rs115129687
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Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PM2PP5_Very_StrongBP4
The NM_000055.4(BCHE):āc.1177G>Cā(p.Gly393Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000726 in 1,612,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (ā ā ).
Frequency
Genomes: š 0.000053 ( 0 hom., cov: 32)
Exomes š: 0.000075 ( 0 hom. )
Consequence
BCHE
NM_000055.4 missense
NM_000055.4 missense
Scores
4
9
6
Clinical Significance
Conservation
PhyloP100: 2.16
Genes affected
BCHE (HGNC:983): (butyrylcholinesterase) This gene encodes a cholinesterase enzyme and member of the type-B carboxylesterase/lipase family of proteins. The encoded enzyme exhibits broad substrate specificity and is involved in the detoxification of poisons including organophosphate nerve agents and pesticides, and the metabolism of drugs including cocaine, heroin and aspirin. Humans homozygous for certain mutations in this gene exhibit prolonged apnea after administration of the muscle relaxant succinylcholine. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 3-165829857-C-G is Pathogenic according to our data. Variant chr3-165829857-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 225301.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP4
Computational evidence support a benign effect (MetaRNN=0.3460163). . Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCHE | NM_000055.4 | c.1177G>C | p.Gly393Arg | missense_variant | 2/4 | ENST00000264381.8 | NP_000046.1 | |
BCHE | NR_137636.2 | n.1295G>C | non_coding_transcript_exon_variant | 2/5 | ||||
BCHE | NR_137635.2 | n.110+7457G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BCHE | ENST00000264381.8 | c.1177G>C | p.Gly393Arg | missense_variant | 2/4 | 1 | NM_000055.4 | ENSP00000264381 | P1 | |
LINC01322 | ENST00000651449.1 | n.1008-16035C>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152056Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000116 AC: 29AN: 249686Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 134928
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GnomAD4 exome AF: 0.0000746 AC: 109AN: 1460424Hom.: 0 Cov.: 31 AF XY: 0.0000771 AC XY: 56AN XY: 726430
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74412
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2Uncertain:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Deficiency of butyrylcholinesterase Pathogenic:2Uncertain:1
Uncertain significance, flagged submission | reference population | Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center | Mar 18, 2016 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Jun 16, 2017 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 24, 2022 | Variant summary: BCHE c.1177G>C (p.Gly393Arg) 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 damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00012 in 249686 control chromosomes, predominantly at a frequency of 0.0013 within the East Asian subpopulation in the gnomAD database. This frequency is not significantly higher than estimated for a pathogenic variant in BCHE causing Deficiency Of Butyrylcholine Esterase (0.00012 vs 0.016), allowing no conclusion about variant significance. c.1177G>C has been reported in the literature as BCHE*365R (p.Gly365Arg) or silent allele in homozygous and compound heterozygous genotypes among multiple Japanese individuals affected with Deficiency Of Butyrylcholine Esterase (example, Hada_1992, Sakamoto_2001, Maekawa_1997). These data indicate that the variant is very likely to be associated with disease. At least two publications report experimental evidence evaluating an impact on protein function (example, Hada_1992, Sakamoto_2001). The most pronounced variant effect results in absence of normal serum Butyrylcholine Esterase enzyme activity. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as pathogenic and one laboratory classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Pathogenic
D
MutationAssessor
Benign
L
MutationTaster
Benign
D;N
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Pathogenic
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Gain of solvent accessibility (P = 0.0584);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at