NM_001382.4:c.699dupC
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001382.4(DPAGT1):c.699dupC(p.Thr234HisfsTer116) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000806 in 1,613,380 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001382.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DPAGT1 | NM_001382.4 | c.699dupC | p.Thr234HisfsTer116 | frameshift_variant | Exon 5 of 9 | ENST00000354202.9 | NP_001373.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000660 AC: 1AN: 151578Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251390Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135858
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461802Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727206
GnomAD4 genome AF: 0.00000660 AC: 1AN: 151578Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73964
ClinVar
Submissions by phenotype
DPAGT1-congenital disorder of glycosylation;C3553645:Congenital myasthenic syndrome 13 Pathogenic:1
This sequence change creates a premature translational stop signal (p.Thr234Hisfs*116) in the DPAGT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DPAGT1 are known to be pathogenic (PMID: 22742743). This variant is present in population databases (rs397515321, gnomAD 0.002%). This premature translational stop signal has been observed in individual(s) with congenital myasthenic syndrome (PMID: 22742743). ClinVar contains an entry for this variant (Variation ID: 36920). For these reasons, this variant has been classified as Pathogenic. -
Congenital myasthenic syndrome 13 Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at