MN1 p.Ser472=
c.1416G>A · VCV4947310
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00802%, 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 2.6 | GERP 0.89, phastCons 1 |
| Overall | ||
| CADD | 15.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00802%
African / African-American · 6/74,848 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.000499%
8/1,603,998 alleles · very rare
exomes 5/1,451,684 · genomes 3/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00802% | 12,475 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,034 |
| South Asian | 0.0011% | 90,674 |
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.Ser472=
- Coding
- c.1416G>A
- MANE Select
- NM_002430
- Type
- single nucleotide variant
- Location
- chr22:27799128 (GRCh38)
- Gene constraint
- LOEUF 0.482 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 42.47
- Residue 472
- a UniProt-annotated variant site (in cebalid)
Similar variants
- MN1 p.Ser472Ter Pathogenic ★ 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-ser472 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown