HNRNPA3
protein-codingheterogeneous nuclear ribonucleoprotein A3, the group of RNA binding motif containing|Heterogeneous nuclear ribonucleoproteins|MicroRNA protein coding host genes
Gene summary
Enables RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Located in nucleoplasm. Part of catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Jun 2026]
- HNRPA3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.4 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 HNRNPA3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_194247.4. 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 | 0 | |||||
| missense | 20 | 20 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 0 | 0 | 29 | 0 | 0 | 29 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_919223.1 | 10 | MANE Select | |
| Ensembl | ENSP00000376309.2 | 10 | MANE Select | |
| RefSeq | NP_001317176.1 | 10 | Standard | |
| RefSeq | NP_001317177.1 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Spliceosome - Homo sapiens (human)
- Metabolism of RNA
- mRNA Splicing - Major Pathway
- mRNA Splicing
- Processing of Capped Intron-Containing Pre-mRNA
Biological Process
- mRNA splicing, via spliceosome
- RNA metabolic process
- mRNA transport
Molecular Function
- RNA binding
- mRNA binding
- protein binding
- RNA transmembrane transporter activity
Cellular Component
- nucleus
- nucleoplasm
- cytoplasm
- postsynaptic density
- ribonucleoprotein granule
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000392524
- Coding exons
- 10
- Length
- 11396
- Individuals with no LoFs
- 125742
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 125744
- p
- 0.00000795
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.64 | 63 | 212 | 0.297 | 0.0000110 | 2439 |
| Missense (PolyPhen) | 5 | 39.822 | 0.12556 | 593 | ||
| Synonymous | -1.37 | 81 | 66.7 | 1.21 | 0.00000331 | 721 |
| Loss of Function | 3.98 | 1 | 20.4 | 0.0491 | 0.00000102 | 269 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in cytoplasmic trafficking of RNA. Binds to the cis-acting response element, A2RE. May be involved in pre-mRNA splicing. {ECO:0000269|PubMed:11886857}.;
Recessive Scores
- pRec
- 0.0925
Intolerance Scores
- LoFtool
- 0.198
- RVIS EVS
- -0.27
- RVIS percentile EVS
- 33.97
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.731
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |