rs137854431
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1PM2PP3PP5_Very_Strong
The NM_004614.5(TK2):c.323C>T(p.Thr108Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000378 in 1,614,060 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
Consequence
NM_004614.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251080Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135726
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461870Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 727240
GnomAD4 genome AF: 0.000125 AC: 19AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74350
ClinVar
Submissions by phenotype
Mitochondrial DNA depletion syndrome, myopathic form Pathogenic:7Other:1
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The TK2 c.323C>T (p.Thr108Met) variant is a missense variant. Across a selection of the available literature, this variant, also described as p.Thr77Met, has been reported in 12 individuals, including seven homozygotes and five compound heterozygotes, from nine families from varying ethnic backgrounds with myopathic mitochondrial DNA depletion syndrome (Mancuso et al. 2002; Mancuso et al. 2003; Wang et al. 2005; Oskoui et al. 2006; Behin et al. 2012; Paradas et al. 2013; Chanprasert et al. 2013; Martin-Hernandez et al. 2017). The clinical symptoms reported among these cases were diverse but generally included a period of normal development after birth followed by onset of myopathy with progression to respiratory failure and early death; however, a few individuals surviving to adulthood and showing slower disease progression are reported. The p.Thr108Met variant was absent from 120 control alleles and is reported at a frequency of 0.000226 in the Latino population of the Genome Aggregation Consortium. Wang et al. (2005) demonstrated that the p.Thr108Met variant enzyme had approximately 3-4% of the activity and approximately 0.5% of the efficiency of the wild type enzyme. Modeling of the TK2 enzyme showed that the Thr108 residue lies in helix four and is involved in active site formation, and an alteration at this residue could disrupt hydrogen bonding (Wang et al. 2005). Based on the collective evidence and application of the ACMG criteria, the p.Thr108Met variant is classified as pathogenic for TK2-related mitochondrial DNA depletion myopathy. -
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
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Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000012710, PMID:12391347, PS1_S). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 15639197, PS3_S). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.853, 3CNET: 0.91, PP3_P). A missense variant is a common mechanism associated with Mitochondrial DNA depletion syndrome 2 (myopathic type) (PP2_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000046, PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
The NM_004614:c.323C>T missense variant corresponds to a nucleotide change in a hot spot region in exon 5 of the TK2 gene, which predicts a change at protein level from threonine to methionine at position 108. This variant is found at low frequency in population databases (Genome Aggregation Database) and has multiple reports (ClinVar variation ID: 12710) as pathogenic. Bioinformatic algorithms predict it as deleterious (REVEL=0.85) in coincidence with functional studies described in the literature (PMID: 15639197). For these reasons, we have classified this variant as Pathogenic, according to the following ACMG criteria: PS3, PM1, PM2, PM3, PP3. This variant was found in a homozygous state in the proband. (HPO: 0003202; 0001324; 0003200; 0003737; 0030059). -
The c.323C>T (p.Thr108Met) missense variant in the TK2 gene has been previously reported in six affected individuals from three families with autosomal recessive Mitochondrial DNA depletion syndrome, and this variant was shown to segregate with disease within these families (Tritschler et al.,1992; Mancuso et al., 2002; Mancuso et al., 2005; Paradas et al., 2013). Affected individuals have harbored this missense variant in trans with other missense variants (H121N, R192K), an in-frame deletion (K202del), and a nonsense variant (Q125*). This variant is located in exon 5, a known mutational hotspot (Mancuso et al., 2003). This c.323C>T variant also lies within the α4 helix of TK2, which is important for enzyme dimerization and nucleoside recognition (Mancuso et al., 2003). Functional studies have shown this variant reduces protein expression, enzymatic activity, and catalytic efficiency of TK2 (Mancuso et al., 2002; Wang et al., 2005; Villarroya et al., 2009). In addition, this variant also leads to reduced enzymatic activity of mitochondrial respiratory chain complexes (complexes I, III, and IV) and reduced cytochrome-c oxidase activity (Mancuso et al., 2002; Mancuso et al., 2003). This variant is absent from two control population databases (Exome Sequencing Project [ESP] and 1000 Genomes) and present at a low frequency in a third control population database (ExAC = 0.009%). Multiple lines of computational evidence suggest a deleterious effect (GERP = 4.97; PolyPhen = 1; SIFT = 0.026), and reputable diagnostic laboratories have reported this variant as pathogenic. Therefore, this collective evidence supports the classification of the c.323C>T (p.Thr108Met) as a recessive Pathogenic variant for Mitochondrial DNA depletion syndrome. -
The missense variant c.323C>T p.Thr108Met in the TK2 gene has been reported previously in a compound heterozygous and homozygous state in individuals affected with mitochondrial DNA depletion syndrome. Functional studies have shown this variant reduces protein expression, enzymatic activity, and catalytic efficiency of TK2 Wang et al., 2005; Mancuso et al., 2003. This variant is reported with the allele frequency 0.004% in the gnomAD and novel in not in any individuals 1000 genome database. It is submitted to ClinVar as Pathogenic. The amino acid Threonine at position 108 is changed to a Methionine changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted as damaging by SIFT. The amino acid change p.Thr108Met in TK2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -
not provided Pathogenic:3
This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 108 of the TK2 protein (p.Thr108Met). This variant is present in population databases (rs137854431, gnomAD 0.02%). This missense change has been observed in individuals with mtDNA depletion syndrome (PMID: 12391347, 12873860, 15639197, 16908738, 22345218, 23303857, 28812460). This variant is also known as T77M. ClinVar contains an entry for this variant (Variation ID: 12710). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on TK2 protein function. Experimental studies have shown that this missense change affects TK2 function (PMID: 12391347, 12873860, 15639197, 19265691, 24484525, 28812460). For these reasons, this variant has been classified as Pathogenic. -
Published functional studies found this variant is associated with a significant decrease in enzyme efficiency and catalytic activity compared to wild-type (PMID: 15639197); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.(T77M); This variant is associated with the following publications: (PMID: 28217183, 29602790, 16908738, 19265691, 18021809, 12873860, 1734306, 23303857, 26925861, 27839525, 28812460, 29625556, 25948719, 32140910, 31589614, 36344503, 33486010, 32161153, 12391347, 22345218, 15639197, 31060578) -
TK2: PP4:Strong, PM1, PM2, PM3, PS3:Supporting -
Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 3 Pathogenic:1
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Mitochondrial DNA depletion syndrome Pathogenic:1
Variant summary: TK2 c.323C>T (p.Thr108Met) results in a non-conservative amino acid change located in the deoxynucleoside kinase domain (IPR031314) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.4e-05 in 251080 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in TK2 causing TK2-Related Mitochondrial DNA Depletion Syndrome (4.4e-05 vs 0.0011), allowing no conclusion about variant significance. c.323C>T has been reported in the literature in multiple homozygous and compound heterozygous individuals affected with TK2-Related Mitochondrial DNA Depletion Syndrome (e.g. Wang_2005, Camara_2015). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function (Wang_2005). The most pronounced variant effect results in <10% of enzyme activity versus the WT protein. The following publications have been ascertained in the context of this evaluation (PMID: 25948719, 15639197). ClinVar contains an entry for this variant (Variation ID: 12710). Based on the evidence outlined above, the variant was classified as pathogenic. -
TK2-related disorder Pathogenic:1
The TK2 c.323C>T variant is predicted to result in the amino acid substitution p.Thr108Met. This particular substitution has been shown to lead to an approximately 100-fold decrease in the enzyme efficiency of thymidine kinase 2 (TK2) (defined as “T77M” in Wang et al. 2005. PubMed ID: 15639197). The p.Thr108Met substitution has also been repeatedly reported as “T77M” or “T108M” in patients with mitochondrial DNA depletion syndrome (Mancuso et al. 2003. PubMed ID: 12873860; Mancuso et al. 2002. PubMed ID: 12391347; Oskoui et al. 2006. PubMed ID: 16908738). This variant is reported in 0.023% of alleles in individuals of Latino descent in gnomAD. This variant is interpreted as pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at