KPNA7

karyopherin subunit alpha 7, the group of Importins|Armadillo repeat containing

Basic information

Region (hg38): 7:99173571-99250075

Links

ENSG00000185467 ∙ NCBI:402569 ∙ OMIM:614107 ∙ HGNC:21839 ∙ Uniprot:A9QM74 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• partial corpus callosum agenesis-cerebellar vermis hypoplasia with posterior fossa cysts syndrome (Supportive), mode of inheritance: AR
• oocyte/zygote/embryo maturation arrest 17 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Oocyte/zygote/embryo maturation arrest 17	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Obstetric	36647821

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KPNA7 gene.

• not provided (440 variants)
• Inborn genetic diseases (30 variants)
• Oocyte/zygote/embryo maturation arrest 17 (5 variants)
• Intellectual disability, mild (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KPNA7 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			5	107	6	118
missense			202	5	4	211
nonsense			14			14
start loss			1			1
frameshift			17			17
inframe indel			2			2
splice donor/acceptor (+/-2bp)			6			6
splice region			15	13	3	31
non coding			2	36	4	42
Total	0	0	249	148	14

Variants in KPNA7

This is a list of pathogenic ClinVar variants found in the KPNA7 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-99173710-A-AT			Uncertain significance (Oct 03, 2023)
7-99173713-T-G			Uncertain significance (Sep 01, 2022)
7-99173720-T-C			Likely benign (May 20, 2023)
7-99173726-T-C			Benign (Nov 27, 2023)
7-99173728-C-T			Uncertain significance (Jul 26, 2022)
7-99173729-A-G			Likely benign (Jul 19, 2023)
7-99173735-T-C			Uncertain significance (Feb 04, 2022)
7-99173750-T-C			Likely benign (Oct 17, 2022)
7-99173752-G-A			Uncertain significance (Apr 16, 2021)
7-99173752-G-T			Uncertain significance (Aug 28, 2021)
7-99173753-G-T		Oocyte/zygote/embryo maturation arrest 17	Uncertain significance (Aug 23, 2022)
7-99173759-G-A			Likely benign (Aug 03, 2017)
7-99173772-A-G			Uncertain significance (Aug 09, 2022)
7-99173777-T-C		KPNA7-related disorder	Likely benign (Dec 06, 2023)
7-99173786-A-G			Likely benign (May 24, 2022)
7-99173789-T-C			Likely benign (Nov 01, 2022)
7-99173794-C-T			Uncertain significance (Nov 24, 2021)
7-99173800-G-A			Likely benign (Sep 25, 2022)
7-99173805-G-C			Likely benign (Oct 03, 2023)
7-99173808-T-C			Likely benign (Oct 02, 2022)
7-99173813-A-T			Benign (Jan 27, 2024)
7-99173813-ACT-A			Likely benign (Sep 07, 2023)
7-99177900-C-T			Likely benign (Dec 24, 2021)
7-99177902-C-T			Benign (Jan 28, 2024)
7-99177903-G-A			Likely benign (Jan 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KPNA7	protein_coding	protein_coding	ENST00000327442	10	33933

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.38e-15	0.0206	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.907	238	281	0.848	0.0000160	3327
Missense in Polyphen		75	96.747	0.77522		1223
Synonymous	1.13	104	120	0.869	0.00000756	1042
Loss of Function	0.236	23	24.3	0.948	0.00000147	254

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions in nuclear protein import. {ECO:0000250}.
• Pathway: Disease;NS1 Mediated Effects on Host Pathways;Host Interactions with Influenza Factors;Influenza Infection;Infectious disease (Consensus)

Intolerance Scores

• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.15

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.296

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kpna7
• Phenotype: cellular 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: protein import into nucleus;modulation by virus of host process
• Cellular component: nucleoplasm;cytosol
• Molecular function: protein binding;protein transporter activity;nuclear import signal receptor activity