MCM9 p.Ser690=
c.2070A>G · VCV4893874
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.23%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.013 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.7 | GERP -3.6 |
| Overall | ||
| CADD | 1.324 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.23%
African / African-American · 899/73,168 alleles
Filtering AF
1.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.14%
Overall
0.0647%
1,003/1,550,540 alleles · low-frequency
exomes 489/1,398,230 · genomes 514/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.23% | 81 |
| Middle Eastern | 0.0835% | 1,198 |
| Remaining individualsnot grpmax-eligible | 0.0782% | 1,279 |
| Admixed American | 0.0608% | 1,645 |
| South Asian | 0.00238% | 42,028 |
| European (non-Finnish) | 0.00166% | 60,366 |
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
- MCM9
- Protein
- p.Ser690=
- Coding
- c.2070A>G
- MANE Select
- NM_017696
- Type
- single nucleotide variant
- Location
- chr6:118816186 (GRCh38)
- Gene constraint
- LOEUF 0.916 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.24 · 6 PDB
- Residue 690
- the 'disordered' region
Similar variants
- MCM9 c.1151-1G>A Pathogenic/Likely pathogenic ★★ same type
- MCM9 p.Arg132Ter Pathogenic/Likely pathogenic ★★ same type
- MCM9 p.Ala812Thr Uncertain significance ★★ ⚠ same type
- MCM9 p.Arg168Gln Uncertain significance ★★ ⚠ same type
- MCM9 p.Asp298Asn Uncertain significance ★★ ⚠ same type
- MCM9 p.Arg424= Benign/Likely benign ★★ same type
- MCM9 p.Arg666Trp Likely benign ★★ same type
- MCM9 p.Asn304Ser Likely benign ★★ ⚠ 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/mcm9-p-ser690 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown