MRPS34 p.Ala172=
c.516C>T · rs1406560076 · VCV1667040
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00178%, nfe)
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 -0.03 | GERP -3.1, phastCons 0.46 |
| Overall | ||
| CADD | 4.433 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00178%
European (non-Finnish) · 21/1,180,018 alleles
Filtering AF
0.00114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000971%
Overall
0.0013%
21/1,612,836 alleles · very rare
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.Ala172=
- Coding
- c.516C>T
- MANE Select
- NM_023936
- dbSNP
- rs1406560076
- Type
- single nucleotide variant
- Location
- chr16:1772362 (GRCh38)
- Gene constraint
- LOEUF 1.89 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.20 · 85 PDB
- Residue 172
- an α-helix; 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 p.Ala172Thr Uncertain significance ★ same residue
- 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
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-ala172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown