MRPS34 p.Val164=
c.492G>A · rs942465730 · VCV2174517
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.01%, amr)
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 1.1 | GERP -2.2, phastCons 1 |
| Overall | ||
| CADD | 6.918 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/60,002 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.000434%
7/1,611,872 alleles · very rare
exomes 5/1,459,686 · genomes 2/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 10,000 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,462 |
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
- MRPS34
- Protein
- p.Val164=
- Coding
- c.492G>A
- MANE Select
- NM_023936
- dbSNP
- rs942465730
- Type
- single nucleotide variant
- Location
- chr16:1772386 (GRCh38)
- Gene constraint
- LOEUF 1.89 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.20 · 85 PDB
- Residue 164
- a β-strand; a UniProt-annotated variant site (in coxpd32; significant decrease in protein levels; destabilizes the small ribosomal subunit resulting in impaired mitochondrial translation)
Similar variants
- MRPS34 c.322-10G>A Pathogenic ★★ same type
- MRPS34 p.Glu23Lys Uncertain significance ★★ ⚠ same type
- MRPS34 p.Ile196Lys Uncertain significance ★★ ⚠ same type
- MRPS34 p.Lys144Asn Uncertain significance ★★ ⚠ same type
- MRPS34 p.Met135Thr Uncertain significance ★★ same type
- MRPS34 c.322-19C>T Likely benign ★★ same type
- MRPS34 c.364+9C>T Benign/Likely benign ★★ same type
- MRPS34 c.*63A>G 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/mrps34-p-val164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown