Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 18%, afr) — too common for a highly-penetrant pathogenic allele
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 -2.9 | GERP -2.1 |
| Overall | ||
| CADD | 0.419 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
18%
African / African-American · 13,500/74,950 alleles
Filtering AF
17.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 17.7%
Overall
8.48%
136,683/1,612,354 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 18% | 6 |
| East Asian | 16.8% | 6 |
| Middle Eastern | 14.8% | 7 |
| Ashkenazi Jewishnot grpmax-eligible | 13.3% | 8 |
| South Asian | 10.4% | 10 |
| Admixed American | 10.3% | 10 |
| Remaining individualsnot grpmax-eligible | 9.67% | 10 |
| Amishnot grpmax-eligible | 9.56% | 10 |
| European (non-Finnish) | 7.32% | 14 |
| Finnishnot grpmax-eligible | 4.29% | 23 |
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.Ser81=
- Coding
- c.243T>C
- MANE Select
- NM_030928
- dbSNP
- rs475667
- Type
- single nucleotide variant
- Location
- chr16:88804559 (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 81
- the 'disordered' region
Similar variants
- CDT1 p.Ser81Asn 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.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
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-ser81 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown