ESD

protein-coding

esterase D

Gene summary

This gene encodes a serine hydrolase that belongs to the esterase D family. The encoded enzyme is active toward numerous substrates including O-acetylated sialic acids, and it may be involved in the recycling of sialic acids. This gene is used as a genetic marker for retinoblastoma and Wilson's disease. [provided by RefSeq, Feb 2009]

MANE transcript

NM_001984.2

Inheritance

—

ClinVar variants

U:35B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr13:46,771,256-46,797,420

External References & Databases

Ensembl (ENSG00000139684)

Transcript & Mutation Effects

hg38 • Region Span ~26.2 kb

Loading mutation effect viewer...

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 ESD variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 31

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001984.2. 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			2 clinvar	1 clinvar	1 clinvar	4
missense			32 clinvar		1 clinvar	33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	35	1	2	38

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001984.2	RefSeq	NP_001975.1	8	MANE Select
ENST00000378720.8	Ensembl	ENSP00000367992.3	8	MANE Select
ENST00000378697.5	Ensembl	ENSP00000367969.1	7	Standard
ENST00000378697.6	Ensembl	ENSP00000367969.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Phase I biotransformations, non P450
Glutathione conjugation
Phase II - Conjugation of compounds
Biological oxidations
Metabolism

Biological Process

biological_process
formaldehyde catabolic process
glutathione derivative biosynthetic process

Molecular Function

protein binding
hydrolase activity, acting on ester bonds
S-formylglutathione hydrolase activity
identical protein binding
methylumbelliferyl-acetate deacetylase activity

Cellular Component

endoplasmic reticulum lumen
cytosol
cytoplasmic vesicle
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378720
Coding exons: 8
Length: 25977
Individuals with no LoFs: 125626
Homozygous LoFs: 2
Heterozygous LoFs: 89
Defined: 125717
p: 0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.398	129	142	0.906	0.00000626	1854
Missense (PolyPhen)		41	54.577	0.75124		691
Synonymous	0.747	41	47.6	0.862	0.00000213	498
Loss of Function	1.12	12	17.0	0.708	8.77e-7	206

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00042	0.00042	rare
South Asian	0.0010	0.00088	notable
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Serine hydrolase involved in the detoxification of formaldehyde. {ECO:0000269|PubMed:3770744, ECO:0000269|PubMed:4768551}.;

Recessive Scores

pRec: 0.541

Intolerance Scores

LoFtool: 0.811
RVIS EVS: 0.1
RVIS percentile EVS: 61.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.859

Gene Damage Prediction

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