ESPL1

extra spindle pole bodies like 1, separase

Basic information

Region (hg38): 12:53268299-53293638

Links

ENSG00000135476 ∙ NCBI:9700 ∙ OMIM:604143 ∙ HGNC:16856 ∙ Uniprot:Q14674 ∙ 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 ESPL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ESPL1 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				11	1	12
missense			74	11	7	92
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	75	22	9

Variants in ESPL1

This is a list of pathogenic ClinVar variants found in the ESPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-53268793-T-C		ESPL1-related disorder	Likely benign (Aug 07, 2019)
12-53269059-C-T		ESPL1-related disorder	Likely benign (Mar 25, 2019)
12-53269117-C-G		not specified	Uncertain significance (Jan 24, 2024)
12-53269139-C-T		not specified	Uncertain significance (Dec 15, 2023)
12-53269170-G-C		not specified	Uncertain significance (May 03, 2023)
12-53269180-C-G		not specified	Uncertain significance (Oct 29, 2021)
12-53269289-C-T		ESPL1-related disorder	Benign (Jun 17, 2019)
12-53269327-G-A		not specified	Uncertain significance (Aug 08, 2023)
12-53269343-A-G		not specified	Uncertain significance (Jan 17, 2023)
12-53269376-G-A		not specified	Uncertain significance (May 10, 2022)
12-53269612-C-T		not specified	Uncertain significance (Jul 05, 2022)
12-53269652-G-A		not specified	Likely benign (Apr 05, 2023)
12-53269667-T-G		not specified	Uncertain significance (Sep 06, 2022)
12-53269675-C-T		not specified	Uncertain significance (Jan 22, 2024)
12-53269676-C-A		not specified	Uncertain significance (Feb 28, 2023)
12-53269738-C-T		not specified	Likely benign (Mar 16, 2023)
12-53269744-C-A		not specified	Uncertain significance (Mar 27, 2023)
12-53269927-C-G		not specified	Uncertain significance (Oct 04, 2022)
12-53269937-C-T		not specified	Uncertain significance (Oct 24, 2023)
12-53269955-A-C		not specified	Uncertain significance (Feb 01, 2023)
12-53269991-G-A		not specified	Uncertain significance (Feb 27, 2023)
12-53270012-T-C		not specified	Likely benign (Oct 26, 2022)
12-53270720-A-C		not specified	Uncertain significance (Nov 09, 2023)
12-53270728-C-T		ESPL1-related disorder	Likely benign (Sep 18, 2019)
12-53270756-G-T		not specified	Uncertain significance (Aug 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ESPL1	protein_coding	protein_coding	ENST00000257934	30	25345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.19e-10	125570	0	177	125747	0.000704

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.31	755	1.17e+3	0.645	0.0000675	13530
Missense in Polyphen		116	314.68	0.36863		3910
Synonymous	1.51	447	489	0.913	0.0000262	4579
Loss of Function	8.38	9	99.0	0.0909	0.00000550	1061

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00473	0.00474
Ashkenazi Jewish	0.000904	0.000893
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000772	0.000765
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Caspase-like protease, which plays a central role in the chromosome segregation by cleaving the SCC1/RAD21 subunit of the cohesin complex at the onset of anaphase. During most of the cell cycle, it is inactivated by different mechanisms. {ECO:0000269|PubMed:10411507, ECO:0000269|PubMed:11509732}.
• Pathway: Cell cycle - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);Cell Cycle;Regulation of sister chromatid separation at the metaphase-anaphase transition;DroToll-like;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.291
• rvis_EVS: 1.8
• rvis_percentile_EVS: 96.89

Haploinsufficiency Scores

• pHI: 0.201
• hipred: Y
• hipred_score: 0.691
• ghis: 0.443

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.494

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Espl1
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; embryo phenotype; liver/biliary system phenotype; hematopoietic system 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; neoplasm; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype

Zebrafish Information Network

• Gene name: espl1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curvature

Gene ontology

• Biological process: mitotic sister chromatid segregation;meiotic spindle organization;mitotic cytokinesis;proteolysis;apoptotic process;establishment of mitotic spindle localization;homologous chromosome segregation;positive regulation of mitotic metaphase/anaphase transition;negative regulation of sister chromatid cohesion;meiotic chromosome separation
• Cellular component: nucleus;cytoplasm;centrosome;cytosol;mitotic spindle
• Molecular function: catalytic activity;cysteine-type endopeptidase activity;protein binding;cysteine-type peptidase activity