NCBP3
protein-codingnuclear cap binding subunit 3
Gene summary
Enables RNA 7-methylguanosine cap binding activity and mRNA binding activity. Involved in defense response to virus; mRNA export from nucleus; and snRNA export from nucleus. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jun 2026]
- C17orf85
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~44.1 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 NCBP3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001114118.3. 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 | 1 | 1 | ||||
| missense | 81 | 3 | 84 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 82 | 4 | 0 | 86 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001107590.1 | 13 | MANE Select | |
| Ensembl | ENSP00000373657.4 | 13 | MANE Select | |
| RefSeq | NP_001385423.1 | 14 | Standard | |
| Ensembl | ENSP00000467742.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- 7-methylguanosine mRNA capping
- mRNA transport
- defense response to virus
Molecular Function
- RNA 7-methylguanosine cap binding
- RNA binding
- mRNA binding
- protein binding
Cellular Component
- nucleus
- cytoplasm
- nuclear speck
- RNA cap binding complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000389005
- Coding exons
- 13
- Length
- 35086
- Individuals with no LoFs
- 125744
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125747
- p
- 0.0000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.32 | 232 | 355 | 0.654 | 0.0000211 | 4074 |
| Missense (PolyPhen) | 88 | 134.06 | 0.6564 | 1480 | ||
| Synonymous | -0.114 | 133 | 131 | 1.01 | 0.00000801 | 1145 |
| Loss of Function | 5.02 | 3 | 35.0 | 0.0856 | 0.00000223 | 408 |
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 | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Associates with NCBP1/CBP80 to form an alternative cap- binding complex (CBC) which plays a key role in mRNA export. NCBP3 serves as adapter protein linking the capped RNAs (m7GpppG-capped RNA) to NCBP1/CBP80. Unlike the conventional CBC with NCBP2 which binds both small nuclear RNA (snRNA) and messenger (mRNA) and is involved in their export from the nucleus, the alternative CBC with NCBP3 does not bind snRNA and associates only with mRNA thereby playing a role in only mRNA export. The alternative CBC is particularly important in cellular stress situations such as virus infections and the NCBP3 activity is critical to inhibit virus growth (PubMed:26382858). {ECO:0000269|PubMed:26382858}.;
Intolerance Scores
- RVIS EVS
- 0.33
- RVIS percentile EVS
- 73.41
Essentials
- Essential (gene trap)
- N