ESD

esterase D

Basic information

Region (hg38): 13:46771256-46797420

Links

ENSG00000139684 ∙ NCBI:2098 ∙ OMIM:133280 ∙ HGNC:3465 ∙ Uniprot:P10768 ∙ 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 ESD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ESD 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	2
missense			12		1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	2

Variants in ESD

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

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

Position	Type	Phenotype	Significance	ClinVar
13-46771452-G-A			Benign (Aug 08, 2018)
13-46771471-A-G		not specified	Uncertain significance (Apr 05, 2023)
13-46771486-T-C		not specified	Uncertain significance (Jan 26, 2022)
13-46777466-C-T		not specified	Uncertain significance (Jan 18, 2022)
13-46777476-C-T		not specified	Uncertain significance (May 31, 2023)
13-46777499-G-A		not specified	Uncertain significance (May 17, 2023)
13-46777529-C-G		not specified	Uncertain significance (Dec 13, 2022)
13-46777532-T-C			Benign (Jan 30, 2018)
13-46777574-T-C		not specified	Uncertain significance (Jun 11, 2021)
13-46781570-T-A		not specified	Uncertain significance (Jun 19, 2024)
13-46782688-C-T		not specified	Uncertain significance (Mar 07, 2023)
13-46782692-C-T		not specified	Uncertain significance (Mar 04, 2024)
13-46782700-G-A			Benign/Likely benign (Sep 01, 2022)
13-46782744-C-G		not specified	Uncertain significance (Dec 01, 2022)
13-46784339-T-C		not specified	Uncertain significance (Nov 13, 2023)
13-46787080-G-C		not specified	Uncertain significance (Dec 22, 2023)
13-46791376-C-G		not specified	Uncertain significance (Jun 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ESD	protein_coding	protein_coding	ENST00000378720	8	25977

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.39e-7	0.666	125626	2	89	125717	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.398	129	142	0.906	0.00000626	1854
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000455	0.000452
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000425	0.000422
Middle Eastern	0.000109	0.000109
South Asian	0.00102	0.000882
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine hydrolase involved in the detoxification of formaldehyde. {ECO:0000269|PubMed:3770744, ECO:0000269|PubMed:4768551}.
• Pathway: Phase I biotransformations, non P450;Glutathione conjugation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;formaldehyde oxidation (Consensus)

Recessive Scores

• pRec: 0.541

Intolerance Scores

• loftool: 0.811
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.408
• hipred: N
• hipred_score: 0.401
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.859

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Esd

Gene ontology

• Biological process: biological_process;formaldehyde catabolic process;glutathione derivative biosynthetic process
• Cellular component: endoplasmic reticulum lumen;cytosol;cytoplasmic vesicle;extracellular exosome
• Molecular function: protein binding;hydrolase activity, acting on ester bonds;S-formylglutathione hydrolase activity;identical protein binding;methylumbelliferyl-acetate deacetylase activity;carboxylic ester hydrolase activity