ESCO1

protein-coding

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

Gene summary

Enables identical protein binding activity; protein-lysine-acetyltransferase activity; and zinc ion binding activity. Involved in peptidyl-lysine acetylation; post-translational protein acetylation; and regulation of DNA replication. Located in chromatin. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_052911.3

Inheritance

—

ClinVar variants

U:112B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr18:21,529,281-21,600,884

External References & Databases

Ensembl (ENSG00000141446)

Transcript & Mutation Effects

hg38 • Region Span ~71.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ESCO1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 107

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052911.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			107 clinvar	1 clinvar		108
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	112	2	0	114

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052911.3	RefSeq	NP_443143.2	9	MANE Select
ENST00000269214.10	Ensembl	ENSP00000269214.4	9	MANE Select
ENST00000383276.1	Ensembl	ENSP00000372763.1	7	Standard
ENST00000383276.2	Ensembl	ENSP00000372763.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Establishment of Sister Chromatid Cohesion
S Phase
Cell Cycle
Cell Cycle, Mitotic

Biological Process

regulation of DNA replication
sister chromatid cohesion
peptidyl-lysine acetylation
post-translational protein acetylation

Molecular Function

N-acetyltransferase activity
zinc ion binding
acetyltransferase activity
peptide-lysine-N-acetyltransferase activity

Cellular Component

chromatin
nucleoplasm
chromosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000269214
Coding exons: 9
Length: 71604
Individuals with no LoFs: 125645
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125647
p: 0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.431	398	423	0.941	0.0000207	5571
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000088	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.338
RVIS EVS: -0.24
RVIS percentile EVS: 36.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.888

Gene Damage Prediction

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