MSR1 p.Arg362=
c.1086G>A · rs4338104 · VCV3060145
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 100%, mid) — too common for a highly-penetrant pathogenic allele
Conditions
1
MSR1-related disorder
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 -0.004 | GERP -4.5, phastCons 0.94 |
| Overall | ||
| CADD | 2.071 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
100%
Middle Eastern · 6,058/6,058 alleles
Filtering AF
99.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 99.8%
Overall
100%
1,609,363/1,609,998 alleles · common
exomes 1,461,478/1,461,800 · genomes 147,885/148,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asian | 100% | 1 |
| South Asian | 100% | 1 |
| Finnishnot grpmax-eligible | 100% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 100% | 1 |
| Amishnot grpmax-eligible | 100% | 1 |
| Middle Easterngrpmax | 100% | 1 |
| European (non-Finnish) | 100% | 1 |
| Remaining individualsnot grpmax-eligible | 100% | 1 |
| Admixed American | 99.9% | 1 |
| African / African-American | 99.2% | 1 |
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
- MSR1
- Protein
- p.Arg362=
- Coding
- c.1086G>A
- MANE Select
- NM_138715
- dbSNP
- rs4338104
- Type
- single nucleotide variant
- Location
- chr8:16120554 (GRCh38)
- Gene constraint
- LOEUF 1.366 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.74 · 1 PDB
- Residue 362
- a β-strand; the srcr domain
Disease context
MSR1-related disorder
Similar variants
- MSR1 c.630+7G>A Likely benign same condition
- MSR1 c.-5+6386C>A Likely benign same condition
- MSR1 p.Ile181Val Likely benign same condition
- MSR1 p.Met118Ile Likely benign same condition
- MSR1 p.Val244= Likely benign same condition
- MSR1 c.1034-17_1034-10del Benign same condition
- MSR1 p.Asp174Tyr Uncertain significance ★★ ⚠ same type
- MSR1 c.103+1G>T Likely benign ★★ 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/msr1-p-arg362 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown