MN1 p.Pro102=
c.306G>C · rs45531332 · VCV716252
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.43%, afr)
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 -5.3 | GERP -4.1 |
| Overall | ||
| CADD | 6.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.43%
African / African-American · 1,801/74,068 alleles
Filtering AF
2.34%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.3%
Overall
0.125%
1,975/1,583,922 alleles · low-frequency
exomes 940/1,431,580 · genomes 1,035/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.43% | 41 |
| Middle Eastern | 0.187% | 533 |
| Remaining individualsnot grpmax-eligible | 0.12% | 836 |
| Admixed American | 0.102% | 983 |
| European (non-Finnish) | 0.00266% | 37,617 |
| South Asian | 0.00232% | 43,056 |
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
- MN1
- Protein
- p.Pro102=
- Coding
- c.306G>C
- MANE Select
- NM_002430
- dbSNP
- rs45531332
- Type
- single nucleotide variant
- Location
- chr22:27800238 (GRCh38)
- Gene constraint
- LOEUF 0.482 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 42.47
- Residue 102
- the 'disordered' region
Similar variants
- MN1 p.Pro102Ala Uncertain significance ★ ⚠ same residue
- MN1 p.Gln1273Ter Pathogenic ★★ same type
- MN1 p.Lys455Ter Likely pathogenic ★★ same type
- MN1 p.Trp1248Ter Pathogenic/Likely pathogenic ★★ same type
- MN1 p.Ala38Asp Uncertain significance ★★ ⚠ same type
- MN1 p.Gly1092Arg Uncertain significance ★★ ⚠ same type
- MN1 p.Gly120Val Uncertain significance ★★ ⚠ same type
- MN1 p.Gly161Arg 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/mn1-p-pro102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown