PRPF31 p.Pro342=
c.1026G>A · rs760509641 · VCV1657029
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00353%, sas)
Conditions
1
inherited retinal dystrophy
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 -11 | GERP -2.5 |
| Overall | ||
| CADD | 0.182 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00353%
South Asian · 3/85,026 alleles
Filtering AF
0.00193%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00168%
Overall
0.00224%
35/1,561,374 alleles · very rare
exomes 32/1,409,242 · genomes 3/152,132 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00353% | 28,342 |
| European (non-Finnish) | 0.00269% | 37,217 |
| East Asian | 0.00231% | 43,322 |
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
- PRPF31
- Protein
- p.Pro342=
- Coding
- c.1026G>A
- MANE Select
- NM_015629
- dbSNP
- rs760509641
- Type
- single nucleotide variant
- Location
- chr19:54128153 (GRCh38)
- Gene constraint
- LOEUF 0.347 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.69 · 30 PDB
- Residue 342
- the 'disordered' region; an α-helix
Similar variants
- PRPF31 c.1074-2A>G Pathogenic ★★ same condition
- PRPF31 c.1074-2A>T Pathogenic ★★ same condition
- PRPF31 c.1146+5G>T Likely pathogenic ★★ same condition
- PRPF31 c.238+1G>A Pathogenic ★★ same condition
- PRPF31 c.323-1G>C Pathogenic/Likely pathogenic ★★ same condition
- PRPF31 c.421-2A>G Pathogenic ★★ same condition
- PRPF31 c.527+1G>T Pathogenic ★★ same condition
- PRPF31 c.698-1G>A Pathogenic ★★ 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/prpf31-p-pro342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown