KPNA1
karyopherin subunit alpha 1, the group of Armadillo repeat containing|Importins
Basic information
Region (hg38): 3:122421901-122514945
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 KPNA1 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 | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 0 | 1 |
Variants in KPNA1
This is a list of pathogenic ClinVar variants found in the KPNA1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-122427065-T-C | not specified | Uncertain significance (Jun 29, 2022) | ||
| 3-122427541-A-C | not specified | Uncertain significance (Dec 16, 2022) | ||
| 3-122427709-C-T | not specified | Uncertain significance (Dec 06, 2021) | ||
| 3-122433726-C-T | Benign (Dec 31, 2019) | |||
| 3-122433751-C-T | not specified | Uncertain significance (Mar 15, 2024) | ||
| 3-122437270-T-C | not specified | Uncertain significance (Feb 17, 2024) | ||
| 3-122449602-C-T | not specified | Uncertain significance (Feb 14, 2023) | ||
| 3-122449719-C-A | not specified | Uncertain significance (Apr 11, 2023) | ||
| 3-122451993-G-C | not specified | Uncertain significance (Nov 09, 2021) | ||
| 3-122453917-T-C | not specified | Uncertain significance (Jan 04, 2024) | ||
| 3-122464008-T-A | not specified | Uncertain significance (Aug 21, 2023) | ||
| 3-122467335-A-G | not specified | Uncertain significance (Aug 16, 2021) | ||
| 3-122467404-G-A | not specified | Uncertain significance (Feb 06, 2024) | ||
| 3-122496474-T-C | not specified | Uncertain significance (Jan 22, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KPNA1 | protein_coding | protein_coding | ENST00000344337 | 13 | 92997 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.998 | 0.00182 | 125738 | 0 | 7 | 125745 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.20 | 131 | 282 | 0.464 | 0.0000139 | 3537 |
| Missense in Polyphen | 34 | 114.32 | 0.29741 | 1427 | ||
| Synonymous | 1.13 | 87 | 101 | 0.857 | 0.00000509 | 1017 |
| Loss of Function | 4.72 | 3 | 31.6 | 0.0948 | 0.00000171 | 362 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000932 | 0.0000924 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000352 | 0.0000327 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Functions in nuclear protein import as an adapter protein for nuclear receptor KPNB1. Binds specifically and directly to substrates containing either a simple or bipartite NLS motif. 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. In vitro, mediates the nuclear import of human cytomegalovirus UL84 by recognizing a non- classical NLS.;
- Pathway
- Influenza A - Homo sapiens (human);Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Disease;HIV Life Cycle;Host Interactions of HIV factors;HIV Infection;Vpr-mediated nuclear import of PICs;Transport of Ribonucleoproteins into the Host Nucleus;Influenza Life Cycle;NS1 Mediated Effects on Host Pathways;Host Interactions with Influenza Factors;Influenza Infection;Infectious disease;Activation of DNA fragmentation factor;Apoptosis induced DNA fragmentation;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Interactions of Vpr with host cellular proteins;Class I PI3K signaling events mediated by Akt;Integration of provirus;Early Phase of HIV Life Cycle
(Consensus)
Recessive Scores
- pRec
- 0.256
Intolerance Scores
- loftool
- 0.260
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 37.11
Haploinsufficiency Scores
- pHI
- 0.917
- hipred
- Y
- hipred_score
- 0.768
- ghis
- 0.627
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.846
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kpna1
- Phenotype
- endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; hematopoietic system 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); reproductive system phenotype;
Gene ontology
- Biological process
- regulation of DNA recombination;apoptotic DNA fragmentation;NLS-bearing protein import into nucleus;modulation by virus of host process;intracellular transport of virus;postsynapse to nucleus signaling pathway
- Cellular component
- nucleus;nuclear pore;nucleoplasm;cytoplasm;cytosol;postsynaptic density;dendrite;host cell;glutamatergic synapse
- Molecular function
- protein binding;nuclear localization sequence binding;protein transporter activity;nuclear import signal receptor activity