MRPL19 p.Phe200=
c.600T>C · rs567728815 · VCV2651081
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0602%, eas)
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 -4.5 | GERP -4.4 |
| Overall | ||
| CADD | 4.552 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0602%
East Asian · 27/44,852 alleles
Filtering AF
0.0424%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0365%
Overall
0.00421%
68/1,613,810 alleles · ultra-rare
exomes 60/1,461,602 · genomes 8/152,208 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0602% | 1,661 |
| South Asian | 0.034% | 2,938 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,943 |
| European (non-Finnish) | 8.48e-05% | 1,179,857 |
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
- MRPL19
- Protein
- p.Phe200=
- Coding
- c.600T>C
- MANE Select
- NM_014763
- dbSNP
- rs567728815
- Type
- single nucleotide variant
- Location
- chr2:75654860 (GRCh38)
- Gene constraint
- LOEUF 1.373 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.98 · 93 PDB
Similar variants
- MRPL19 c.658-9C>A Likely benign ★★ same type
- MRPL19 p.Ala288Val Uncertain significance ★ ⚠ same type
- MRPL19 p.Arg118His Uncertain significance ★ ⚠ same type
- MRPL19 p.Arg182Trp Uncertain significance ★ ⚠ same type
- MRPL19 p.Arg232Cys Uncertain significance ★ ⚠ same type
- MRPL19 p.Arg232His Uncertain significance ★ ⚠ same type
- MRPL19 p.Arg235His Uncertain significance ★ ⚠ same type
- MRPL19 p.Arg271Lys 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/mrpl19-p-phe200 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown