IPO9

importin 9, the group of MicroRNA protein coding host genes|Importins

Basic information

Region (hg38): 1:201829149-201884291

Links

ENSG00000198700 ∙ NCBI:55705 ∙ ∙ HGNC:19425 ∙ Uniprot:Q96P70 ∙ 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 IPO9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IPO9 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					1	1
missense			45			45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	0	1

Variants in IPO9

This is a list of pathogenic ClinVar variants found in the IPO9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-201829243-G-A		not specified	Uncertain significance (Dec 27, 2022)
1-201829246-C-A		not specified	Uncertain significance (May 09, 2023)
1-201829304-T-G		not specified	Uncertain significance (Dec 07, 2024)
1-201847323-G-T		not specified	Uncertain significance (Dec 12, 2024)
1-201848472-C-T			Uncertain significance (May 08, 2023)
1-201848576-G-C		not specified	Uncertain significance (Jan 15, 2025)
1-201852113-G-T		not specified	Uncertain significance (Dec 27, 2022)
1-201852126-C-G		not specified	Uncertain significance (Sep 01, 2021)
1-201854622-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-201854674-G-A		not specified	Uncertain significance (Nov 13, 2024)
1-201854679-A-G		not specified	Uncertain significance (Jan 16, 2025)
1-201854706-G-A		not specified	Uncertain significance (Sep 14, 2023)
1-201855144-A-G		not specified	Uncertain significance (Jul 30, 2024)
1-201855156-A-T		not specified	Uncertain significance (Oct 02, 2023)
1-201855159-T-A		not specified	Uncertain significance (Oct 02, 2023)
1-201855834-A-G		not specified	Uncertain significance (Dec 07, 2021)
1-201855837-C-G		not specified	Uncertain significance (Jul 15, 2024)
1-201855839-C-A		not specified	Uncertain significance (Nov 13, 2023)
1-201855855-A-T		not specified	Uncertain significance (Jul 29, 2023)
1-201855867-C-T		not specified	Uncertain significance (Sep 09, 2024)
1-201855914-A-G		not specified	Uncertain significance (Feb 24, 2025)
1-201857115-A-T		not specified	Uncertain significance (Feb 25, 2025)
1-201857151-C-A		not specified	Uncertain significance (May 20, 2024)
1-201858498-G-A		not specified	Uncertain significance (Oct 09, 2024)
1-201858988-C-T		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IPO9	protein_coding	protein_coding	ENST00000361565	24	55154

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000955	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.28	356	578	0.616	0.0000308	6831
Missense in Polyphen		52	147.02	0.35369		1664
Synonymous	1.00	196	215	0.913	0.0000114	2038
Loss of Function	6.15	7	57.2	0.122	0.00000291	624

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000106	0.000106
Ashkenazi Jewish	0.000308	0.000298
East Asian	0.0000548	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000546	0.0000527
Middle Eastern	0.0000548	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions in nuclear protein import as nuclear transport receptor (PubMed:11823430). Serves as receptor for nuclear localization signals (NLS) in cargo substrates (PubMed:11823430). Is thought to mediate docking of the importin/substrate complex to the nuclear pore complex (NPC) through binding to nucleoporin and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism (PubMed:11823430). At the nucleoplasmic side of the NPC, Ran binds to the importin, the importin/substrate complex dissociates and importin is re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran (PubMed:11823430). 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 (PubMed:11823430). Mediates the nuclear import of RPS7, RPL18A, RPL6, histone H2A, histone H2B and histone (PubMed:11823430). Prevents the cytoplasmic aggregation of RPS7 and RPL18A by shielding exposed basic domains (PubMed:11823430). Mediates the nuclear import of actin (By similarity). {ECO:0000250|UniProtKB:Q91YE6, ECO:0000269|PubMed:11823430}.

Recessive Scores

• pRec: 0.335

Intolerance Scores

• loftool: 0.252
• rvis_EVS: -1.29
• rvis_percentile_EVS: 5.03

Haploinsufficiency Scores

• pHI: 0.967
• hipred: Y
• hipred_score: 0.673
• ghis: 0.675

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.806

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ipo9
• 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)

Gene ontology

• Biological process: protein import into nucleus
• Cellular component: nuclear envelope;cytoplasm;cytosol;membrane
• Molecular function: protein binding;Ran GTPase binding;protein transporter activity;histone binding