CTC1 p.Pro1165=
c.3495G>T · VCV4933629
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000508%, nfe)
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 -0.072 | GERP -3.3, phastCons 0.086 |
| Overall | ||
| CADD | 2.488 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000508%
European (non-Finnish) · 6/1,180,006 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.00041%
6/1,461,894 alleles · very rare
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
- CTC1
- Protein
- p.Pro1165=
- Coding
- c.3495G>T
- MANE Select
- NM_025099
- Type
- single nucleotide variant
- Location
- chr17:8228522 (GRCh38)
- Gene constraint
- LOEUF 0.776 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.01 · 7 PDB
Similar variants
- CTC1 p.Pro1165Leu Uncertain significance ★★ ⚠ same residue
- CTC1 c.1617+5G>T Pathogenic/Likely pathogenic ★★ same type
- CTC1 c.1818+1G>A Likely pathogenic ★★ same type
- CTC1 c.2386-1G>A Likely pathogenic ★★ same type
- CTC1 c.2758+1G>T Pathogenic/Likely pathogenic ★★ same type
- CTC1 c.3221+1G>A Likely pathogenic ★★ same type
- CTC1 p.Ala227Val Pathogenic ★★ ⚠ same type
- CTC1 p.Arg108Ter Pathogenic ★★ 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/ctc1-p-pro1165 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown