MST1R p.Arg910=
c.2730G>A · rs540237920 · VCV3043026
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.493%, sas)
Conditions
1
MST1R-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.259 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.001 | GERP -2, phastCons 0.78 |
| Overall | ||
| CADD | 2.875 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.493%
South Asian · 439/89,088 alleles
Filtering AF
0.455%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.44%
Overall
0.0284%
456/1,605,504 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.493% | 203 |
| Middle Eastern | 0.0332% | 3,011 |
| Remaining individualsnot grpmax-eligible | 0.0225% | 4,438 |
| European (non-Finnish) | 8.5e-05% | 1,175,880 |
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
- MST1R
- Protein
- p.Arg910=
- Coding
- c.2730G>A
- MANE Select
- NM_002447
- dbSNP
- rs540237920
- Type
- single nucleotide variant
- Location
- chr3:49896027 (GRCh38)
- Gene constraint
- LOEUF 0.985 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.23 · 4 PDB
Disease context
MST1R-related disorder
Similar variants
- MST1R p.Arg910Gln Benign ★★ same residue
- MST1R p.Arg910Trp Uncertain significance ★ ⚠ same residue
- MST1R c.3811-10C>A Benign same condition
- MST1R p.Arg1335Gly Benign same condition
- MST1R p.Arg322Gln Benign same condition
- MST1R p.Arg455= Likely benign same condition
- MST1R p.Asn778Thr Likely benign same condition
- MST1R p.Asp805= Likely benign same condition
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/mst1r-p-arg910 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown