CTC1 p.Pro944fs
c.2831del · rs199473677 · VCV31000
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 17 of 23 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.9 | GERP -3.5, phastCons 0.98 |
| Overall | ||
| CADD | 28.5 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Finnishnot grpmax-eligible | 0.331% | 302 |
| Middle Easterngrpmax | 0.033% | 3,029 |
| Remaining individualsnot grpmax-eligible | 0.0304% | 3,290 |
| African / African-American | 0.0133% | 7,503 |
| European (non-Finnish) | 0.00805% | 12,421 |
| South Asian | 0.0022% | 45,538 |
| Admixed American | 0.00167% | 60,016 |
Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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.Pro944fs
- Coding
- c.2831del
- MANE Select
- NM_025099
- dbSNP
- rs199473677
- Type
- Deletion
- Location
- chr17:8230396 (GRCh38)
- Gene constraint
- LOEUF 0.776 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.01 · 7 PDB
Disease context
Also linked: Coats plus syndromedyskeratosis congenitacerebroretinal microangiopathy with calcifications and cysts 1
Similar variants
- CTC1 p.Pro944Leu Uncertain significance ★ ⚠ same residue
- CTC1 p.Pro944Ser Uncertain significance ★ ⚠ same residue
- CTC1 p.Asp405fs Pathogenic/Likely pathogenic ★★ same condition
- CTC1 p.Glu454fs Pathogenic/Likely pathogenic ★★ same condition
- CTC1 p.Glu557fs Pathogenic/Likely pathogenic ★★ same condition
- CTC1 p.His726fs Pathogenic/Likely pathogenic ★★ same condition
- CTC1 p.Leu1007fs Pathogenic/Likely pathogenic ★★ same condition
- CTC1 p.Pro999fs Pathogenic/Likely pathogenic ★★ same condition
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-pro944fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown