NM_000754.4:c.480C>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_000754.4(COMT):​c.480C>G​(p.Asp160Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as drug response (no stars).

Frequency

Genomes: not found (cov: 33)

Consequence

COMT
NM_000754.4 missense

Scores

5
14

Clinical Significance

drug response no assertion criteria provided O:1

Conservation

PhyloP100: 0.278
Variant links:
Genes affected
COMT (HGNC:2228): (catechol-O-methyltransferase) Catechol-O-methyltransferase catalyzes the transfer of a methyl group from S-adenosylmethionine to catecholamines, including the neurotransmitters dopamine, epinephrine, and norepinephrine. This O-methylation results in one of the major degradative pathways of the catecholamine transmitters. In addition to its role in the metabolism of endogenous substances, COMT is important in the metabolism of catechol drugs used in the treatment of hypertension, asthma, and Parkinson disease. COMT is found in two forms in tissues, a soluble form (S-COMT) and a membrane-bound form (MB-COMT). The differences between S-COMT and MB-COMT reside within the N-termini. Several transcript variants are formed through the use of alternative translation initiation sites and promoters. [provided by RefSeq, Sep 2008]
MIR4761 (HGNC:41591): (microRNA 4761) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.33496627).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COMTNM_000754.4 linkc.480C>G p.Asp160Glu missense_variant Exon 4 of 6 ENST00000361682.11 NP_000745.1 P21964-1A0A140VJG8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COMTENST00000361682.11 linkc.480C>G p.Asp160Glu missense_variant Exon 4 of 6 1 NM_000754.4 ENSP00000354511.6 P21964-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
35
GnomAD4 genome
Cov.:
33

ClinVar

Significance: drug response
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Tramadol response Other:1
Apr 28, 2018
Bruce Budowle Laboratory, University of North Texas Health Science Center
Significance: drug response
Review Status: no assertion criteria provided
Collection Method: research

- T:M1 = postmortem ratio or tramadol to O-desmethyltramadol; t-MP = model-based clustered metabolizer phenotype inferred from T:M1

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Uncertain
0.022
T
BayesDel_noAF
Benign
-0.21
CADD
Benign
17
DANN
Uncertain
0.99
DEOGEN2
Benign
0.20
T;.;T;T;T;T;.
Eigen
Benign
-0.057
Eigen_PC
Benign
-0.063
FATHMM_MKL
Uncertain
0.78
D
LIST_S2
Benign
0.72
.;T;.;.;T;T;T
M_CAP
Benign
0.024
T
MetaRNN
Benign
0.33
T;T;T;T;T;T;T
MetaSVM
Benign
-0.85
T
MutationAssessor
Benign
1.8
L;.;L;L;.;L;.
PrimateAI
Uncertain
0.48
T
PROVEAN
Benign
-2.1
N;N;N;.;N;N;N
REVEL
Uncertain
0.32
Sift
Benign
0.097
T;T;T;.;D;T;T
Sift4G
Benign
0.12
T;T;T;T;T;T;T
Polyphen
0.0030
B;B;B;B;.;B;.
Vest4
0.24
MutPred
0.56
Loss of catalytic residue at K159 (P = 0.1122);Loss of catalytic residue at K159 (P = 0.1122);Loss of catalytic residue at K159 (P = 0.1122);Loss of catalytic residue at K159 (P = 0.1122);Loss of catalytic residue at K159 (P = 0.1122);Loss of catalytic residue at K159 (P = 0.1122);.;
MVP
0.76
MPC
0.25
ClinPred
0.38
T
GERP RS
3.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.67
gMVP
0.46

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1601529589; hg19: chr22-19951279; API