CDCA7 p.Glu281del
c.825GGA[4] · rs754083976 · VCV1975130
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0154%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.6 | GERP -4.9 |
| Overall | ||
| CADD | 18.68 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (GGA)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0154%
Admixed American · 9/58,586 alleles
Filtering AF
0.00854%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00669%
Overall
0.00311%
50/1,608,150 alleles · ultra-rare
exomes 50/1,456,114 · genomes 0/152,036 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0154% | 6,510 |
| South Asian | 0.0145% | 6,919 |
| East Asian | 0.0135% | 7,428 |
| African / African-American | 0.00537% | 18,616 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0034% | 29,420 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,234 |
| Finnishnot grpmax-eligible | 0.00156% | 63,914 |
| European (non-Finnish) | 0.00127% | 78,536 |
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.Glu281del
- Coding
- c.825GGA[4]
- MANE Select
- NM_031942
- dbSNP
- rs754083976
- Type
- Microsatellite
- Location
- chr2:173364920 (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 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-glu281del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown