CDCA7 p.Thr292=
c.876C>T · rs148421045 · VCV1559555
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0199%, amr)
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 -0.13 | GERP -3.1 |
| Overall | ||
| CADD | 11.73 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0199%
Admixed American · 10/50,154 alleles
Filtering AF
0.0107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00821%
Overall
0.00266%
42/1,578,232 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0199% | 5,015 |
| South Asian | 0.00586% | 17,063 |
| Remaining individualsnot grpmax-eligible | 0.00491% | 20,386 |
| European (non-Finnish) | 0.00206% | 48,657 |
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.Thr292=
- Coding
- c.876C>T
- MANE Select
- NM_031942
- dbSNP
- rs148421045
- Type
- single nucleotide variant
- Location
- chr2:173364971 (GRCh38)
- Gene constraint
- LOEUF 0.676 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.93 · 2 PDB
- Residue 292
- a turn
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-thr292 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown