MTMR1 p.Arg650=
c.1950C>T · rs782415979 · VCV2661637
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0265%, sas)
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 -7.3 | GERP -4.2 |
| Overall | ||
| CADD | 0.175 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0265%
South Asian · 15/56,569 alleles
Filtering AF
0.0163%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0132%
Overall
0.00356%
43/1,208,144 alleles · ultra-rare
exomes 41/1,095,957 · genomes 2/112,187 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0265% | 3,771 |
| Remaining individualsnot grpmax-eligible | 0.00632% | 15,824 |
| European (non-Finnish) | 0.0028% | 35,774 |
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
- MTMR1
- Protein
- p.Arg650=
- Coding
- c.1950C>T
- MANE Select
- NM_001306144
- dbSNP
- rs782415979
- Type
- single nucleotide variant
- Location
- chrX:150762657 (GRCh38)
- Structure
- AlphaFold pLDDT 85.72 · 1 PDB
- Residue 650
- the 'required for dimerization' region; the 'disordered' region
Similar variants
- MTMR1 c.1081-305A>G Benign ★★ same type
- MTMR1 c.1081-4G>A Benign ★★ same type
- MTMR1 c.277-41C>T Benign ★★ same type
- MTMR1 c.448-137G>A Benign ★★ same type
- MTMR1 p.Gly642= Benign ★★ same type
- MTMR1 c.253-1G>T Uncertain significance ★ same type
- MTMR1 p.Ala116Val Uncertain significance ★ ⚠ same type
- MTMR1 p.Ala223Ser 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/mtmr1-p-arg650 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown