PRPF3

Chr 1

pre-mRNA processing factor 3

Also known as: HPRP3, HPRP3P, PRP3, Prp3p, RP18, SNRNP90

NCBI Gene: 9129ENSG00000117360UniProt: O43395

The removal of introns from nuclear pre-mRNAs occurs on complexes called spliceosomes, which are made up of 4 small nuclear ribonucleoprotein (snRNP) particles and an undefined number of transiently associated splicing factors. This gene product is one of several proteins that associate with U4 and U6 snRNPs. Mutations in this gene are associated with retinitis pigmentosa-18. [provided by RefSeq, Jul 2008]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtRetinitis pigmentosa 18

Clinical highlights

Gene-disease validity (ClinGen)
retinitis pigmentosa 18 · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Curated gene-level mechanism — a prior for triage, not a per-variant call.
0
Active trials
7
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.07
LOEUF· LoF intol.
Multiple*
Mechanism· predicted
📖
GeneReview available — PRPF3
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?
0.07LOEUF
pLI 1.000
Z-score 6.12
OE 0.00 (0.00–0.07)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?
3.85Z-score
OE missense 0.44 (0.38–0.50)
160 obs / 367.6 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?
LoF OE?0.00 (0.00–0.07)
0≤0.351.4
Missense OE?0.44 (0.38–0.50)
0≤0.61.4
Synonymous OE?0.94
0≤1.21.6
LoF obs/exp: 0 / 43.6Missense obs/exp: 160 / 367.6Syn Z: 0.57

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PRPF3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients