PRPF3 p.Arg89=
c.267A>G · rs782538822 · VCV1944638
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.022%, sas)
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 4 | GERP -0.55, phastCons 1 |
| Overall | ||
| CADD | 10.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.022%
South Asian · 20/91,072 alleles
Filtering AF
0.0145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0121%
Overall
0.00161%
26/1,613,116 alleles · ultra-rare
exomes 24/1,460,886 · genomes 2/152,230 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.022% | 4,554 |
| East Asian | 0.0111% | 8,974 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,400 |
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
- PRPF3
- Protein
- p.Arg89=
- Coding
- c.267A>G
- MANE Select
- NM_004698
- dbSNP
- rs782538822
- Type
- single nucleotide variant
- Location
- chr1:150325872 (GRCh38)
- Gene constraint
- LOEUF 0.087 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.75 · 30 PDB
- Residue 89
- the 'disordered' region
Similar variants
- PRPF3 p.Arg89Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- PRPF3 p.Arg449Gly Pathogenic/Likely pathogenic ★★ same type
- PRPF3 p.His499Pro Pathogenic ★★ same type
- PRPF3 p.Pro493Ser Pathogenic ★★ same type
- PRPF3 p.Thr494Met Pathogenic ★★ same type
- PRPF3 p.Ala489Pro Uncertain significance ★★ ⚠ same type
- PRPF3 p.Arg641Gln Uncertain significance ★★ ⚠ same type
- PRPF3 p.Asp43Gly 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/prpf3-p-arg89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown