CDT1 p.Pro15=
c.45C>T · rs774050803 · VCV2182468
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, 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 -2.2 | GERP -2 |
| Overall | ||
| CADD | 7.009 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
European (non-Finnish) · 37/1,110,816 alleles
Filtering AF
0.00246%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00214%
Overall
0.00271%
40/1,475,560 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00333% | 30,022 |
| Remaining individualsnot grpmax-eligible | 0.00183% | 54,782 |
| African / African-American | 0.00147% | 68,168 |
| South Asian | 0.00121% | 82,896 |
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
- CDT1
- Protein
- p.Pro15=
- Coding
- c.45C>T
- MANE Select
- NM_030928
- dbSNP
- rs774050803
- Type
- single nucleotide variant
- Location
- chr16:88803876 (GRCh38)
- Gene constraint
- LOEUF 1.737 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.51 · 6 PDB
- Residue 15
- the 'disordered' region
Similar variants
- CDT1 c.832+1G>A Pathogenic/Likely pathogenic ★★ same type
- CDT1 p.Arg462Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- CDT1 p.Ala11Val Uncertain significance ★★ ⚠ same type
- CDT1 p.Ala144Ser Uncertain significance ★★ ⚠ same type
- CDT1 p.Ala167Thr Uncertain significance ★★ ⚠ same type
- CDT1 p.Ala217Val Uncertain significance ★★ ⚠ same type
- CDT1 p.Ala414Ser Uncertain significance ★★ ⚠ same type
- CDT1 p.Ala431Thr 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/cdt1-p-pro15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown