CDC6 p.Pro55=
c.165C>T · rs142289528 · VCV210619
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.96%, mid)
Conditions
1
Meier-Gorlin syndrome 5
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 1.1 | GERP -2, phastCons 1 |
| Overall | ||
| CADD | 12.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.96%
Middle Eastern · 119/6,062 alleles
Filtering AF
1.68%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.57%
Overall
0.156%
2,524/1,613,974 alleles · low-frequency
exomes 2,339/1,461,724 · genomes 185/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.96% | 51 |
| Amishnot grpmax-eligible | 0.768% | 130 |
| South Asian | 0.637% | 157 |
| Ashkenazi Jewishnot grpmax-eligible | 0.442% | 226 |
| Remaining individualsnot grpmax-eligible | 0.208% | 481 |
| Admixed American | 0.147% | 682 |
| European (non-Finnish) | 0.122% | 819 |
| African / African-American | 0.032% | 3,125 |
| Finnishnot grpmax-eligible | 0.00625% | 16,007 |
| East Asian | 0.00223% | 44,872 |
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
- CDC6
- Protein
- p.Pro55=
- Coding
- c.165C>T
- MANE Select
- NM_001254
- dbSNP
- rs142289528
- Type
- single nucleotide variant
- Location
- chr17:40289585 (GRCh38)
- Gene constraint
- LOEUF 0.99 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.85 · 7 PDB
- Residue 55
- the 'disordered' region
Similar variants
- CDC6 p.Arg378His Uncertain significance ★★ same condition
- CDC6 p.Lys531Glu Uncertain significance ★★ ⚠ same condition
- CDC6 p.Val282Ala Uncertain significance ★★ ⚠ same condition
- CDC6 c.*653C>A Likely benign ★★ same condition
- CDC6 p.Asp295Asn Benign ★★ same condition
- CDC6 p.Cys146= Benign ★★ same condition
- CDC6 p.Ser504= Benign ★★ same condition
- CDC6 p.Thr299Met Benign ★★ ⚠ same condition
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/cdc6-p-pro55 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown