Is PRPF31 p.Arg293fs (c.877del) pathogenic?

PRPF31 p.Arg293fs (c.877del) is classified Pathogenic in PRPF31 (ClinVar, Single submitter, 1 submitter; last evaluated 2014-01-01). Associated with inherited retinal dystrophy.

What condition is associated with PRPF31 p.Arg293fs (c.877del)?

PRPF31 p.Arg293fs (c.877del) is associated with inherited retinal dystrophy (ClinVar).

PRPF31 p.Arg293fs

c.877del · VCV3249720

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

inherited retinal dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 9 of 14
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: PRPF31
Protein: p.Arg293fs
Coding: c.877del
MANE Select: NM_015629
Type: Deletion
Location: chr19:54126547 (GRCh38)
Gene constraint: LOEUF 0.347 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 77.69 · 30 PDB
Residue 293: the nop domain; a functional site (interaction with u4 snrna and u4atac snrna); an α-helix

Full PRPF31 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

inherited retinal dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRPF31 c.1067_1073+8del Pathogenic ★★ same condition
PRPF31 c.528-39_531del Pathogenic/Likely pathogenic ★★ same condition
PRPF31 c.(1146+1_1147-1 Pathogenic ★ same condition
PRPF31 c.(238+1_239-1 Pathogenic ★ same condition
PRPF31 c.845_855+1del Pathogenic ★ same condition
PRPF31 c.(855+1_856-1 Pathogenic ★ same condition
PRPF31 p.Gly381fs Pathogenic ★ same condition
PRPF31 p.Lys401fs Likely 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-arg293fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown