PRPF4 p.Lys155=
c.465A>G · rs11552582 · VCV1165174
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 51.5%, sas) — too common for a highly-penetrant pathogenic allele
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 3 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 8.943 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
51.5%
South Asian · 46,704/90,652 alleles
Filtering AF
51.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 51%
Overall
35.8%
573,700/1,603,410 alleles · common
exomes 518,090/1,451,650 · genomes 55,610/151,760 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 51.5% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 47.9% | 2 |
| East Asian | 43.9% | 2 |
| African / African-American | 43.4% | 2 |
| Amishnot grpmax-eligible | 41.4% | 2 |
| Remaining individualsnot grpmax-eligible | 37% | 3 |
| Middle Eastern | 35.8% | 3 |
| European (non-Finnish) | 34.3% | 3 |
| Finnishnot grpmax-eligible | 29.4% | 3 |
| Admixed American | 24.2% | 4 |
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.Lys155=
- Coding
- c.465A>G
- MANE Select
- NM_001244926
- dbSNP
- rs11552582
- Type
- single nucleotide variant
- Location
- chr9:113282718 (GRCh38)
- Gene constraint
- LOEUF 0.294 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.33 · 25 PDB
Similar variants
- PRPF4 p.Lys155Thr 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-lys155 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown