IPO13

importin 13, the group of Importins

Basic information

Region (hg38): 1:43946949-43968022

Links

ENSG00000117408 ∙ NCBI:9670 ∙ OMIM:610411 ∙ HGNC:16853 ∙ Uniprot:O94829 ∙ 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 IPO13 gene.

• Inborn genetic diseases (22 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IPO13 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	2	3
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	2

Variants in IPO13

This is a list of pathogenic ClinVar variants found in the IPO13 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-43947638-C-G		not specified	Uncertain significance (May 26, 2022)
1-43949418-C-T		not specified	Uncertain significance (Jan 18, 2023)
1-43949502-A-G		not specified	Uncertain significance (May 26, 2022)
1-43949664-G-A		not specified	Uncertain significance (Jun 24, 2022)
1-43949668-T-G		not specified	Uncertain significance (Jun 09, 2022)
1-43949799-C-G		not specified	Uncertain significance (Oct 20, 2023)
1-43949874-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-43949916-C-T		not specified	Uncertain significance (Dec 14, 2022)
1-43949940-C-T		not specified	Uncertain significance (May 04, 2022)
1-43949959-A-C			Likely benign (Nov 01, 2023)
1-43950059-A-G		not specified	Uncertain significance (Feb 21, 2024)
1-43950063-A-T		IPO13-related disorder	Likely benign (Apr 27, 2023)
1-43956324-G-A		IPO13-related disorder • not specified	Uncertain significance (Dec 21, 2023)
1-43956379-G-A		not specified	Uncertain significance (Mar 29, 2023)
1-43956409-C-T		not specified	Uncertain significance (Jan 07, 2022)
1-43956414-C-G		not specified	Uncertain significance (Apr 25, 2023)
1-43957301-C-G		not specified	Uncertain significance (Jun 11, 2021)
1-43958090-A-G		not specified	Uncertain significance (Mar 01, 2024)
1-43958124-C-T		not specified	Uncertain significance (Oct 30, 2023)
1-43958811-A-G			Benign (Dec 31, 2019)
1-43958834-A-G		not specified	Uncertain significance (Jul 07, 2022)
1-43960252-G-T		not specified	Uncertain significance (Nov 21, 2022)
1-43960877-C-T		not specified	Uncertain significance (Jan 04, 2024)
1-43960978-A-G		not specified	Uncertain significance (Mar 21, 2022)
1-43961187-G-A		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IPO13	protein_coding	protein_coding	ENST00000372343	20	21084

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000168	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.49	312	540	0.578	0.0000308	6270
Missense in Polyphen		27	77.08	0.35029		948
Synonymous	2.15	178	218	0.815	0.0000119	1951
Loss of Function	6.11	5	53.0	0.0944	0.00000290	536

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000969	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions in nuclear protein import as nuclear transport receptor. Serves as receptor for nuclear localization signals (NLS) in cargo substrates. 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. 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. 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 (By similarity). Mediates the nuclear import of UBC9, the RBM8A/MAGOH complex, PAX6 and probably other members of the paired homeobox family. Also mediates nuclear export of eIF-1A, and the cytoplasmic release of eIF-1A is triggered by the loading of import substrates onto IPO13. {ECO:0000250, ECO:0000269|PubMed:11447110, ECO:0000269|PubMed:15143176}.

Recessive Scores

• pRec: 0.270

Intolerance Scores

• loftool: 0.274
• rvis_EVS: -1.22
• rvis_percentile_EVS: 5.6

Haploinsufficiency Scores

• pHI: 0.692
• hipred: Y
• hipred_score: 0.728
• ghis: 0.610

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ipo13
• 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)

Zebrafish Information Network

• Gene name: ipo13
• Affected structure: retinal outer plexiform layer
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: protein import into nucleus
• Cellular component: nucleus;cytoplasm
• Molecular function: protein binding;Ran GTPase binding;protein transporter activity