CDCA7 p.Lys15=
c.45G>A · rs139753635 · VCV720862
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.144%, nfe)
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 6 | GERP -0.16, phastCons 1 |
| Overall | ||
| CADD | 6.008 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.144%
European (non-Finnish) · 1,700/1,179,846 alleles
Filtering AF
0.138%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.136%
Overall
0.115%
1,863/1,613,806 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.144% | 694 |
| Admixed American | 0.13% | 769 |
| Middle Eastern | 0.116% | 866 |
| Remaining individualsnot grpmax-eligible | 0.0912% | 1,096 |
| African / African-American | 0.0133% | 7,504 |
| South Asian | 0.011% | 9,101 |
| Finnishnot grpmax-eligible | 0.00156% | 64,018 |
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
- CDCA7
- Protein
- p.Lys15=
- Coding
- c.45G>A
- MANE Select
- NM_031942
- dbSNP
- rs139753635
- Type
- single nucleotide variant
- Location
- chr2:173358735 (GRCh38)
- Gene constraint
- LOEUF 0.676 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.93 · 2 PDB
Similar variants
- CDCA7 p.Lys15del Uncertain significance ★ same residue
- CDCA7 c.384+2T>C Uncertain significance ★★ same type
- CDCA7 p.Ala157Val Uncertain significance ★★ ⚠ same type
- CDCA7 p.Ala391Gly Uncertain significance ★★ ⚠ same type
- CDCA7 p.Arg134Leu Uncertain significance ★★ ⚠ same type
- CDCA7 p.Arg134Trp Uncertain significance ★★ ⚠ same type
- CDCA7 p.Arg171Cys Uncertain significance ★★ ⚠ same type
- CDCA7 p.Arg171Leu 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/cdca7-p-lys15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown