ESCO1

establishment of sister chromatid cohesion N-acetyltransferase 1, the group of Lysine acetyltransferases

Basic information

Region (hg38): 18:21529281-21600884

Links

ENSG00000141446 ∙ NCBI:114799 ∙ OMIM:609674 ∙ HGNC:24645 ∙ Uniprot:Q5FWF5 ∙ 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 ESCO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ESCO1 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			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	33	2	0

Variants in ESCO1

This is a list of pathogenic ClinVar variants found in the ESCO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-21532570-T-C		not specified	Uncertain significance (Mar 18, 2024)
18-21532625-G-C		not specified	Uncertain significance (Aug 21, 2023)
18-21536044-A-T		not specified	Uncertain significance (Mar 08, 2024)
18-21540013-G-GAT			Benign (Apr 19, 2018)
18-21564221-A-C		not specified	Uncertain significance (Sep 28, 2022)
18-21564276-T-C		not specified	Uncertain significance (Oct 12, 2021)
18-21564292-G-C		not specified	Uncertain significance (Oct 29, 2021)
18-21564297-G-A		not specified	Uncertain significance (Jun 07, 2024)
18-21566167-G-T		not specified	Uncertain significance (Dec 06, 2022)
18-21568013-C-A		not specified	Uncertain significance (Oct 14, 2023)
18-21568081-C-G		not specified	Uncertain significance (May 05, 2022)
18-21573319-T-G		not specified	Uncertain significance (Jun 11, 2021)
18-21573324-G-A		not specified	Uncertain significance (Jul 14, 2021)
18-21573343-T-C		not specified	Uncertain significance (Dec 27, 2022)
18-21573457-C-T		not specified	Uncertain significance (May 26, 2024)
18-21573520-T-C		not specified	Uncertain significance (Jan 30, 2024)
18-21573564-A-G		not specified	Uncertain significance (Jun 07, 2024)
18-21573686-C-G		not specified	Uncertain significance (Mar 03, 2023)
18-21573754-G-A		not specified	Uncertain significance (Nov 13, 2023)
18-21573831-T-C		not specified	Uncertain significance (Oct 27, 2023)
18-21573861-A-G		not specified	Uncertain significance (Mar 17, 2023)
18-21573871-A-G		not specified	Uncertain significance (Nov 18, 2022)
18-21573960-G-A		not specified	Uncertain significance (Oct 05, 2022)
18-21573985-G-C		not specified	Uncertain significance (Feb 27, 2024)
18-21574015-G-C		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ESCO1	protein_coding	protein_coding	ENST00000269214	9	71604

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000452	125645	0	2	125647	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.431	398	423	0.941	0.0000207	5571
Missense in Polyphen		68	135.1	0.50334		1719
Synonymous	0.188	144	147	0.980	0.00000748	1516
Loss of Function	5.34	2	37.1	0.0539	0.00000193	490

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)	0.00000892	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acetyltransferase required for the establishment of sister chromatid cohesion (PubMed:15958495, PubMed:18614053). Couples the processes of cohesion and DNA replication to ensure that only sister chromatids become paired together. In contrast to the structural cohesins, the deposition and establishment factors are required only during S phase. Acts by mediating the acetylation of cohesin component SMC3 (PubMed:18614053). {ECO:0000269|PubMed:14576321, ECO:0000269|PubMed:15958495, ECO:0000269|PubMed:18614053, ECO:0000269|PubMed:19907496, ECO:0000269|PubMed:27112597, ECO:0000269|PubMed:27803161}.
• Pathway: Establishment of Sister Chromatid Cohesion;S Phase;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.338
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.23

Haploinsufficiency Scores

• pHI: 0.877
• hipred: Y
• hipred_score: 0.771
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.888

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Esco1
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of DNA replication;sister chromatid cohesion;peptidyl-lysine acetylation;post-translational protein acetylation
• Cellular component: chromatin;nucleoplasm;chromosome
• Molecular function: N-acetyltransferase activity;zinc ion binding;acetyltransferase activity;peptide-lysine-N-acetyltransferase activity