KPNA2

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

Basic information

Region (hg38): 17:68035635-68047364

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	2
missense			16			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	Type	Phenotype	Significance	ClinVar
17-68037170-G-A		not specified	Uncertain significance (Mar 07, 2024)
17-68037443-G-A		not specified	Uncertain significance (Jan 26, 2022)
17-68037460-G-A		not specified	Uncertain significance (Jul 20, 2021)
17-68037463-A-G		not specified	Uncertain significance (Nov 15, 2023)
17-68037464-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-68037470-C-T		not specified	Uncertain significance (Sep 27, 2022)
17-68037480-A-C		not specified	Uncertain significance (Feb 05, 2024)
17-68040682-C-T		not specified	Uncertain significance (Jan 16, 2024)
17-68042150-A-G		not specified	Uncertain significance (Nov 30, 2022)
17-68042210-C-T		not specified	Uncertain significance (Aug 29, 2023)
17-68042280-A-T			Benign (Sep 19, 2018)
17-68042309-C-T		not specified	Uncertain significance (Sep 13, 2023)
17-68042314-A-G		not specified	Uncertain significance (Sep 16, 2021)
17-68042917-T-G		not specified	Uncertain significance (Feb 27, 2023)
17-68043944-A-C		not specified	Uncertain significance (Mar 19, 2024)
17-68044059-T-C			Benign (Dec 31, 2019)
17-68044357-G-A		not specified	Uncertain significance (Jan 08, 2024)
17-68044400-A-T		not specified	Uncertain significance (Aug 19, 2021)
17-68045919-G-A		not specified	Uncertain significance (Jan 23, 2024)

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

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