NM_003647.3:c.486dupA
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_003647.3(DGKE):c.486dupA(p.Val163SerfsTer3) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
DGKE
NM_003647.3 frameshift
NM_003647.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0550
Publications
2 publications found
Genes affected
DGKE (HGNC:2852): (diacylglycerol kinase epsilon) Diacylglycerol kinases are thought to be involved mainly in the regeneration of phosphatidylinositol (PI) from diacylglycerol in the PI-cycle during cell signal transduction. When expressed in mammalian cells, DGK-epsilon shows specificity for arachidonyl-containing diacylglycerol. DGK-epsilon is expressed predominantly in testis. [provided by RefSeq, Jul 2008]
TRIM25 (HGNC:12932): (tripartite motif containing 25) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein is an RNA binding protein, functions as a ubiquitin E3 ligase and is involved in multiple cellular processes, including regulation of antiviral innate immunity. [provided by RefSeq, Sep 2021]
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 12 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-56844039-C-CA is Pathogenic according to our data. Variant chr17-56844039-C-CA is described in CliVar as Pathogenic. Clinvar id is 135639.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-56844039-C-CA is described in CliVar as Pathogenic. Clinvar id is 135639.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-56844039-C-CA is described in CliVar as Pathogenic. Clinvar id is 135639.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-56844039-C-CA is described in CliVar as Pathogenic. Clinvar id is 135639.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-56844039-C-CA is described in CliVar as Pathogenic. Clinvar id is 135639.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-56844039-C-CA is described in CliVar as Pathogenic. Clinvar id is 135639.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely pathogenic; risk factor
Submissions summary: Pathogenic:1Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Atypical hemolytic-uremic syndrome Pathogenic:1
-
Richard Lifton Laboratory, Yale University School of Medicine
Significance:Likely pathogenic
Review Status:no assertion criteria provided
Collection Method:literature only
- -
Hemolytic uremic syndrome, atypical, susceptibility to, 7 Other:1
May 01, 2013
OMIM
Significance:risk factor
Review Status:no assertion criteria provided
Collection Method:literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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