rs16448
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_130439.3(MXI1):c.*113_*122del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000061 in 901,546 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000099 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000053 ( 0 hom. )
Consequence
MXI1
NM_130439.3 3_prime_UTR
NM_130439.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.42
Genes affected
MXI1 (HGNC:7534): (MAX interactor 1, dimerization protein) Expression of the c-myc gene, which produces an oncogenic transcription factor, is tightly regulated in normal cells but is frequently deregulated in human cancers. The protein encoded by this gene is a transcriptional repressor thought to negatively regulate MYC function, and is therefore a potential tumor suppressor. This protein inhibits the transcriptional activity of MYC by competing for MAX, another basic helix-loop-helix protein that binds to MYC and is required for its function. Defects in this gene are frequently found in patients with prostate tumors. Three alternatively spliced transcripts encoding different isoforms have been described. Additional alternatively spliced transcripts may exist but the products of these transcripts have not been verified experimentally. [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 |
---|---|---|---|---|---|---|---|
MXI1 | NM_130439.3 | c.*113_*122del | 3_prime_UTR_variant | 6/6 | ENST00000332674.9 | ||
MXI1 | NM_001008541.1 | c.*113_*122del | 3_prime_UTR_variant | 5/5 | |||
MXI1 | NM_005962.5 | c.*113_*122del | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MXI1 | ENST00000332674.9 | c.*113_*122del | 3_prime_UTR_variant | 6/6 | 1 | NM_130439.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000991 AC: 15AN: 151422Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000533 AC: 40AN: 750004Hom.: 0 AF XY: 0.0000508 AC XY: 19AN XY: 373870
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at