KPNA2

karyopherin subunit alpha 2, the group of Importins|Armadillo repeat containing

Basic information

Region (hg38): 17:68035636-68047364

Previous symbols: [ "RCH1" ]

Links

ENSG00000182481

∙ NCBI:3838 ∙ OMIM:600685 ∙ HGNC:6395 ∙ Uniprot:P52292 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KPNA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KPNA2 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					2 clinvar	2
missense			16 clinvar			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	2

Variants in KPNA2

This is a list of pathogenic ClinVar variants found in the KPNA2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
17-68037170-G-A	not specified	Uncertain significance (Mar 07, 2024)	3116176
17-68037443-G-A	not specified	Uncertain significance (Jan 26, 2022)	2273444
17-68037460-G-A	not specified	Uncertain significance (Jul 20, 2021)	2238220
17-68037463-A-G	not specified	Uncertain significance (Nov 15, 2023)	3116172
17-68037464-C-T	not specified	Uncertain significance (Feb 15, 2023)	2485318
17-68037470-C-T	not specified	Uncertain significance (Sep 27, 2022)	2313760
17-68037480-A-C	not specified	Uncertain significance (Feb 05, 2024)	3116173
17-68037494-A-T	not specified	Uncertain significance (Dec 09, 2024)	3535661
17-68040682-C-T	not specified	Uncertain significance (Jan 16, 2024)	3116174
17-68042150-A-G	not specified	Uncertain significance (Nov 30, 2022)	2330228
17-68042210-C-T	not specified	Uncertain significance (Aug 29, 2023)	2621933
17-68042280-A-T		Benign (Sep 19, 2018)	717516
17-68042309-C-T	not specified	Uncertain significance (Sep 13, 2023)	2623789
17-68042314-A-G	not specified	Uncertain significance (Sep 16, 2021)	2249751
17-68042917-T-G	not specified	Uncertain significance (Feb 27, 2023)	2489532
17-68043944-A-C	not specified	Uncertain significance (Mar 19, 2024)	3289235
17-68044059-T-C		Benign (Dec 31, 2019)	769922
17-68044357-G-A	not specified	Uncertain significance (Jan 08, 2024)	3116170
17-68044400-A-T	not specified	Uncertain significance (Aug 19, 2021)	2407988
17-68045919-G-A	not specified	Uncertain significance (Jan 23, 2024)	3116171

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KPNA2	protein_coding	protein_coding	ENST00000537025	10	11324

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.541	0.459	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.368	268	286	0.939	0.0000150	3457
Missense in Polyphen		42	60.718	0.69173		932
Synonymous	-1.47	124	105	1.18	0.00000571	1060
Loss of Function	3.60	5	24.0	0.208	0.00000121	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000170	0.000169
Ashkenazi Jewish	0.000601	0.000595
East Asian	0.00	0.00
Finnish	0.0000650	0.0000462
European (Non-Finnish)	0.0000619	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

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.;
Pathway: Influenza A - Homo sapiens (human);DNA Repair;Disease;DNA Double-Strand Break Repair;role of ran in mitotic spindle regulation;NS1 Mediated Effects on Host Pathways;Host Interactions with Influenza Factors;Influenza Infection;Infectious disease;mechanism of protein import into the nucleus;Signaling events mediated by TCPTP;Sensing of DNA Double Strand Breaks;TNFalpha;DNA Double Strand Break Response;Regulation of cytoplasmic and nuclear SMAD2/3 signaling;Role of Calcineurin-dependent NFAT signaling in lymphocytes (Consensus)

Recessive Scores

pRec: 0.486

Intolerance Scores

loftool: 0.372
rvis_EVS: 0.51
rvis_percentile_EVS: 80.2

Haploinsufficiency Scores

pHI: 0.988
hipred: Y
hipred_score: 0.734
ghis: 0.571

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: H
gene_indispensability_pred: N
gene_indispensability_score: 0.126

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Kpna2
Phenotype

Gene ontology

Biological process: regulation of DNA recombination;DNA metabolic process;NLS-bearing protein import into nucleus;modulation by virus of host process;postsynapse to nucleus signaling pathway
Cellular component: nucleoplasm;cytoplasm;cytosol;membrane;extrinsic component of postsynaptic specialization membrane;glutamatergic synapse
Molecular function: RNA binding;protein binding;nuclear localization sequence binding;protein transporter activity;histone deacetylase binding;nuclear import signal receptor activity