ClinVar Miner

Submissions for variant NM_000055.4(BCHE):c.635C>T (p.Ala212Val)

gnomAD frequency: 0.00254  dbSNP: rs114706984
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000412062 SCV000486272 likely pathogenic Deficiency of butyrylcholinesterase 2016-04-28 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000412062 SCV000916010 likely pathogenic Deficiency of butyrylcholinesterase 2017-09-07 criteria provided, single submitter clinical testing The BCHE c.635C>T (p.Ala212Val) missense variant, also referred to as p.Ala184Val, has been identified in at least four studies and seven individuals with low BChE activity, including in one in a homozygous state, in three in a compound heterozygous state, and in three in a heterozygous state (Greenberg et al. 1995; Levano et al. 2005; Mikami et al. 2008; Jasiecki et al. 2016). Two of the compound heterozygous individuals were found to have prolonged duration of succinylcholine action during routine anesthetic administration (Greenberg et al. 1995; Levano et al. 2005). The p.Ala212Val variant is reported at a frequency of 0.00419 in the European-American population of the Exome Sequencing Project. Based on the evidence, the p.Ala212Val is classified as likely pathogenic for butyrylcholinesterase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001844157 SCV002103784 uncertain significance not specified 2023-03-16 criteria provided, single submitter clinical testing Variant summary: BCHE c.635C>T (p.Ala212Val; aka. 551C>T, A184V or SC variant) results in a non-conservative amino acid change located in the Carboxylesterase, type B domain (IPR002018) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0021 in 250210 control chromosomes in the gnomAD database, including 1 homozygote. This frequency is lower than the estimated maximum expected for a pathogenic variant in BCHE causing Deficiency of Butyrylcholine Esterase (0.0021 vs 0.016), allowing no conclusion about variant significance. c.635C>T has been reported in the literature in at least two compound heterozygous individuals with a prolonged response to Succinylcholine (Greenberg_1995, Levano_2005), a homozygous blood donor whose enzyme activity was not specified (Mikami_2008) and as a compound heterozygous genotype in a healthy Polish individual with normal Butrylcholine esterase activity, but abnormal Dibucaine number (Jasiecki_2016). At least one publication reports reduced plasma cholinesterase activity in compound heterozygous individual (Greenberg_1995), however this result doesn't allow conclusions for the individual effect of the variant. Six other ClinVar submitters (evaluation after 2014) have cited the variant with conflicting assessments, classifying the variant as likely pathogenic (n = 4), pathogenic (n = 1), and uncertain significance (n = 1). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.
GeneDx RCV002244851 SCV002513661 uncertain significance not provided 2022-04-25 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 31589614, 18300943, 22750491, 20589221, 15731589, 7618741, 27109752)
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein RCV002252109 SCV002523882 pathogenic See cases 2020-12-02 criteria provided, single submitter clinical testing ACMG classification criteria: PS3, PS4, PM3, BP4
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV000412062 SCV002767576 likely pathogenic Deficiency of butyrylcholinesterase 2022-05-27 criteria provided, single submitter clinical testing Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as likely pathogenic. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0106 - This gene is known to be associated with autosomal recessive disease. (N) 0200 - Variant is predicted to result in a missense amino acid change from alanine to valine (exon 2). (N) 0251 - Variant is heterozygous. (N) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (593 heterozygotes, 1 homozygote). (P) 0503 - Missense variant consistently predicted to be tolerated or not conserved in mammals with a minor amino acid change. (B) 0600 - Variant is located in an annotated domain or motif (COesterase domain; NCBI, PDB). (N) 0705 - No comparable variants have previous evidence for pathogenicity. (N) 0801 - Strong previous evidence of pathogenicity in several unrelated individuals, both compound heterozygote (PMID:27109752, PMID:7618741) and homozygote (PMID:18300943). (P) 0905 - No segregation evidence has been identified for this variant. (N) 1002 - Moderate functional evidence supporting abnormal protein function, where mutant protein showed 70% of normal protein function (PMID:25448037). (P) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV002244851 SCV003800197 likely pathogenic not provided 2023-08-23 criteria provided, single submitter clinical testing The BCHE c.635C>T; p.Ala212Val variant, also published as Ala184Val, is reported in the literature as occurring in the homozygous state, compound heterozygous state, and heterozygous state, with at least two of the compound heterozygous individuals experiencing prolonged duration of succinylcholine action during routine anesthetic administration and reduced BChE activity (Greenberg 1995, Levano 2005, Mikami 2008). The variant is also listed in the ClinVar database (Variation ID: 370854), and is found in the general population with an overall allele frequency of 0.2% (595/281,610 alleles, including 1 homozygote) in the Genome Aggregation Database (v2.1.1). Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.365). Based on available information, the p.Ala212Val variant is classified as likely pathogenic. References: Greenberg CP et al. Prolonged response to succinylcholine: a new variant of plasma cholinesterase that is identified as normal by traditional phenotyping methods. Anesth Analg. 1995 Aug;81(2):419-21. PMID: 7618741. Levano S et al. Genotyping the butyrylcholinesterase in patients with prolonged neuromuscular block after succinylcholine. Anesthesiology. 2005 Mar;102(3):531-5. PMID: 15731589. Mikami LR et al. Five new naturally occurring mutations of the BCHE gene and frequencies of 12 butyrylcholinesterase alleles in a Brazilian population. Pharmacogenet Genomics. 2008 Mar;18(3):213-8. PMID: 18300943.

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