PROKR2 p.Phe50=
c.150C>T · rs149123899 · VCV697956
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.1 | GERP -4.2 |
| Overall | ||
| CADD | 1.549 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.199%
African / African-American · 149/75,038 alleles
Filtering AF
0.172%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.163%
Overall
0.0137%
221/1,614,208 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.199% | 504 |
| South Asian | 0.0329% | 3,036 |
| East Asian | 0.029% | 3,452 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,813 |
| Admixed American | 0.00833% | 12,006 |
| Finnishnot grpmax-eligible | 0.00468% | 21,347 |
| European (non-Finnish) | 0.0011% | 90,772 |
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
- PROKR2
- Protein
- p.Phe50=
- Coding
- c.150C>T
- MANE Select
- NM_144773
- dbSNP
- rs149123899
- Type
- single nucleotide variant
- Location
- chr20:5314220 (GRCh38)
- Gene constraint
- LOEUF 1.492 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.50
Similar variants
- PROKR2 p.Arg164Gln Likely pathogenic ★★ same type
- PROKR2 p.Glu231Lys Likely pathogenic ★★ ⚠ same type
- PROKR2 p.Tyr316Ter Likely pathogenic ★★ same type
- PROKR2 p.Ala103Val Uncertain significance ★★ ⚠ same type
- PROKR2 p.Ala129Thr Uncertain significance ★★ ⚠ same type
- PROKR2 p.Ala156Thr Uncertain significance ★★ same type
- PROKR2 p.Arg135Cys Uncertain significance ★★ ⚠ same type
- PROKR2 p.Arg248Trp 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/prokr2-p-phe50 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown