MRPS7 p.Phe41=
c.123C>T · rs199887365 · VCV1539518
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0178%, eas)
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 1.1 | GERP -0.58, phastCons 0.92 |
| Overall | ||
| CADD | 8.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0178%
East Asian · 8/44,886 alleles
Filtering AF
0.00883%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00641%
Overall
0.000681%
11/1,614,092 alleles · ultra-rare
exomes 9/1,461,790 · genomes 2/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0178% | 5,611 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
| South Asian | 0.0011% | 91,086 |
| European (non-Finnish) | 8.47e-05% | 1,179,994 |
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.Phe41=
- Coding
- c.123C>T
- MANE Select
- NM_015971
- dbSNP
- rs199887365
- Type
- single nucleotide variant
- Location
- chr17:75262536 (GRCh38)
- Gene constraint
- LOEUF 0.758 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 87.29 · 86 PDB
Similar variants
- MRPS7 p.Phe41Leu 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-phe41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown