PRPF4 p.Arg196=
c.588A>C · rs200829645 · VCV1124888
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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.18 | GERP -4.3, phastCons 0.99 |
| Overall | ||
| CADD | 10.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,968 alleles
Overall
0.000186%
3/1,613,860 alleles · very rare
exomes 2/1,461,874 · genomes 1/151,986 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,968 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,500 |
| European (non-Finnish) | 8.47e-05% | 1,179,980 |
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.Arg196=
- Coding
- c.588A>C
- MANE Select
- NM_001244926
- dbSNP
- rs200829645
- Type
- single nucleotide variant
- Location
- chr9:113283416 (GRCh38)
- Gene constraint
- LOEUF 0.294 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.33 · 25 PDB
- Residue 196
- an α-helix
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-arg196 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown