TRMU p.Gln2=
c.6G>A · rs758055404 · VCV1083033
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0118%, 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 3 | GERP -1, phastCons 1 |
| Overall | ||
| CADD | 4.944 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0118%
South Asian · 10/85,050 alleles
Filtering AF
0.00633%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00482%
Overall
0.000967%
15/1,551,782 alleles · ultra-rare
exomes 15/1,399,434 · genomes 0/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0118% | 8,505 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,362 |
| African / African-American | 0.00136% | 73,368 |
| European (non-Finnish) | 0.00026% | 384,166 |
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
- TRMU
- Protein
- p.Gln2=
- Coding
- c.6G>A
- MANE Select
- NM_018006
- dbSNP
- rs758055404
- Type
- single nucleotide variant
- Location
- chr22:46335770 (GRCh38)
- Gene constraint
- LOEUF 1.276 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.60
Similar variants
- TRMU p.Gln2Ter Pathogenic/Likely pathogenic ★★ same residue
- TRMU c.1019-1G>A Likely pathogenic ★★ same type
- TRMU c.1102-3C>G Likely pathogenic ★★ same type
- TRMU c.248+1G>A Pathogenic/Likely pathogenic ★★ same type
- TRMU c.249-2A>G Likely pathogenic ★★ same type
- TRMU c.355+1G>C Likely pathogenic ★★ same type
- TRMU c.355+1G>T Likely pathogenic ★★ same type
- TRMU c.478+1G>A Likely pathogenic ★★ 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/trmu-p-gln2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown