chr2-73926913-G-A
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Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1PS1_ModeratePM2PP5_Moderate
The NM_080916.3(DGUOK):c.3G>A(p.Met1?) variant causes a start lost change. The variant allele was found at a frequency of 0.000013 in 1,613,274 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
DGUOK
NM_080916.3 start_lost
NM_080916.3 start_lost
Scores
6
5
1
Clinical Significance
Conservation
PhyloP100: 3.68
Genes affected
DGUOK (HGNC:2858): (deoxyguanosine kinase) In mammalian cells, the phosphorylation of purine deoxyribonucleosides is mediated predominantly by two deoxyribonucleoside kinases, cytosolic deoxycytidine kinase and mitochondrial deoxyguanosine kinase. The protein encoded by this gene is responsible for phosphorylation of purine deoxyribonucleosides in the mitochondrial matrix. In addition, this protein phosphorylates several purine deoxyribonucleoside analogs used in the treatment of lymphoproliferative disorders, and this phosphorylation is critical for the effectiveness of the analogs. Alternative splice variants encoding different protein isoforms have been described for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 14 ACMG points.
PVS1
Start lost variant, no new inframe start found.
PS1
Another start lost variant in NM_080916.3 (DGUOK) was described as [Pathogenic] in ClinVar as 2734235
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 2-73926913-G-A is Pathogenic according to our data. Variant chr2-73926913-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 1324223.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGUOK | NM_080916.3 | c.3G>A | p.Met1? | start_lost | 1/7 | ENST00000264093.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGUOK | ENST00000264093.9 | c.3G>A | p.Met1? | start_lost | 1/7 | 1 | NM_080916.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250446Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135600
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GnomAD4 exome AF: 0.0000110 AC: 16AN: 1461070Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 726886
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74360
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2023 | This sequence change affects the initiator methionine of the DGUOK mRNA. The next in-frame methionine is located at codon 18. This variant is present in population databases (rs534297082, gnomAD 0.006%). Disruption of the initiator codon has been observed in individuals with mitochondrial DNA depletion syndrome (PMID: 16908739, 21107780). ClinVar contains an entry for this variant (Variation ID: 1324223). For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Pathogenic
D
MutationTaster
Benign
N;N;N
Sift4G
Pathogenic
D;D;D
Polyphen
0.92
.;P;.
Vest4
MutPred
Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);
MVP
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at