BCHE

butyrylcholinesterase

Basic information

Region (hg38): 3:165772904-165837462

Previous symbols: [ "CHE1", "CHE2" ]

Links

ENSG00000114200 ∙ NCBI:590 ∙ OMIM:177400 ∙ HGNC:983 ∙ Uniprot:P06276 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• butyrylcholinesterase deficiency (Definitive), mode of inheritance: Unknown
• butyrylcholinesterase deficiency (Definitive), mode of inheritance: AR
• butyrylcholinesterase deficiency (Supportive), mode of inheritance: AR
• butyrylcholinesterase deficiency (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Butyrlcholinesterase deficiency	AR	Pharmacogenomic	Individuals have prolonged apnea upon use of specific anesthetics (ie, suxamethonium, succinylcholine)	Biochemical	13711731; 14465122; 4984470; 3741370; 3225823; 2915989; 2911599; 2013061; 1662391; 1349196; 1415224; 8554068; 9543549; 9302273; 9110359; 9388484; 10190327; 10699053; 12881446; 16788378; 18075469; 18555211; 21029050

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BCHE gene.

• Deficiency of butyrylcholinesterase (5 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCHE 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			7	5	1	13
missense	1	7	56	3		67
nonsense	3	18	1			22
start loss						0
frameshift	2	18	3			23
inframe indel			2			2
splice donor/acceptor (+/-2bp)		3				3
splice region			2		1	3
non coding			12	2	2	16
Total	6	46	81	10	3

Highest pathogenic variant AF is 0.000328

Variants in BCHE

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

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

Position	Type	Phenotype	Significance	ClinVar
3-165772915-G-C		Deficiency of butyrylcholinesterase	Uncertain significance (Jan 12, 2018)
3-165772982-A-G		Deficiency of butyrylcholinesterase	Uncertain significance (Jan 12, 2018)
3-165773033-C-T		Deficiency of butyrylcholinesterase	Likely benign (Jan 12, 2018)
3-165773066-A-T		Deficiency of butyrylcholinesterase	Uncertain significance (Jan 13, 2018)
3-165773088-G-GA		Deficiency of butyrylcholinesterase	Benign (Jun 14, 2016)
3-165773097-A-G		Deficiency of butyrylcholinesterase	Uncertain significance (Jan 13, 2018)
3-165773101-T-G		Deficiency of butyrylcholinesterase	Uncertain significance (Jan 13, 2018)
3-165773145-T-C		Deficiency of butyrylcholinesterase	Uncertain significance (Jan 12, 2018)
3-165773193-C-T		Deficiency of butyrylcholinesterase	Benign (Jan 12, 2018)
3-165773202-C-T		Deficiency of butyrylcholinesterase	Likely benign (Jan 13, 2018)
3-165773208-G-A		Deficiency of butyrylcholinesterase	Uncertain significance (Jan 12, 2018)
3-165773243-A-T		Deficiency of butyrylcholinesterase	Uncertain significance (Jan 12, 2018)
3-165773330-T-C		Deficiency of butyrylcholinesterase	Uncertain significance (Jan 12, 2018)
3-165773343-C-A		Deficiency of butyrylcholinesterase	Uncertain significance (Jan 12, 2018)
3-165773369-G-A		Deficiency of butyrylcholinesterase	Uncertain significance (Jan 12, 2018)
3-165773388-AC-A		not specified	Uncertain significance (Dec 07, 2023)
3-165773389-C-A		Deficiency of butyrylcholinesterase	Uncertain significance (Jan 12, 2018)
3-165773391-C-G			Likely benign (Nov 01, 2022)
3-165773397-A-G			Likely benign (May 01, 2023)
3-165773410-C-A		Inborn genetic diseases	Uncertain significance (May 21, 2024)
3-165773414-T-C		Inborn genetic diseases	Uncertain significance (Jun 16, 2024)
3-165773421-G-A		Deficiency of butyrylcholinesterase	Uncertain significance (Jan 13, 2018)
3-165773455-T-C		Deficiency of butyrylcholinesterase • Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 21, 2022)
3-165773470-C-CCTGCTTTCCACTCCCATT		Deficiency of butyrylcholinesterase	Uncertain significance (May 10, 2017)
3-165773491-G-A		Inborn genetic diseases	Uncertain significance (Apr 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCHE	protein_coding	protein_coding	ENST00000264381	3	64569

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-13	0.0420	125436	1	301	125738	0.00120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.04	367	315	1.16	0.0000152	3975
Missense in Polyphen		139	113.99	1.2195		1409
Synonymous	0.128	107	109	0.984	0.00000536	1125
Loss of Function	0.341	21	22.8	0.923	0.00000120	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00170	0.00169
Ashkenazi Jewish	0.00506	0.00507
East Asian	0.00294	0.00294
Finnish	0.00	0.00
European (Non-Finnish)	0.000874	0.000853
Middle Eastern	0.00294	0.00294
South Asian	0.00150	0.00147
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Esterase with broad substrate specificity. Contributes to the inactivation of the neurotransmitter acetylcholine. Can degrade neurotoxic organophosphate esters. {ECO:0000269|PubMed:19452557, ECO:0000269|PubMed:19542320}.
• Disease: DISEASE: Butyrylcholinesterase deficiency (BCHED) [MIM:617936]: An autosomal recessive metabolic condition characterized by increased sensitivity to certain anesthetic drugs, including the muscle relaxants succinylcholine or mivacurium. BCHED results in slower hydrolysis of these drugs and, consequently, a prolonged neuromuscular block, leading to apnea. The duration of the prolonged apnea varies significantly depending on the extent of the enzyme deficiency. {ECO:0000269|PubMed:10404729, ECO:0000269|PubMed:11928765, ECO:0000269|PubMed:12881446, ECO:0000269|PubMed:1306123, ECO:0000269|PubMed:1349196, ECO:0000269|PubMed:1415224, ECO:0000269|PubMed:15563885, ECO:0000269|PubMed:15781196, ECO:0000269|PubMed:1611188, ECO:0000269|PubMed:16788378, ECO:0000269|PubMed:17700357, ECO:0000269|PubMed:18075469, ECO:0000269|PubMed:18300943, ECO:0000269|PubMed:25054547, ECO:0000269|PubMed:25264279, ECO:0000269|PubMed:2915989, ECO:0000269|PubMed:7634491, ECO:0000269|PubMed:8554068, ECO:0000269|PubMed:8680411, ECO:0000269|PubMed:9110359, ECO:0000269|PubMed:9191541, ECO:0000269|PubMed:9388484, ECO:0000269|PubMed:9543549, ECO:0000269|PubMed:9694584}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Irinotecan Pathway, Pharmacokinetics;Irinotecan Pathway, Pharmacodynamics;Heroin Metabolism Pathway;Irinotecan Action Pathway;Heroin Action Pathway;Irinotecan Metabolism Pathway;Irinotecan Pathway;Heroin metabolism;Cocaine metabolism;Peptide hormone metabolism;Metabolism of lipids;Synthesis, secretion, and deacylation of Ghrelin;Metabolism of proteins;Metabolism;Synthesis of PC;Neuronal System;Neurotransmitter clearance;Transmission across Chemical Synapses;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.505

Intolerance Scores

• loftool: 0.416
• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.21

Haploinsufficiency Scores

• pHI: 0.243
• hipred: N
• hipred_score: 0.250
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.536

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bche
• 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: learning;negative regulation of cell population proliferation;neuroblast differentiation;choline metabolic process;response to alkaloid;cocaine metabolic process;negative regulation of synaptic transmission;response to glucocorticoid;response to folic acid
• Cellular component: extracellular region;nuclear envelope lumen;endoplasmic reticulum lumen;membrane;blood microparticle
• Molecular function: amyloid-beta binding;catalytic activity;acetylcholinesterase activity;cholinesterase activity;hydrolase activity, acting on ester bonds;enzyme binding;choline binding;identical protein binding