MRPS23 p.Pro180=
c.540T>C · rs149198678 · VCV3030896
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0733%, afr)
Conditions
1
MRPS23-related disorder
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 -1.6 | GERP -3.8 |
| Overall | ||
| CADD | 0.283 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0733%
African / African-American · 55/75,070 alleles
Filtering AF
0.0577%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0522%
Overall
0.0044%
71/1,614,210 alleles · ultra-rare
exomes 46/1,461,854 · genomes 25/152,356 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0733% | 1,365 |
| Middle Eastern | 0.066% | 1,516 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,929 |
| European (non-Finnish) | 0.000424% | 236,007 |
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.Pro180=
- Coding
- c.540T>C
- MANE Select
- NM_016070
- dbSNP
- rs149198678
- Type
- single nucleotide variant
- Location
- chr17:57839816 (GRCh38)
- Gene constraint
- LOEUF 1.117 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.21 · 85 PDB
- Residue 180
- the 'disordered' region
Disease context
MRPS23-related disorder
Similar variants
- MRPS23 p.Pro180Arg Uncertain significance ★ same residue
- MRPS23 p.Gly81Ser Likely benign same condition
- 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
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-pro180 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown