chrX-43693357-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_000240.4(MAOA):āc.235C>Gā(p.Arg79Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000183 in 1,095,376 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 Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R79H) has been classified as Uncertain significance.
Frequency
Consequence
NM_000240.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAOA | NM_000240.4 | c.235C>G | p.Arg79Gly | missense_variant | 3/15 | ENST00000338702.4 | |
MAOA | NM_001270458.2 | c.-165C>G | 5_prime_UTR_variant | 4/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAOA | ENST00000338702.4 | c.235C>G | p.Arg79Gly | missense_variant | 3/15 | 1 | NM_000240.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 0.00000183 AC: 2AN: 1095376Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 360850
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.235C>G (p.R79G) alteration is located in exon 3 (coding exon 3) of the MAOA gene. This alteration results from a C to G substitution at nucleotide position 235, causing the arginine (R) at amino acid position 79 to be replaced by a glycine (G). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at