MN1 p.Val595=
c.1785G>A · rs45554336 · VCV777678
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 29.3%, 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 -0.33, phastCons 1 |
| Overall | ||
| CADD | 8.694 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
29.3%
African / African-American · 21,377/73,026 alleles
Filtering AF
28.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 28.8%
Overall
1.58%
24,281/1,534,322 alleles · common
exomes 11,573/1,382,026 · genomes 12,708/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 29.3% | 3 |
| Admixed American | 2.1% | 48 |
| Remaining individualsnot grpmax-eligible | 2.08% | 48 |
| Middle Eastern | 1.15% | 87 |
| Ashkenazi Jewishnot grpmax-eligible | 0.158% | 633 |
| South Asian | 0.0607% | 1,646 |
| European (non-Finnish) | 0.0371% | 2,696 |
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.Val595=
- Coding
- c.1785G>A
- MANE Select
- NM_002430
- dbSNP
- rs45554336
- Type
- single nucleotide variant
- Location
- chr22:27798759 (GRCh38)
- Gene constraint
- LOEUF 0.482 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 42.47
- Residue 595
- a UniProt-annotated variant site (in cebalid); the 'disordered' region
Similar variants
- MN1 p.Val595Met Likely benign ★★ same residue
- MN1 p.Val595_Gly596insHisGlyGlyProVal 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
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-val595 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown