chr17-56834856-C-CACCT
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Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_003647.3(DGKE):c.62_65dup(p.Ile23ProfsTer20) 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 (★).
Frequency
Genomes: not found (cov: 33)
Consequence
DGKE
NM_003647.3 frameshift
NM_003647.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.29
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]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 25 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-56834856-C-CACCT is Pathogenic according to our data. Variant chr17-56834856-C-CACCT is described in ClinVar as [Pathogenic]. Clinvar id is 1179079.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGKE | NM_003647.3 | c.62_65dup | p.Ile23ProfsTer20 | frameshift_variant | 2/12 | ENST00000284061.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGKE | ENST00000284061.8 | c.62_65dup | p.Ile23ProfsTer20 | frameshift_variant | 2/12 | 1 | NM_003647.3 | P1 | |
DGKE | ENST00000572810.1 | c.62_65dup | p.Ile23ProfsTer20 | frameshift_variant | 2/2 | 1 | |||
DGKE | ENST00000576869.5 | n.210_213dup | non_coding_transcript_exon_variant | 2/6 | 1 | ||||
C17orf67 | ENST00000487705.1 | n.285+3632_285+3633insAGGT | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248412Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134650
GnomAD3 exomes
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248412
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134650
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GnomAD4 exome Cov.: 31
GnomAD4 exome
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GnomAD4 genome Cov.: 33
GnomAD4 genome
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33
Bravo
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Immunoglobulin-mediated membranoproliferative glomerulonephritis Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jun 30, 2021 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at