MRPS7 p.Pro218=
c.654C>T · VCV4936982
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00441%, nfe)
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 -5.4 | GERP -3.7 |
| Overall | ||
| CADD | 0.427 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00441%
European (non-Finnish) · 52/1,180,040 alleles
Filtering AF
0.00342%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0031%
Overall
0.00353%
57/1,614,018 alleles · very rare
exomes 55/1,461,804 · genomes 2/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00441% | 22,693 |
| African / African-American | 0.004% | 24,981 |
| Admixed American | 0.00167% | 60,008 |
| South Asian | 0.0011% | 91,092 |
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.Pro218=
- Coding
- c.654C>T
- MANE Select
- NM_015971
- Type
- single nucleotide variant
- Location
- chr17:75265848 (GRCh38)
- Gene constraint
- LOEUF 0.758 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 87.29 · 86 PDB
- Residue 218
- an α-helix
Similar variants
- MRPS7 p.Pro218Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro218 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown