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GeneE
5 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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PRPF38A
pre-mRNA processing factor 38A
Chromosome 1 · 1p32.3
NCBI Gene: 84950Ensembl: ENSG00000134748.14HGNC: HGNC:25930UniProt: Q8NAV1
83PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Hub Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
RNA bindingprotein bindingmRNA splicing, via spliceosomenucleusneurodegenerative diseaseEar-patella-short stature syndromeMeier-Gorlin syndromeresponse to statin
✦AI Summary

PRPF38A is a pre-mRNA splicing factor that functions as a component of the U2-type spliceosome, a ribonucleoprotein complex essential for mRNA processing 1. The protein localizes to nuclear speckles, dynamic nuclear bodies involved in splicing regulation, where it forms droplet-like structures and physically interacts with MFAP1 2. PRPF38A's spatial organization within the nucleus regulates splicing activity; relocation of PRPF38A to the nuclear lamina induces intron retention, demonstrating that subcellular localization controls splicing factor function 3. Clinically, PRPF38A represents a vulnerability in basal-A triple-negative breast cancer cells; knockdown of PRPF38A causes widespread intron retention in genes critical for protein homeostasis, mitosis, and apoptosis, and splicing inhibition shows therapeutic potential when combined with proteasome inhibitors 1. Additionally, genomic variants near PRPF38A influence its expression and are associated with pediatric bone accrual, suggesting roles in osteoblast differentiation and bone development 4. These findings position PRPF38A as both a fundamental splicing regulator and a potential therapeutic target in cancer and skeletal diseases.

Sources cited
1
PRPF38A localizes to nuclear speckles, forms droplet-like structures with MFAP1, and its localization precedes nuclear speckle formation
PMID: 32609799
2
PRPF38A relocation to the nuclear lamina induces intron retention, demonstrating spatial regulation of splicing activity
PMID: 35869234
3
PRPF38A is a spliceosome component and dependency gene in basal-A TNBC; knockdown causes intron retention in genes affecting protein homeostasis, mitosis, and apoptosis
PMID: 28878028
4
Genomic variants near PRPF38A influence its expression and are associated with pediatric bone accrual
PMID: 33397451
⚠Limited data available — This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.27Weak
Ear-patella-short stature syndromeOpen Targets
0.12Weak
Meier-Gorlin syndromeOpen Targets
0.12Weak
response to statinOpen Targets
0.05Suggestive
atrial fibrillationOpen Targets
0.05Suggestive
hemolytic anemiaOpen Targets
0.02Suggestive
osteosarcomaOpen Targets
0.01Suggestive
sarcomaOpen Targets
0.01Suggestive
neoplasmOpen Targets
0.00Suggestive
colorectal carcinomaOpen Targets
0.00Suggestive
hepatocellular carcinomaOpen Targets
0.00Suggestive
IGA glomerulonephritisOpen Targets
0.00Suggestive
triple-negative breast cancerOpen Targets
0.00Suggestive
acute myeloid leukemiaOpen Targets
0.00Suggestive
cervical cancerOpen Targets
0.00Suggestive
clear cell renal carcinomaOpen Targets
0.00Suggestive
esophageal cancerOpen Targets
0.00Suggestive
gastric cancerOpen Targets
0.00Suggestive
hereditary breast carcinomaOpen Targets
0.00Suggestive
Uterine CarcinosarcomaOpen Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
HNRNPA1L3Shared pathway100%RBMXL1Shared pathway100%RBMY1EShared pathway100%RBMY1DShared pathway100%RBM44Shared pathway100%HNRNPA3Shared pathway100%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
58%
Brain
44%
Lung
33%
Heart
27%
Liver
27%
Gene Interaction Network
Click a node to explore
PRPF38AHNRNPA1L3RBMXL1RBMY1ERBMY1DRBM44HNRNPA3
PROTEIN STRUCTURE
Preparing viewer…
PDB4RZ9 · 1.28 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.40Moderately Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.21 [0.12–0.40]
RankingsWhere PRPF38A stands among ~20K protein-coding genes
  • #5,751of 20,598
    Most Researched83
  • #2,010of 17,882
    Most Constrained (LOEUF)0.40 · top quartile
Genes detectedPRPF38A
Sources retrieved5 papers
Response time—
📄 Sources
5
1
Tyramide signal amplification mass spectrometry (TSA-MS) ratio identifies nuclear speckle proteins.
PMID: 32609799
J Cell Biol · 2020
1.00
2
Recruitment of a splicing factor to the nuclear lamina for its inactivation.
PMID: 35869234
Commun Biol · 2022
0.80
3
Basal-A Triple-Negative Breast Cancer Cells Selectively Rely on RNA Splicing for Survival.
PMID: 28878028
Mol Cancer Ther · 2017
0.60
4
Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual.
PMID: 33397451
Genome Biol · 2021
0.40
5
Identification of a novel fusion gene, RUNX1-PRPF38A, in acute myeloid leukemia.
PMID: 28263028
Int J Lab Hematol · 2017
0.20