KPNB1
karyopherin subunit beta 1, the group of Armadillo repeat containing|Importins
Basic information
Region (hg38): 17:47649476-47685505
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 KPNB1 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 1 |
Variants in KPNB1
This is a list of pathogenic ClinVar variants found in the KPNB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-47652785-C-T | not specified | Uncertain significance (Sep 26, 2023) | ||
| 17-47657005-C-T | not specified | Uncertain significance (Dec 14, 2023) | ||
| 17-47658554-T-C | not specified | Uncertain significance (Nov 10, 2022) | ||
| 17-47663138-A-G | not specified | Uncertain significance (Jul 27, 2021) | ||
| 17-47664181-G-A | not specified | Uncertain significance (Feb 02, 2024) | ||
| 17-47670775-A-C | not specified | Uncertain significance (Jan 13, 2023) | ||
| 17-47676459-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
| 17-47676479-T-C | Benign (Jul 31, 2017) | |||
| 17-47680594-G-A | not specified | Uncertain significance (Jun 10, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KPNB1 | protein_coding | protein_coding | ENST00000290158 | 21 | 36030 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 3.59e-8 | 125723 | 0 | 4 | 125727 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 5.93 | 109 | 472 | 0.231 | 0.0000233 | 5745 |
| Missense in Polyphen | 10 | 137.84 | 0.072545 | 1661 | ||
| Synonymous | 0.804 | 161 | 175 | 0.923 | 0.00000878 | 1681 |
| Loss of Function | 6.54 | 1 | 51.8 | 0.0193 | 0.00000272 | 594 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000293 | 0.0000293 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000883 | 0.00000879 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.0000328 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Functions in nuclear protein import, either in association with an adapter protein, like an importin-alpha subunit, which binds to nuclear localization signals (NLS) in cargo substrates, or by acting as autonomous nuclear transport receptor. Acting autonomously, serves itself as NLS receptor. Docking of the importin/substrate complex to the nuclear pore complex (NPC) is mediated by KPNB1 through binding to nucleoporin FxFG repeats and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to importin-beta and the three components separate and importin-alpha and -beta are re- exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran from importin. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus. Mediates autonomously the nuclear import of ribosomal proteins RPL23A, RPS7 and RPL5. Binds to a beta-like import receptor binding (BIB) domain of RPL23A. In association with IPO7 mediates the nuclear import of H1 histone. In vitro, mediates nuclear import of H2A, H2B, H3 and H4 histones. In case of HIV-1 infection, binds and mediates the nuclear import of HIV-1 Rev. Imports SNAI1 and PRKCI into the nucleus. {ECO:0000269|PubMed:10228156, ECO:0000269|PubMed:11891849, ECO:0000269|PubMed:19386897, ECO:0000269|PubMed:24699649, ECO:0000269|PubMed:9687515}.;
- Pathway
- RNA transport - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Neutrophil degranulation;Disease;role of ran in mitotic spindle regulation;Metabolism of lipids;Interactions of Rev with host cellular proteins;Host Interactions of HIV factors;HIV Infection;Transport of Ribonucleoproteins into the Host Nucleus;Influenza Life Cycle;NS1 Mediated Effects on Host Pathways;Host Interactions with Influenza Factors;Influenza Infection;Regulation of cholesterol biosynthesis by SREBP (SREBF);Infectious disease;Innate Immune System;Immune System;Metabolism;Activation of DNA fragmentation factor;Apoptosis induced DNA fragmentation;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Metabolism of steroids;TGF_beta_Receptor;mechanism of protein import into the nucleus;Signaling events mediated by TCPTP;Nuclear import of Rev protein;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Regulation of cytoplasmic and nuclear SMAD2/3 signaling;Role of Calcineurin-dependent NFAT signaling in lymphocytes
(Consensus)
Recessive Scores
- pRec
- 0.559
Intolerance Scores
- loftool
- 0.0409
- rvis_EVS
- -0.62
- rvis_percentile_EVS
- 17.16
Haploinsufficiency Scores
- pHI
- 0.999
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.614
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.981
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kpnb1
- Phenotype
- normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- obsolete protein import into nucleus, translocation;apoptotic DNA fragmentation;protein import into nucleus;NLS-bearing protein import into nucleus;ribosomal protein import into nucleus;mitotic chromosome movement towards spindle pole;mitotic metaphase plate congression;modulation by virus of host process;astral microtubule organization;Ran protein signal transduction;establishment of mitotic spindle localization;neutrophil degranulation;establishment of protein localization;regulation of cholesterol biosynthetic process;intracellular transport of virus;mitotic spindle assembly
- Cellular component
- extracellular region;nuclear envelope;nuclear pore;nucleoplasm;cytoplasm;cytosol;cytoplasmic stress granule;membrane;nuclear membrane;nuclear periphery;specific granule lumen;host cell;extracellular exosome;endoplasmic reticulum tubular network;ficolin-1-rich granule lumen
- Molecular function
- RNA binding;protein binding;nuclear localization sequence binding;zinc ion binding;Ran GTPase binding;protein transporter activity;enzyme binding;protein domain specific binding;Hsp90 protein binding