15-74891395-AC-ACC
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_002435.3(MPI):c.166dupC(p.Arg56ProfsTer8) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,816 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_002435.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251476Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135908
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461816Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727204
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
MPI-congenital disorder of glycosylation Pathogenic:5
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This sequence change creates a premature translational stop signal (p.Arg56Profs*8) in the MPI gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MPI are known to be pathogenic (PMID: 19862844). This variant is present in population databases (rs786204593, gnomAD 0.0009%). This premature translational stop signal has been observed in individuals with congenital disorders of glycosylation type Ib (PMID: 10980531, 18928705). ClinVar contains an entry for this variant (Variation ID: 188967). For these reasons, this variant has been classified as Pathogenic. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at