PRPF4 p.Tyr511=
c.1533T>C · VCV3706971
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 0.067 | GERP 0.071, phastCons 0.97 |
| Overall | ||
| CADD | 5.959 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,024 alleles
Overall
0.000124%
2/1,614,208 alleles · very rare
exomes 2/1,461,884 · genomes 0/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,024 |
| European (non-Finnish) | 8.47e-05% | 1,180,030 |
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.Tyr511=
- Coding
- c.1533T>C
- MANE Select
- NM_001244926
- Type
- single nucleotide variant
- Location
- chr9:113291627 (GRCh38)
- Gene constraint
- LOEUF 0.294 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.33 · 25 PDB
- Residue 511
- a β-strand
Similar variants
- PRPF4 p.Tyr511Cys Uncertain significance ★ ⚠ same residue
- 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
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-tyr511 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown