PRPF8 p.Pro913=
c.2739C>T · rs780783091 · VCV3028457
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
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 -7.5 | GERP -5.3 |
| Overall | ||
| CADD | 0.115 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,024 alleles
Overall
6.2e-05%
1/1,613,962 alleles · very rare
exomes 0/1,461,894 · genomes 1/152,068 · joint denominator
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
- PRPF8
- Protein
- p.Pro913=
- Coding
- c.2739C>T
- MANE Select
- NM_006445
- dbSNP
- rs780783091
- Type
- single nucleotide variant
- Location
- chr17:1675753 (GRCh38)
- Gene constraint
- LOEUF 0.26 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.20 · 100 PDB
- Residue 913
- an α-helix; the 'reverse transcriptase homology domain' region
Similar variants
- PRPF8 p.Pro913Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro913 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown