22-50488027-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_017584.6(MIOX):c.319C>T(p.Arg107Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000285 in 1,613,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017584.6 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIOX | NM_017584.6 | c.319C>T | p.Arg107Trp | missense_variant | Exon 4 of 10 | ENST00000216075.11 | NP_060054.4 | |
MIOX | XM_005261925.5 | c.181C>T | p.Arg61Trp | missense_variant | Exon 3 of 9 | XP_005261982.1 | ||
MIOX | XM_011530705.3 | c.319C>T | p.Arg107Trp | missense_variant | Exon 4 of 6 | XP_011529007.1 | ||
MIOX | XM_047441443.1 | c.319C>T | p.Arg107Trp | missense_variant | Exon 4 of 9 | XP_047297399.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIOX | ENST00000216075.11 | c.319C>T | p.Arg107Trp | missense_variant | Exon 4 of 10 | 1 | NM_017584.6 | ENSP00000216075.6 | ||
MIOX | ENST00000395732.7 | c.319C>T | p.Arg107Trp | missense_variant | Exon 4 of 10 | 1 | ENSP00000379081.3 | |||
MIOX | ENST00000395733.7 | c.319C>T | p.Arg107Trp | missense_variant | Exon 4 of 8 | 1 | ENSP00000379082.3 | |||
MIOX | ENST00000451761.1 | c.304C>T | p.Arg102Trp | missense_variant | Exon 3 of 9 | 3 | ENSP00000409894.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000599 AC: 15AN: 250372Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135574
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461424Hom.: 0 Cov.: 33 AF XY: 0.0000275 AC XY: 20AN XY: 727014
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.319C>T (p.R107W) alteration is located in exon 4 (coding exon 4) of the MIOX gene. This alteration results from a C to T substitution at nucleotide position 319, causing the arginine (R) at amino acid position 107 to be replaced by a tryptophan (W). 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