MRPS23 p.Ala2=
c.6A>C · rs775066859 · VCV1900553
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -11 | GERP -4.2 |
| Overall | ||
| CADD | 1.861 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,068 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000834%
Overall
0.00126%
20/1,592,338 alleles · ultra-rare
exomes 18/1,440,572 · genomes 2/151,766 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,068 |
| European (non-Finnish) | 0.00162% | 61,812 |
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
- MRPS23
- Protein
- p.Ala2=
- Coding
- c.6A>C
- MANE Select
- NM_016070
- dbSNP
- rs775066859
- Type
- single nucleotide variant
- Location
- chr17:57850005 (GRCh38)
- Gene constraint
- LOEUF 1.117 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.21 · 85 PDB
- Residue 2
- a modified residue (n-acetylalanine)
Similar variants
- MRPS23 p.Arg42Lys Uncertain significance ★★ ⚠ same type
- MRPS23 p.Arg98Trp Uncertain significance ★★ ⚠ same type
- MRPS23 p.Ser14Phe Uncertain significance ★★ same type
- MRPS23 c.215+12G>C Benign ★★ same type
- MRPS23 p.Arg21= Likely benign ★★ same type
- MRPS23 p.Gly136= Benign ★★ same type
- MRPS23 p.His142= Benign/Likely benign ★★ same type
- MRPS23 p.Pro59His 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/mrps23-p-ala2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown