chr4-961105-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001347.4(DGKQ):c.2671G>A(p.Gly891Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,459,648 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001347.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DGKQ | NM_001347.4 | c.2671G>A | p.Gly891Arg | missense_variant | Exon 22 of 23 | ENST00000273814.8 | NP_001338.2 | |
DGKQ | XM_047449687.1 | c.2758G>A | p.Gly920Arg | missense_variant | Exon 22 of 23 | XP_047305643.1 | ||
DGKQ | XM_011513411.2 | c.2671G>A | p.Gly891Arg | missense_variant | Exon 22 of 23 | XP_011511713.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DGKQ | ENST00000273814.8 | c.2671G>A | p.Gly891Arg | missense_variant | Exon 22 of 23 | 1 | NM_001347.4 | ENSP00000273814.3 | ||
DGKQ | ENST00000509465.5 | c.2470G>A | p.Gly824Arg | missense_variant | Exon 21 of 22 | 5 | ENSP00000425862.1 | |||
DGKQ | ENST00000515182.1 | c.316G>A | p.Gly106Arg | missense_variant | Exon 4 of 5 | 5 | ENSP00000421756.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000812 AC: 2AN: 246400Hom.: 0 AF XY: 0.00000747 AC XY: 1AN XY: 133924
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459648Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 726134
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2671G>A (p.G891R) alteration is located in exon 22 (coding exon 22) of the DGKQ gene. This alteration results from a G to A substitution at nucleotide position 2671, causing the glycine (G) at amino acid position 891 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at