CTC1 p.Ala900=
c.2700T>G · rs1597376096 · VCV735672
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0106%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.97 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -3.2, phastCons 1 |
| Overall | ||
| CADD | 10.56 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0106%
European (non-Finnish) · 125/1,175,396 alleles
Filtering AF
0.00909%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00847%
Overall
0.00839%
135/1,609,122 alleles · ultra-rare
exomes 135/1,456,812 · genomes 0/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0106% | 9,403 |
| South Asian | 0.0055% | 18,197 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,775 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,586 |
| African / African-American | 0.00133% | 74,980 |
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.Ala900=
- Coding
- c.2700T>G
- MANE Select
- NM_025099
- dbSNP
- rs1597376096
- Type
- single nucleotide variant
- Location
- chr17:8230621 (GRCh38)
- Gene constraint
- LOEUF 0.776 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.01 · 7 PDB
- Residue 900
- a β-strand
Similar variants
- CTC1 p.Ala900Thr Uncertain significance ★★ same residue
- CTC1 p.Ala900Val 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
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-ala900 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown