MRPS23 p.Pro158=
c.474A>G · VCV3616981
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
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 0.22 | GERP -0.02, phastCons 0.02 |
| Overall | ||
| CADD | 3.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,922 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000372%
6/1,614,066 alleles · very rare
exomes 4/1,461,886 · genomes 2/152,180 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,461 |
| Admixed American | 0.00167% | 59,986 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
| European (non-Finnish) | 0.000169% | 590,023 |
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.Pro158=
- Coding
- c.474A>G
- MANE Select
- NM_016070
- Type
- single nucleotide variant
- Location
- chr17:57839882 (GRCh38)
- Gene constraint
- LOEUF 1.117 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.21 · 85 PDB
- Residue 158
- the 'disordered' region
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-pro158 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown