chrX-43781451-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000898.5(MAOB):āc.1022T>Cā(p.Met341Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000189 in 1,059,389 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 23)
Exomes š: 0.0000019 ( 0 hom. 1 hem. )
Consequence
MAOB
NM_000898.5 missense
NM_000898.5 missense
Scores
1
10
6
Clinical Significance
Conservation
PhyloP100: 6.38
Genes affected
MAOB (HGNC:6834): (monoamine oxidase B) The protein encoded by this gene belongs to the flavin monoamine oxidase family. It is a enzyme located in the mitochondrial outer membrane. It catalyzes the oxidative deamination of biogenic and xenobiotic amines and plays an important role in the metabolism of neuroactive and vasoactive amines in the central nervous sysytem and peripheral tissues. This protein preferentially degrades benzylamine and phenylethylamine. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAOB | NM_000898.5 | c.1022T>C | p.Met341Thr | missense_variant | 9/15 | ENST00000378069.5 | |
MAOB | XM_017029524.3 | c.974T>C | p.Met325Thr | missense_variant | 9/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAOB | ENST00000378069.5 | c.1022T>C | p.Met341Thr | missense_variant | 9/15 | 1 | NM_000898.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 genomes
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23
GnomAD3 exomes AF: 0.00000621 AC: 1AN: 160929Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 49095
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GnomAD4 exome AF: 0.00000189 AC: 2AN: 1059389Hom.: 0 Cov.: 22 AF XY: 0.00000301 AC XY: 1AN XY: 331849
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GnomAD4 genome Cov.: 23
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23
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.1022T>C (p.M341T) alteration is located in exon 9 (coding exon 9) of the MAOB gene. This alteration results from a T to C substitution at nucleotide position 1022, causing the methionine (M) at amino acid position 341 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
DEOGEN2
Pathogenic
D
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Uncertain
D
MetaSVM
Uncertain
D
MutationAssessor
Benign
L
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
B
Vest4
MutPred
Loss of sheet (P = 0.0126);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at