KPNA5

karyopherin subunit alpha 5, the group of Armadillo repeat containing|Importins

Basic information

Region (hg38): 6:116681186-116741867

Links

ENSG00000196911 ∙ NCBI:3841 ∙ OMIM:604545 ∙ HGNC:6398 ∙ Uniprot:O15131 ∙ 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 KPNA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KPNA5 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						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in KPNA5

This is a list of pathogenic ClinVar variants found in the KPNA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-116689344-A-C		not specified	Uncertain significance (May 16, 2024)
6-116689355-A-C		not specified	Uncertain significance (Jun 01, 2023)
6-116689357-G-A		not specified	Uncertain significance (Jul 20, 2021)
6-116692311-G-A		not specified	Uncertain significance (Jan 24, 2024)
6-116692374-A-G		not specified	Uncertain significance (Mar 01, 2023)
6-116702076-G-T		not specified	Uncertain significance (Mar 29, 2024)
6-116716235-A-G		not specified	Uncertain significance (Feb 10, 2022)
6-116722211-A-C		not specified	Uncertain significance (Aug 14, 2023)
6-116722282-C-G		not specified	Uncertain significance (Jan 20, 2023)
6-116726620-A-G		not specified	Uncertain significance (Jun 28, 2022)
6-116732190-A-C		not specified	Uncertain significance (Mar 25, 2024)
6-116732280-T-C		not specified	Uncertain significance (Dec 07, 2021)
6-116732289-A-G		not specified	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KPNA5	protein_coding	protein_coding	ENST00000368564	14	60680

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000135	1.00	125681	0	60	125741	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	213	271	0.785	0.0000129	3542
Missense in Polyphen		97	118.44	0.81895		1515
Synonymous	1.38	72	88.5	0.813	0.00000415	989
Loss of Function	3.12	12	30.6	0.392	0.00000157	379

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000560	0.000547
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000172	0.000163
Finnish	0.000280	0.000277
European (Non-Finnish)	0.000229	0.000220
Middle Eastern	0.000172	0.000163
South Asian	0.000310	0.000294
Other	0.000346	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. Mediates nuclear import of STAT1 homodimers and STAT1/STAT2 heterodimers by recognizing non- classical NLSs of STAT1 and STAT2 through ARM repeats 8-9. Recognizes influenza A virus nucleoprotein through ARM repeat 7-9 In vitro, mediates the nuclear import of human cytomegalovirus UL84 by recognizing a non-classical NLS.
• Pathway: Disease;NS1 Mediated Effects on Host Pathways;Host Interactions with Influenza Factors;Influenza Infection;Infectious disease (Consensus)

Intolerance Scores

• loftool: 0.854
• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.09

Haploinsufficiency Scores

• pHI: 0.947
• hipred: N
• hipred_score: 0.473
• ghis: 0.665

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.616

Gene Damage Prediction

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

Gene ontology

• Biological process: NLS-bearing protein import into nucleus;modulation by virus of host process
• Cellular component: nuclear pore;nucleoplasm;cytosol
• Molecular function: protein binding;nuclear localization sequence binding;protein transporter activity;nuclear import signal receptor activity