MRPS7 p.Pro39=
c.117T>C · rs115955242 · VCV392386
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.199%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.4 | GERP -3.1 |
| Overall | ||
| CADD | 1.757 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.199%
African / African-American · 149/75,044 alleles
Filtering AF
0.172%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.163%
Overall
0.0103%
166/1,614,110 alleles · rare
exomes 74/1,461,790 · genomes 92/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.199% | 504 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,813 |
| Admixed American | 0.01% | 10,005 |
| South Asian | 0.00329% | 30,363 |
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
- MRPS7
- Protein
- p.Pro39=
- Coding
- c.117T>C
- MANE Select
- NM_015971
- dbSNP
- rs115955242
- Type
- single nucleotide variant
- Location
- chr17:75262530 (GRCh38)
- Gene constraint
- LOEUF 0.758 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 87.29 · 86 PDB
Similar variants
- MRPS7 p.Arg166Cys Uncertain significance ★★ ⚠ same type
- MRPS7 p.Arg192Gln Uncertain significance ★★ ⚠ same type
- MRPS7 p.Arg192Trp Uncertain significance ★★ ⚠ same type
- MRPS7 p.Arg21Gln Uncertain significance ★★ ⚠ same type
- MRPS7 p.Arg240Cys Uncertain significance ★★ ⚠ same type
- MRPS7 p.Glu138Lys Uncertain significance ★★ ⚠ same type
- MRPS7 p.Glu67Gln Uncertain significance ★★ ⚠ same type
- MRPS7 p.Met229Thr 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/mrps7-p-pro39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown