MSMO1 p.Asn124=
c.372T>C · rs148185089 · VCV1666596
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0617%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>G here scores Δ0.20 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.28 | GERP -3.3, phastCons 0.044 |
| Overall | ||
| CADD | 11.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0617%
Admixed American · 37/60,006 alleles
Filtering AF
0.0522%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0508%
Overall
0.0459%
741/1,613,614 alleles · ultra-rare
exomes 684/1,461,270 · genomes 57/152,344 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0617% | 1,622 |
| European (non-Finnish) | 0.0558% | 1,793 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,975 |
| Finnishnot grpmax-eligible | 0.0281% | 3,555 |
| African / African-American | 0.00799% | 12,509 |
| South Asian | 0.0011% | 91,072 |
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
- MSMO1
- Protein
- p.Asn124=
- Coding
- c.372T>C
- MANE Select
- NM_006745
- dbSNP
- rs148185089
- Type
- single nucleotide variant
- Location
- chr4:165337905 (GRCh38)
- Gene constraint
- LOEUF 0.901 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.13
- Residue 124
- a UniProt-annotated variant site (in)
Similar variants
- MSMO1 p.Asn124Ser Benign ★★ same residue
- MSMO1 p.Ala60Gly Uncertain significance ★★ ⚠ same type
- MSMO1 p.Asn236Ser Uncertain significance ★★ ⚠ same type
- MSMO1 p.Gly273Glu Uncertain significance ★★ same type
- MSMO1 p.His105Gln Uncertain significance ★★ ⚠ same type
- MSMO1 p.Ile56Met Uncertain significance ★★ ⚠ same type
- MSMO1 p.Phe137Leu Uncertain significance ★★ ⚠ same type
- MSMO1 p.Trp135Cys 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/msmo1-p-asn124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown