CDC73 p.Glu261del
c.779AAG[1] · rs1676029521 · VCV2067394
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
2
hereditary neoplastic syndrome
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 12 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 20.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,930 alleles
Overall
0.000657%
1/152,186 alleles · very rare
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
- CDC73
- Protein
- p.Glu261del
- Coding
- c.779AAG[1]
- MANE Select
- NM_024529
- dbSNP
- rs1676029521
- Type
- Microsatellite
- Location
- chr1:193147914 (GRCh38)
- Gene constraint
- LOEUF 0.42 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 73.94 · 21 PDB
- Residue 261
- the 'interaction with polr2a and paf1' region; the 'disordered' region; an α-helix
Similar variants
- CDC73 p.Arg229fs Pathogenic ★★ same condition
- CDC73 p.His160fs Pathogenic/Likely pathogenic ★★ same condition
- CDC73 p.Val230fs Pathogenic ★★ same condition
- CDC73 p.Asn66del Uncertain significance ★★ same condition
- CDC73 p.Lys394del Uncertain significance ★★ same condition
- CDC73 c.1316+14TA[6] Likely benign ★★ same condition
- CDC73 p.Arg152fs Pathogenic ★ same condition
- CDC73 p.Glu400fs Pathogenic ★ 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/cdc73-p-glu261del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown