CSE1L

chromosome segregation 1 like, the group of Exportins

Basic information

Region (hg38): 20:49046245-49096960

Links

ENSG00000124207 ∙ NCBI:1434 ∙ OMIM:601342 ∙ HGNC:2431 ∙ Uniprot:P55060 ∙ 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 CSE1L gene.

• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSE1L 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in CSE1L

This is a list of pathogenic ClinVar variants found in the CSE1L region.

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

Position	Type	Phenotype	Significance	ClinVar
20-49063222-G-A		not specified	Uncertain significance (Jan 19, 2024)
20-49063343-T-G		not specified	Uncertain significance (Dec 15, 2021)
20-49066246-A-G		not specified	Uncertain significance (Sep 01, 2021)
20-49066444-G-A		not specified	Uncertain significance (Dec 13, 2021)
20-49067246-A-T		not specified	Uncertain significance (Jan 16, 2024)
20-49067248-G-T		not specified	Uncertain significance (Nov 17, 2022)
20-49068716-C-T		not specified	Uncertain significance (Aug 04, 2023)
20-49070216-A-T		not specified	Uncertain significance (Jun 24, 2022)
20-49070232-A-G		not specified	Uncertain significance (Mar 20, 2023)
20-49070246-G-A		not specified	Uncertain significance (Feb 16, 2023)
20-49072400-A-G		not specified	Uncertain significance (Mar 31, 2023)
20-49072437-A-G		not specified	Uncertain significance (Dec 14, 2021)
20-49072685-A-G		not specified	Uncertain significance (Nov 29, 2023)
20-49075369-A-G		not specified	Uncertain significance (Dec 28, 2023)
20-49075434-G-A		not specified	Uncertain significance (Jan 16, 2024)
20-49084032-A-G		not specified	Uncertain significance (Mar 31, 2023)
20-49084051-C-T		not specified	Uncertain significance (Feb 27, 2024)
20-49084125-C-T		not specified	Uncertain significance (Jun 29, 2023)
20-49084128-C-T		not specified	Uncertain significance (Mar 01, 2024)
20-49085291-C-T		not specified	Uncertain significance (Jul 08, 2022)
20-49085350-C-A		not specified	Uncertain significance (May 06, 2022)
20-49088098-G-A		not specified	Uncertain significance (Jun 21, 2023)
20-49089552-G-A		not specified	Uncertain significance (May 23, 2023)
20-49089643-T-G		not specified	Uncertain significance (Dec 03, 2021)
20-49089720-A-C		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSE1L	protein_coding	protein_coding	ENST00000262982	24	50641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	8.75e-8	125737	0	3	125740	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.85	325	505	0.643	0.0000251	6429
Missense in Polyphen		72	162.66	0.44264		2299
Synonymous	-0.660	195	184	1.06	0.00000982	1800
Loss of Function	6.55	2	53.8	0.0372	0.00000279	662

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Export receptor for importin-alpha. Mediates importin- alpha re-export from the nucleus to the cytoplasm after import substrates (cargos) have been released into the nucleoplasm. In the nucleus binds cooperatively to importin-alpha and to the GTPase Ran in its active GTP-bound form. Docking of this trimeric complex to the nuclear pore complex (NPC) is mediated through binding to nucleoporins. Upon transit of a nuclear export complex into the cytoplasm, disassembling of the complex and hydrolysis of Ran-GTP to Ran-GDP (induced by RANBP1 and RANGAP1, respectively) cause release of the importin-alpha from the export receptor. CSE1L/XPO2 then return to the nuclear compartment and mediate another round of transport. The directionality of nuclear export is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus. {ECO:0000269|PubMed:9323134}.
• Pathway: Direct p53 effectors;p53 pathway (Consensus)

Recessive Scores

• pRec: 0.388

Intolerance Scores

• loftool: 0.279
• rvis_EVS: -1.02
• rvis_percentile_EVS: 8

Haploinsufficiency Scores

• pHI: 0.952
• hipred: Y
• hipred_score: 0.783
• ghis: 0.703

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.899

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cse1l
• 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); embryo phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: cse1l
• Affected structure: enterocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased height

Gene ontology

• Biological process: protein import into nucleus;protein export from nucleus;apoptotic process;cell population proliferation
• Cellular component: nucleus;nuclear envelope;nucleoplasm;cytoplasm;cytosol;membrane;extracellular exosome
• Molecular function: nuclear export signal receptor activity;protein binding;Ran GTPase binding;protein transporter activity