Is PRPF31 p.Pro30fs (c.89_92del) pathogenic?

PRPF31 p.Pro30fs (c.8992del) is classified Pathogenic in PRPF31 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-05-28). Absent from gnomAD; Associated with retinitis pigmentosa.

What condition is associated with PRPF31 p.Pro30fs (c.89_92del)?

PRPF31 p.Pro30fs (c.89_92del) is associated with retinitis pigmentosa (ClinVar).

How common is PRPF31 p.Pro30fs (c.89_92del) in the general population?

PRPF31 p.Pro30fs (c.89_92del) is absent from gnomAD (gnomAD).

How is Retinitis pigmentosa inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

PRPF31 p.Pro30fs

c.89_92del · rs1600324442 · VCV804152

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

retinitis pigmentosa

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 2 of 14
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 1.2, phastCons 1
Region caveats
Repeat context	tandem	GA-rich low complexity · ambiguous alignment · confidence, not pathogenicity

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PRPF31
Protein: p.Pro30fs
Coding: c.89_92del
MANE Select: NM_015629
dbSNP: rs1600324442
Type: Deletion
Location: chr19:54118364 (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

Disease context

retinitis pigmentosa — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Retinitis pigmentosa (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

PRPF31 c.1067_1073+8del Pathogenic ★★ same condition
PRPF31 p.Glu124fs Pathogenic ★★ same condition
PRPF31 p.Glu28fs Pathogenic ★★ same condition
PRPF31 p.Gly317fs Pathogenic/Likely pathogenic ★★ same condition
PRPF31 p.Arg360fs Pathogenic ★ same condition
PRPF31 p.Gly317_Tyr318insTer Pathogenic ★ same condition
PRPF31 p.Gly82fs Pathogenic ★ same condition
PRPF31 p.Ile32fs 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-pro30fs (accessed [today's date]).

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