17-56834892-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000284061.8(DGKE):c.97C>T(p.Pro33Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,620 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P33R) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000284061.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DGKE | NM_003647.3 | c.97C>T | p.Pro33Ser | missense_variant | 2/12 | ENST00000284061.8 | NP_003638.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DGKE | ENST00000284061.8 | c.97C>T | p.Pro33Ser | missense_variant | 2/12 | 1 | NM_003647.3 | ENSP00000284061 | P1 | |
DGKE | ENST00000572810.1 | c.97C>T | p.Pro33Ser | missense_variant | 2/2 | 1 | ENSP00000459295 | |||
DGKE | ENST00000576869.5 | n.245C>T | non_coding_transcript_exon_variant | 2/6 | 1 | |||||
C17orf67 | ENST00000487705.1 | n.285+3597G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250054Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135338
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461382Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727018
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74376
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 23, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with DGKE-related conditions. This variant is present in population databases (rs376469683, gnomAD 0.008%). This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 33 of the DGKE protein (p.Pro33Ser). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at