CDCA7 p.Cys399=
c.1197C>T · rs1192861543 · VCV2158170
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0168%, mid)
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 0.36 | GERP -0.9, phastCons 0.99 |
| Overall | ||
| CADD | 7.488 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0168%
Middle Eastern · 1/5,958 alleles
Filtering AF
8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000439%
7/1,592,866 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0168% | 5,958 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,558 |
| African / African-American | 0.00135% | 73,832 |
| European (non-Finnish) | 0.000342% | 292,791 |
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.Cys399=
- Coding
- c.1197C>T
- MANE Select
- NM_031942
- dbSNP
- rs1192861543
- Type
- single nucleotide variant
- Location
- chr2:173367161 (GRCh38)
- Gene constraint
- LOEUF 0.676 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.93 · 2 PDB
Similar variants
- 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
- CDCA7 p.Arg239Gln 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-cys399 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown