PRPF40A
protein-codingpre-mRNA processing factor 40 homolog A, the group of Spliceosomal A complex
Gene summary
Enables RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Located in nuclear matrix and nuclear speck. [provided by Alliance of Genome Resources, Jun 2026]
- FNBP3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~66.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PRPF40A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001365597.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 1 | 3 | |||
| missense | 69 | 69 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 9 | 9 | ||||
| Total | 0 | 0 | 80 | 0 | 1 | 81 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001352526.1 | 26 | MANE Select | |
| Ensembl | ENSP00000444656.4 | 26 | MANE Select | |
| RefSeq | NP_001341360.1 | 25 | Standard | |
| RefSeq | NP_001341361.1 | 24 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Spliceosome - Homo sapiens (human)
- miR-targeted genes in epithelium - TarBase
- miR-targeted genes in leukocytes - TarBase
- miR-targeted genes in lymphocytes - TarBase
- miR-targeted genes in squamous cell - TarBase
Biological Process
- mRNA splicing, via spliceosome
- cytoskeleton organization
- cell cycle
- regulation of cell shape
- cell migration
Molecular Function
- RNA binding
- protein binding
Cellular Component
- nucleoplasm
- U1 snRNP
- cytosol
- membrane
- nuclear matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000410080
- Coding exons
- 26
- Length
- 66405
- Individuals with no LoFs
- 124621
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 17
- Defined
- 124638
- p
- 0.0000682
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.33 | 261 | 463 | 0.564 | 0.0000236 | 6128 |
| Missense (PolyPhen) | 14 | 36.443 | 0.38416 | 440 | ||
| Synonymous | -2.52 | 181 | 143 | 1.27 | 0.00000703 | 1604 |
| Loss of Function | 5.10 | 14 | 54.7 | 0.256 | 0.00000291 | 738 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000066 | 0.000065 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00011 | 0.00011 | rare |
| South Asian | 0.000034 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Binds to WASL/N-WASP and suppresses its translocation from the nucleus to the cytoplasm, thereby inhibiting its cytoplasmic function (By similarity). Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the control of cell shape and migration. May play a role in cytokinesis. May be involved in pre-mRNA splicing. {ECO:0000250, ECO:0000269|PubMed:21834987}.;
Recessive Scores
- pRec
- 0.178
Intolerance Scores
- LoFtool
- 0.299
- RVIS EVS
- -1.11
- RVIS percentile EVS
- 6.72
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.922
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |