MN1 p.Pro187=
c.561G>T · VCV4947317
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0034%, nfe)
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 -0.61 | GERP -4.5 |
| Overall | ||
| CADD | 5.073 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0034%
European (non-Finnish) · 40/1,176,954 alleles
Filtering AF
0.00256%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00226%
Overall
0.00256%
41/1,603,224 alleles · very rare
exomes 38/1,450,990 · genomes 3/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0034% | 29,424 |
| Finnishnot grpmax-eligible | 0.00172% | 58,056 |
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.Pro187=
- Coding
- c.561G>T
- MANE Select
- NM_002430
- Type
- single nucleotide variant
- Location
- chr22:27799983 (GRCh38)
- Gene constraint
- LOEUF 0.482 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 42.47
- Residue 187
- the 'disordered' region
Similar variants
- MN1 p.Pro187Gln 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-pro187 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown