MCM7 p.Arg653=
c.1959G>A · rs1270206426 · VCV3124387
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 14.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,876 alleles
Overall
6.2e-05%
1/1,613,586 alleles · very rare
exomes 1/1,461,300 · genomes 0/152,286 · joint denominator
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
- MCM7
- Protein
- p.Arg653=
- Coding
- c.1959G>A
- MANE Select
- NM_005916
- dbSNP
- rs1270206426
- Type
- single nucleotide variant
- Location
- chr7:100093133 (GRCh38)
- Gene constraint
- LOEUF 1.305 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.63 · 28 PDB
- Residue 653
- the 'interaction with atrip' region
Similar variants
- MCM7 p.Gly259Ala Pathogenic ★★ ⚠ same type
- MCM7 p.His459= Benign ★★ same type
- MCM7 p.Leu281= Likely benign ★★ same type
- MCM7 p.Thr415= Benign ★★ same type
- MCM7 p.Val622= Benign ★★ same type
- MCM7 p.Arg527Ter Pathogenic ★ same type
- MCM7 p.Gln139Ter Pathogenic ★ same type
- MCM7 p.Gln45Ter Pathogenic ★ 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/mcm7-p-arg653 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown