PRPF8 p.Phe1684=
c.5052C>T · rs1911570557 · VCV3028446
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
inherited retinal dystrophy
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 6.5 | GERP 0.61, phastCons 1 |
| Overall | ||
| CADD | 11.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PRPF8
- Protein
- p.Phe1684=
- Coding
- c.5052C>T
- MANE Select
- NM_006445
- dbSNP
- rs1911570557
- Type
- single nucleotide variant
- Location
- chr17:1659443 (GRCh38)
- Gene constraint
- LOEUF 0.26 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.20 · 100 PDB
- Residue 1684
- an α-helix; the 'restriction endonuclease homology domain' region; the 'involved in interaction with pre-mrna 5' splice site' region
Similar variants
- PRPF8 p.Arg1935His Pathogenic/Likely pathogenic ★★ same condition
- PRPF8 p.Arg2310Gly Pathogenic/Likely pathogenic ★★ same condition
- PRPF8 p.Gln2321Ter Pathogenic/Likely pathogenic ★★ same condition
- PRPF8 p.His2313Pro Likely pathogenic ★★ ⚠ same condition
- PRPF8 p.Pro2301Ser Pathogenic/Likely pathogenic ★★ ⚠ same condition
- PRPF8 p.Thr1931Met Pathogenic/Likely pathogenic ★★ ⚠ same condition
- PRPF8 p.Ala1704Thr Uncertain significance ★★ ⚠ same condition
- PRPF8 p.Ala2299Val Uncertain significance ★★ ⚠ same condition
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/prpf8-p-phe1684 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown