X-43683572-C-T
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_001270458.2(MAOA):c.-267C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000913 in 1,095,740 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_001270458.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAOA | NM_000240.4 | c.133C>T | p.Arg45Trp | missense_variant | 2/15 | ENST00000338702.4 | NP_000231.1 | |
MAOA | NM_001270458.2 | c.-267C>T | 5_prime_UTR_premature_start_codon_gain_variant | 3/16 | NP_001257387.1 | |||
MAOA | NM_001270458.2 | c.-267C>T | 5_prime_UTR_variant | 3/16 | NP_001257387.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAOA | ENST00000338702.4 | c.133C>T | p.Arg45Trp | missense_variant | 2/15 | 1 | NM_000240.4 | ENSP00000340684.3 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 9.13e-7 AC: 1AN: 1095740Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 361178
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Brunner syndrome Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 23, 2015 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Sydney Children's Hospital, SCHN | Nov 10, 2014 | Phenotype consistent with described MAOA deficiency. Functional studies (bioamine levels in blood and urine) consistent with MAOA deficiency. Predicted Pathogenic PROVEAN, SIFT, Mutation Taster. Not listed Exac Database. - |
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Apr 28, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25807999, 11700166) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at