MCM9 p.Ser71=
c.213T>C · rs73521381 · VCV790585
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 8.06%, afr) — too common for a highly-penetrant pathogenic allele
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 -1.3 | GERP -3.5 |
| Overall | ||
| CADD | 3.592 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.06%
African / African-American · 6,050/75,022 alleles
Filtering AF
7.89%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.82%
Overall
0.458%
7,400/1,614,152 alleles · common
exomes 3,871/1,461,860 · genomes 3,529/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.06% | 12 |
| Remaining individualsnot grpmax-eligible | 0.594% | 168 |
| Admixed American | 0.558% | 179 |
| Middle Eastern | 0.511% | 196 |
| Ashkenazi Jewishnot grpmax-eligible | 0.223% | 449 |
| South Asian | 0.0582% | 1,719 |
| European (non-Finnish) | 0.0419% | 2,389 |
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.Ser71=
- Coding
- c.213T>C
- MANE Select
- NM_017696
- dbSNP
- rs73521381
- Type
- single nucleotide variant
- Location
- chr6:118931511 (GRCh38)
- Gene constraint
- LOEUF 0.916 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.24 · 6 PDB
- Residue 71
- an α-helix
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-ser71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown