Is PRPF31 p.Arg293= (c.879G>C) pathogenic?

PRPF31 p.Arg293= (c.879G>C) is classified Likely benign in PRPF31 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-02-13). Absent from gnomAD v4.1.

How common is PRPF31 p.Arg293= (c.879G>C) in the general population?

PRPF31 p.Arg293= (c.879G>C) is absent from gnomAD v4.1 (gnomAD).

PRPF31 p.Arg293=

c.879G>C · VCV4943833

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -0.3	GERP -3.4, phastCons 0.021
Overall
CADD	5.646	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: PRPF31
Protein: p.Arg293=
Coding: c.879G>C
MANE Select: NM_015629
Type: single nucleotide variant
Location: chr19:54126551 (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

Similar variants

PRPF31 p.Arg293Gln Uncertain significance ★ ⚠ same residue
PRPF31 p.Arg293Trp Uncertain significance ★ ⚠ same residue
PRPF31 p.Arg293fs Pathogenic ★ same residue
PRPF31 c.1073+1G>A Pathogenic ★★ same type
PRPF31 c.1074-1G>C Likely pathogenic ★★ same type
PRPF31 c.1074-2A>G Pathogenic ★★ same type
PRPF31 c.1074-2A>T Pathogenic ★★ same type
PRPF31 c.1146+2T>C Pathogenic ★★ 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/prpf31-p-arg293 (accessed [today's date]).

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