CDT1 p.Ala144=
c.432C>G · rs759429997 · VCV1919180
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0379%, eas)
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 -0.99 | GERP -2.5 |
| Overall | ||
| CADD | 1.014 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0379%
East Asian · 17/44,842 alleles
Filtering AF
0.0241%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0198%
Overall
0.00112%
18/1,611,424 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0379% | 2,638 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,340 |
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.Ala144=
- Coding
- c.432C>G
- MANE Select
- NM_030928
- dbSNP
- rs759429997
- Type
- single nucleotide variant
- Location
- chr16:88804842 (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 144
- the 'disordered' region
Similar variants
- CDT1 p.Ala144Ser Uncertain significance ★★ ⚠ same residue
- CDT1 p.Ala144Thr Uncertain significance ★ ⚠ same residue
- 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.Ala167Thr Uncertain significance ★★ ⚠ same type
- CDT1 p.Ala217Val Uncertain significance ★★ ⚠ same type
- CDT1 p.Ala414Ser 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-ala144 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown