CDT1 p.Arg5=
c.15C>A · rs372245967 · VCV723696
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.569%, afr)
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 -1.3 | GERP -2 |
| Overall | ||
| CADD | 8.888 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.569%
African / African-American · 391/68,760 alleles
Filtering AF
0.522%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.504%
Overall
0.0296%
444/1,500,990 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.569% | 176 |
| Admixed American | 0.0455% | 2,199 |
| Remaining individualsnot grpmax-eligible | 0.0427% | 2,343 |
| Middle Eastern | 0.0176% | 5,668 |
| South Asian | 0.00117% | 85,546 |
| European (non-Finnish) | 0.000267% | 374,981 |
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.Arg5=
- Coding
- c.15C>A
- MANE Select
- NM_030928
- dbSNP
- rs372245967
- Type
- single nucleotide variant
- Location
- chr16:88803846 (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 5
- 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-arg5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown