Is PRPF31 p.Pro30= (c.90A>G) pathogenic?

PRPF31 p.Pro30= (c.90A>G) is classified Likely benign in PRPF31 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-06). Absent from gnomAD v4.1.

How common is PRPF31 p.Pro30= (c.90A>G) in the general population?

PRPF31 p.Pro30= (c.90A>G) is absent from gnomAD v4.1 (gnomAD).

PRPF31 p.Pro30=

c.90A>G · rs1399742310 · VCV1665716

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 -10	GERP -2.5
Overall
CADD	0.449	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.Pro30=
Coding: c.90A>G
MANE Select: NM_015629
dbSNP: rs1399742310
Type: single nucleotide variant
Location: chr19:54118368 (GRCh38)
Gene constraint: LOEUF 0.347 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 77.69 · 30 PDB
Residue 30: the 'disordered' region

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

Similar variants

PRPF31 p.Pro30Leu Uncertain significance ★ ⚠ same residue
PRPF31 p.Pro30Ser Uncertain significance ★ ⚠ same residue
PRPF31 p.Pro30fs 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-pro30 (accessed [today's date]).

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