PRPF4 p.Val139=
c.417C>T · rs139273131 · VCV1164910
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.213%, amr)
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 -8.9 | GERP -5.1 |
| Overall | ||
| CADD | 1.447 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.213%
Admixed American · 125/58,812 alleles
Filtering AF
0.182%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.171%
Overall
0.0144%
230/1,601,894 alleles · rare
exomes 152/1,453,452 · genomes 78/148,442 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.213% | 470 |
| East Asian | 0.0516% | 1,940 |
| Remaining individualsnot grpmax-eligible | 0.0129% | 7,750 |
| African / African-American | 0.00682% | 14,672 |
| European (non-Finnish) | 0.00579% | 17,271 |
| Finnishnot grpmax-eligible | 0.0016% | 62,556 |
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
- PRPF4
- Protein
- p.Val139=
- Coding
- c.417C>T
- MANE Select
- NM_001244926
- dbSNP
- rs139273131
- Type
- single nucleotide variant
- Location
- chr9:113282670 (GRCh38)
- Gene constraint
- LOEUF 0.294 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.33 · 25 PDB
Similar variants
- PRPF4 p.Pro314Leu Likely pathogenic ★★ same type
- PRPF4 c.654+4A>T Uncertain significance ★★ same type
- PRPF4 p.Ala195Thr Uncertain significance ★★ ⚠ same type
- PRPF4 p.Ala299Val Uncertain significance ★★ ⚠ same type
- PRPF4 p.Arg206Ser Uncertain significance ★★ ⚠ same type
- PRPF4 p.Arg438Trp Uncertain significance ★★ ⚠ same type
- PRPF4 p.Arg439Cys Uncertain significance ★★ ⚠ same type
- PRPF4 p.Asn241Ser 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/prpf4-p-val139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown