PRP4K p.Arg488=
c.1464C>T · rs532267331 · VCV2656189
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.3%, sas)
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 -1.3 | GERP -4.2 |
| Overall | ||
| CADD | 6.659 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.3%
South Asian · 273/91,058 alleles
Filtering AF
0.271%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.259%
Overall
0.022%
355/1,613,694 alleles · rare
exomes 337/1,461,554 · genomes 18/152,140 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.3% | 334 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,976 |
| Middle Eastern | 0.033% | 3,028 |
| European (non-Finnish) | 0.00458% | 21,848 |
| African / African-American | 0.00267% | 37,484 |
| East Asian | 0.00223% | 44,872 |
| Admixed American | 0.00167% | 59,982 |
| Finnishnot grpmax-eligible | 0.00156% | 63,976 |
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
- PRP4K
- Protein
- p.Arg488=
- Coding
- c.1464C>T
- MANE Select
- NM_003913
- dbSNP
- rs532267331
- Type
- single nucleotide variant
- Location
- chr6:4040823 (GRCh38)
- Structure
- AlphaFold pLDDT 60.24 · 14 PDB
- Residue 488
- the 'disordered' region
Similar variants
- PRP4K p.Ala671Thr Uncertain significance ★ same type
- PRP4K p.Arg10Trp Uncertain significance ★ ⚠ same type
- PRP4K p.Arg183Gln Uncertain significance ★ ⚠ same type
- PRP4K p.Arg191Trp Uncertain significance ★ ⚠ same type
- PRP4K p.Arg308Gln Uncertain significance ★ ⚠ same type
- PRP4K p.Arg308Gly Uncertain significance ★ ⚠ same type
- PRP4K p.Arg344Gly Uncertain significance ★ ⚠ same type
- PRP4K p.Arg348His 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/prp4k-p-arg488 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown