADD | 9.889 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00442%
African / African-American · 3/67,894 alleles
Filtering AF
0.00117%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000625%
Overall
0.000278%
4/1,436,342 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00442% | 22,631 |
| European (non-Finnish) | 9.37e-05% | 1,067,084 |
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.Thr38=
- Coding
- c.114C>A
- MANE Select
- NM_001330
- Type
- single nucleotide variant
- Location
- chr16:30899503 (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-thr38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown