NCBP1
nuclear cap binding protein subunit 1, the group of MIF4G domain containing proteins
Basic information
Region (hg38): 9:97633668-97673748
Previous symbols: [ "NCBP" ]
Links
Phenotypes
GenCC
Source:
- Tourette syndrome (Limited), mode of inheritance: Unknown
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 NCBP1 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 | 1 | |||||
| missense | 34 | 34 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 34 | 0 | 1 |
Variants in NCBP1
This is a list of pathogenic ClinVar variants found in the NCBP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-97633890-G-A | Benign (Apr 01, 2024) | |||
| 9-97640830-C-T | not specified | Uncertain significance (May 30, 2023) | ||
| 9-97643352-G-A | Mycotic Aneurysm, Intracranial | Uncertain significance (Oct 08, 2021) | ||
| 9-97645121-G-A | not specified | Uncertain significance (Mar 02, 2023) | ||
| 9-97645156-G-T | not specified | Uncertain significance (Jun 04, 2024) | ||
| 9-97645189-T-A | not specified | Uncertain significance (Dec 15, 2022) | ||
| 9-97645223-A-G | not specified | Uncertain significance (May 06, 2024) | ||
| 9-97645629-G-T | not specified | Uncertain significance (Apr 18, 2023) | ||
| 9-97645688-T-A | not specified | Uncertain significance (Nov 07, 2024) | ||
| 9-97645722-A-G | not specified | Uncertain significance (Nov 13, 2024) | ||
| 9-97648152-C-T | not specified | Uncertain significance (Jun 13, 2023) | ||
| 9-97650552-A-G | not specified | Uncertain significance (Dec 16, 2021) | ||
| 9-97650569-A-G | not specified | Uncertain significance (Aug 12, 2022) | ||
| 9-97651357-A-C | not specified | Uncertain significance (Dec 22, 2024) | ||
| 9-97653859-C-T | not specified | Uncertain significance (Feb 28, 2025) | ||
| 9-97654890-C-T | not specified | Uncertain significance (Aug 28, 2024) | ||
| 9-97654911-G-A | not specified | Uncertain significance (Nov 14, 2023) | ||
| 9-97654916-G-A | not specified | Uncertain significance (Jan 01, 2025) | ||
| 9-97656030-G-T | not specified | Uncertain significance (Nov 19, 2022) | ||
| 9-97656072-G-C | not specified | Uncertain significance (May 07, 2024) | ||
| 9-97658689-G-A | not specified | Uncertain significance (Jul 11, 2023) | ||
| 9-97661000-A-G | not specified | Uncertain significance (Feb 24, 2025) | ||
| 9-97661045-A-G | not specified | Uncertain significance (Jul 27, 2024) | ||
| 9-97662063-C-T | not specified | Uncertain significance (Feb 21, 2025) | ||
| 9-97662099-A-G | not specified | Uncertain significance (Aug 28, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NCBP1 | protein_coding | protein_coding | ENST00000375147 | 23 | 40123 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 6.26e-8 | 125719 | 0 | 2 | 125721 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.52 | 224 | 429 | 0.522 | 0.0000223 | 5263 |
| Missense in Polyphen | 62 | 165.39 | 0.37488 | 2075 | ||
| Synonymous | 0.658 | 134 | 144 | 0.930 | 0.00000738 | 1398 |
| Loss of Function | 6.44 | 1 | 50.3 | 0.0199 | 0.00000261 | 584 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000883 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the cap-binding complex (CBC), which binds cotranscriptionally 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 and is 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, NCBP1/CBP80 does not bind directly capped RNAs (m7GpppG-capped RNA) but is required to stabilize the movement of the N-terminal loop of NCBP2/CBP20 and lock the CBC into a high affinity cap-binding state with the cap structure. Associates with NCBP3 to form an alternative cap- binding complex (CBC) which plays a key role in mRNA export and is particularly important in cellular stress situations such as virus infections. The conventional CBC with NCBP2 binds both small nuclear RNA (snRNA) and messenger (mRNA) and is involved in their export from the nucleus whereas the alternative CBC with NCBP3 does not bind snRNA and associates only with mRNA thereby playing a role only in mRNA export. NCBP1/CBP80 is required for cell growth and viability (PubMed:26382858). {ECO:0000269|PubMed:11551508, ECO:0000269|PubMed:12093754, ECO:0000269|PubMed:15059963, ECO:0000269|PubMed:15361857, ECO:0000269|PubMed:16186820, ECO:0000269|PubMed:16317009, ECO:0000269|PubMed:17190602, ECO:0000269|PubMed:17873884, ECO:0000269|PubMed:18369367, ECO:0000269|PubMed:19632182, ECO:0000269|PubMed:19648179, ECO:0000269|PubMed:26382858, ECO:0000269|PubMed:7651522, ECO:0000269|PubMed:8069914}.;
- 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
- 0.154
Intolerance Scores
- loftool
- 0.0487
- rvis_EVS
- -0.18
- rvis_percentile_EVS
- 40.36
Haploinsufficiency Scores
- pHI
- 0.0861
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.641
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.958
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ncbp1
- Phenotype
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;spliceosomal complex assembly;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;regulation of translational initiation;histone mRNA metabolic process;RNA splicing;fibroblast growth factor receptor signaling pathway;RNA metabolic process;positive regulation of cell growth;primary miRNA processing;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 mRNA splicing, via spliceosome;nuclear export;pre-mRNA cleavage required for polyadenylation;regulation of mRNA polyadenylation;positive regulation of RNA binding
- Cellular component
- nucleus;nucleoplasm;mitochondrion;cytosol;mRNA cap binding complex;nuclear cap binding complex;RNA cap binding complex;ribonucleoprotein complex
- Molecular function
- RNA cap binding;RNA 7-methylguanosine cap binding;RNA binding;protein binding