MRPL44 p.Arg59=
c.177C>G · rs556415712 · VCV1627694
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0184%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>T here scores Δ0.26 · evaluated, not missing |
|---|---|---|
| Pangolin | Δ0.23 | loss · gain 0.03 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP 4.1 | GERP 3, phastCons 1 |
| Overall | ||
| CADD | 18.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0184%
Middle Eastern · 1/5,438 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000498%
8/1,604,962 alleles · ultra-rare
exomes 7/1,452,614 · genomes 1/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0184% | 5,438 |
| Finnishnot grpmax-eligible | 0.00175% | 57,126 |
| European (non-Finnish) | 0.000509% | 196,530 |
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
- MRPL44
- Protein
- p.Arg59=
- Coding
- c.177C>G
- MANE Select
- NM_022915
- dbSNP
- rs556415712
- Type
- single nucleotide variant
- Location
- chr2:223957649 (GRCh38)
- Gene constraint
- LOEUF 1.194 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.36 · 91 PDB
Similar variants
- MRPL44 p.Arg59Cys Uncertain significance ★ ⚠ same residue
- MRPL44 p.Leu156Arg Pathogenic/Likely pathogenic ★★ same type
- MRPL44 p.Ala37Ser Uncertain significance ★★ ⚠ same type
- MRPL44 p.Arg105Cys Uncertain significance ★★ ⚠ same type
- MRPL44 p.Arg312Trp Uncertain significance ★★ ⚠ same type
- MRPL44 p.Asn249Ser Uncertain significance ★★ ⚠ same type
- MRPL44 p.Asn315Tyr Uncertain significance ★★ ⚠ same type
- MRPL44 p.His13Arg Uncertain significance ★★ ⚠ 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/mrpl44-p-arg59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown