NCBP2
nuclear cap binding protein subunit 2, the group of RNA binding motif containing
Basic information
Region (hg38): 3:196935402-196942594
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCBP2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in NCBP2
This is a list of pathogenic ClinVar variants found in the NCBP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-196937043-C-T | not specified | Uncertain significance (Feb 25, 2025) | ||
| 3-196937546-C-G | not specified | Uncertain significance (Sep 20, 2023) | ||
| 3-196937583-C-T | not specified | Uncertain significance (May 05, 2023) | ||
| 3-196937619-G-A | not specified | Uncertain significance (Dec 26, 2023) | ||
| 3-196939380-A-G | not specified | Uncertain significance (Mar 16, 2022) | ||
| 3-196942458-C-T | not specified | Uncertain significance (Nov 10, 2024) | ||
| 3-196942491-G-C | not specified | Uncertain significance (Jan 31, 2025) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NCBP2 | protein_coding | protein_coding | ENST00000321256 | 4 | 7196 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.400 | 0.592 | 125725 | 0 | 23 | 125748 | 0.0000915 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.15 | 40 | 101 | 0.397 | 0.00000636 | 1015 |
| Missense in Polyphen | 14 | 32.962 | 0.42474 | 334 | ||
| Synonymous | -1.58 | 50 | 37.7 | 1.33 | 0.00000239 | 284 |
| Loss of Function | 2.22 | 2 | 9.32 | 0.215 | 5.64e-7 | 100 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000177 | 0.000177 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000124 | 0.000123 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000980 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the cap-binding complex (CBC), which binds co-transcriptionally to the 5' cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing, translation regulation, nonsense-mediated mRNA decay, RNA-mediated gene silencing (RNAi) by microRNAs (miRNAs) and mRNA export. The CBC complex is involved in mRNA export from the nucleus via its interaction with ALYREF/THOC4/ALY, leading to the recruitment of the mRNA export machinery to the 5' end of mRNA and to mRNA export in a 5' to 3' direction through the nuclear pore. The CBC complex is also involved in mediating U snRNA and intronless mRNAs export from the nucleus. The CBC complex is essential for a pioneer round of mRNA translation, before steady state translation when the CBC complex is replaced by cytoplasmic cap-binding protein eIF4E. The pioneer round of mRNA translation mediated by the CBC complex plays a central role in nonsense-mediated mRNA decay (NMD), NMD only taking place in mRNAs bound to the CBC complex, but not on eIF4E-bound mRNAs. The CBC complex enhances NMD in mRNAs containing at least one exon-junction complex (EJC) via its interaction with UPF1, promoting the interaction between UPF1 and UPF2. The CBC complex is also involved in 'failsafe' NMD, which is independent of the EJC complex, while it does not participate in Staufen-mediated mRNA decay (SMD). During cell proliferation, the CBC complex is also involved in microRNAs (miRNAs) biogenesis via its interaction with SRRT/ARS2, thereby being required for miRNA- mediated RNA interference. The CBC complex also acts as a negative regulator of PARN, thereby acting as an inhibitor of mRNA deadenylation. In the CBC complex, NCBP2/CBP20 recognizes and binds capped RNAs (m7GpppG-capped RNA) but requires NCBP1/CBP80 to stabilize the movement of its N-terminal loop and lock the CBC into a high affinity cap-binding state with the cap structure. The conventional cap-binding complex with NCBP2 binds both small nuclear RNA (snRNA) and messenger (mRNA) and is involved in their export from the nucleus (PubMed:26382858). {ECO:0000269|PubMed:11551508, ECO:0000269|PubMed:15361857, ECO:0000269|PubMed:17190602, ECO:0000269|PubMed:17363367, ECO:0000269|PubMed:17873884, ECO:0000269|PubMed:18369367, ECO:0000269|PubMed:19632182, ECO:0000269|PubMed:26382858}.;
- Pathway
- mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human);Spliceosome - Homo sapiens (human);mRNA Processing;FGFR2 alternative splicing;Signaling by FGFR2;Disease;Signal Transduction;Formation of the HIV-1 Early Elongation Complex;Gene expression (Transcription);Signaling by FGFR;Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;Abortive elongation of HIV-1 transcript in the absence of Tat;HIV Transcription Elongation;Formation of HIV elongation complex in the absence of HIV Tat;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;snRNP Assembly;RNA Polymerase II Pre-transcription Events;Formation of RNA Pol II elongation complex ;RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs;Metabolism of RNA;Processing of Intronless Pre-mRNAs;Processing of Capped Intronless Pre-mRNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Infectious disease;RNA Polymerase II Transcription Elongation;mRNA Splicing - Major Pathway;Transport of the SLBP independent Mature mRNA;Transport of the SLBP Dependant Mature mRNA;Transport of Mature mRNA Derived from an Intronless Transcript;Transport of Mature mRNAs Derived from Intronless Transcripts;Nonsense-Mediated Decay (NMD);Transport of Mature mRNA derived from an Intron-Containing Transcript;Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC);Metabolism of non-coding RNA;Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC);mRNA Capping;Formation of the Early Elongation Complex;SLBP independent Processing of Histone Pre-mRNAs;Signaling by Receptor Tyrosine Kinases;mRNA Splicing - Minor Pathway;mRNA Splicing;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.178
Intolerance Scores
- loftool
- 0.476
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.39
Haploinsufficiency Scores
- pHI
- 0.255
- hipred
- Y
- hipred_score
- 0.816
- ghis
- 0.713
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.991
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Ncbp2
- Phenotype
Zebrafish Information Network
- Gene name
- ncbp2
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- necrotic
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;mRNA splicing, via spliceosome;transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;termination of RNA polymerase II transcription;7-methylguanosine mRNA capping;RNA export from nucleus;mRNA export from nucleus;snRNA export from nucleus;regulation of translational initiation;histone mRNA metabolic process;RNA splicing;fibroblast growth factor receptor signaling pathway;RNA metabolic process;gene silencing by RNA;mRNA 3'-end processing;positive regulation of mRNA 3'-end processing;snRNA transcription by RNA polymerase II;mRNA cis splicing, via spliceosome;positive regulation of RNA export from nucleus;nuclear export;pre-mRNA cleavage required for polyadenylation;regulation of mRNA polyadenylation
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;mRNA cap binding complex;nuclear cap binding complex;RNA cap binding complex
- Molecular function
- RNA cap binding;RNA 7-methylguanosine cap binding;RNA binding;mRNA binding;protein binding;snRNA binding