MN1 p.Pro167=
c.501G>A · VCV4947318
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, 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 -0.002 | GERP -2.5, phastCons 0.2 |
| Overall | ||
| CADD | 9.551 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,168 alleles
Overall
6.24e-05%
1/1,602,066 alleles · very rare
exomes 1/1,449,732 · genomes 0/152,334 · 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
- MN1
- Protein
- p.Pro167=
- Coding
- c.501G>A
- MANE Select
- NM_002430
- Type
- single nucleotide variant
- Location
- chr22:27800043 (GRCh38)
- Gene constraint
- LOEUF 0.482 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 42.47
- Residue 167
- the 'disordered' region
Similar variants
- MN1 p.Pro167Leu 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-pro167 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown