CDT1 p.Ser467=
c.1401C>T · rs151292317 · VCV1543025
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.182%, mid)
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 -20 | GERP -2.8 |
| Overall | ||
| CADD | 0.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.182%
Middle Eastern · 11/6,046 alleles
Filtering AF
0.102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0789%
Overall
0.0112%
180/1,612,912 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.182% | 550 |
| Admixed American | 0.04% | 2,501 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,248 |
| European (non-Finnish) | 0.0103% | 9,672 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0101% | 9,867 |
| African / African-American | 0.00932% | 10,725 |
| East Asian | 0.00223% | 44,884 |
| South Asian | 0.0022% | 45,540 |
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.Ser467=
- Coding
- c.1401C>T
- MANE Select
- NM_030928
- dbSNP
- rs151292317
- Type
- single nucleotide variant
- Location
- chr16:88807406 (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 467
- the 'interaction with lrwd1' 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-ser467 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown