KPNA4

karyopherin subunit alpha 4, the group of Importins|Armadillo repeat containing

Basic information

Region (hg38): 3:160495007-160565571

Links

ENSG00000186432 ∙ NCBI:3840 ∙ OMIM:602970 ∙ HGNC:6397 ∙ Uniprot:O00629 ∙ 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 KPNA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KPNA4 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	6	0	1

Variants in KPNA4

This is a list of pathogenic ClinVar variants found in the KPNA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-160502132-T-C		not specified	Uncertain significance (Jul 19, 2022)
3-160514088-G-A		not specified	Uncertain significance (Apr 27, 2024)
3-160514111-T-C		not specified	Uncertain significance (Jul 12, 2023)
3-160521831-C-T		not specified	Uncertain significance (Feb 12, 2024)
3-160521849-T-C		not specified	Uncertain significance (Apr 08, 2022)
3-160526030-T-C		not specified	Uncertain significance (Nov 09, 2021)
3-160527944-T-A			Benign (Nov 14, 2018)
3-160527991-A-G		not specified	Uncertain significance (Aug 13, 2021)
3-160535827-A-G		not specified	Uncertain significance (May 02, 2024)
3-160535900-T-A			Likely benign (Jul 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KPNA4	protein_coding	protein_coding	ENST00000334256	17	70594

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000106	125658	0	2	125660	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.23	107	251	0.426	0.0000111	3443
Missense in Polyphen		19	97.519	0.19483		1364
Synonymous	0.287	79	82.3	0.960	0.00000371	951
Loss of Function	4.94	1	30.4	0.0329	0.00000146	378

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000883	0.00000880
Middle Eastern	0.0000547	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

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. In vitro, mediates the nuclear import of human cytomegalovirus UL84 by recognizing a non- classical NLS. In vitro, mediates the nuclear import of human cytomegalovirus UL84 by recognizing a non-classical NLS.
• Pathway: Leptin signaling pathway;Disease;NS1 Mediated Effects on Host Pathways;Host Interactions with Influenza Factors;Influenza Infection;Infectious disease (Consensus)

Recessive Scores

• pRec: 0.447

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.865
• hipred: Y
• hipred_score: 0.777
• ghis: 0.581

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.855

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kpna4

Gene ontology

• Biological process: NLS-bearing protein import into nucleus;modulation by virus of host process;response to hydrogen peroxide
• Cellular component: nucleus;nucleoplasm;cytosol;nuclear membrane
• Molecular function: protein binding;protein transporter activity;nuclear import signal receptor activity