rs137854431

chr16-66531432-G-A

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1 PM2 PP3 PP5_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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T108A) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00012 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000029 (0 hom.)
• Consequence: TK2 NM_004614.5 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:11 O:1
• Conservation: PhyloP100: 5.48

Genes affected

TK2 (HGNC:11831): (thymidine kinase 2) This gene encodes a deoxyribonucleoside kinase that specifically phosphorylates thymidine, deoxycytidine, and deoxyuridine. The encoded enzyme localizes to the mitochondria and is required for mitochondrial DNA synthesis. Mutations in this gene are associated with a myopathic form of mitochondrial DNA depletion syndrome. Alternate splicing results in multiple transcript variants encoding distinct isoforms, some of which lack transit peptide, so are not localized to mitochondria. [provided by RefSeq, Dec 2012]

ACMG classification

Verdict is Pathogenic. Variant got 13 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 2 uncertain in NM_004614.5
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.8
• PP5: Variant 16-66531432-G-A is Pathogenic according to our data. Variant chr16-66531432-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 12710.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TK2	NM_004614.5	c.323C>T	p.Thr108Met	missense_variant	5/10	ENST00000544898.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TK2	ENST00000544898.6	c.323C>T	p.Thr108Met	missense_variant	5/10	1	NM_004614.5	P1

Frequencies

GnomAD3 genomes AF: 0.000125 AC: 19 AN: 152190 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00105

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000438 AC: 11 AN: 251080 Hom.: 0 AF XY: 0.0000663 AC XY: 9 AN XY: 135726

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000202

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000353

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000287 AC: 42 AN: 1461870 Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29 AN XY: 727240

Gnomad4 AFR exome AF: 0.0000896

Gnomad4 AMR exome AF: 0.000268

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000348

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000162

Gnomad4 OTH exome AF: 0.0000994

GnomAD4 genome AF: 0.000125 AC: 19 AN: 152190 Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11 AN XY: 74350

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00105

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000138 Hom.: 0

Bravo AF: 0.000234

ExAC AF: 0.0000247 AC: 3

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:11 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Mitochondrial DNA depletion syndrome, myopathic form Pathogenic:6 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Knight Diagnostic Laboratories, Oregon Health and Sciences University	Dec 04, 2015	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. -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Jan 03, 2022	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. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jan 29, 2013	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jun 19, 2019	This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
Pathogenic, criteria provided, single submitter	clinical testing	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	Oct 09, 2023	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). -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Sep 11, 2019	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. -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Feb 18, 2019	This sequence change replaces threonine with methionine at codon 108 of the TK2 protein (p.Thr108Met). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and methionine. This variant is present in population databases (rs137854431, ExAC 0.009%). This variant has been reported in several families and unrelated individuals affected with mtDNA depletion syndrome, both as homozygous or in combination with other heterozygous TK2 variants (PMID: 12391347, 12873860, 15639197, 16908738, 22345218, 23303857, 26925861). It is also known as T77M in the literature. ClinVar contains an entry for this variant (Variation ID: 12710). An experimental study has shown that this missense change results in a dramatic reduction in TK2 activity compared to wild-type protein in vitro (PMID: 15639197). In addition, TK2 activity is markedly reduced in cells from affected individuals with this variant, and there is a noted depletion of mtDNA (PMID: 12391347, 12873860, 19265691, 24484525, 28812460). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Dec 08, 2022	Published functional studies found this variant is associated with a significant decrease in enzyme efficiency and catalytic activity compared to wild-type (Wang et al. 2005); Also known as p.(T77M); This variant is associated with the following publications: (PMID: 22345218, 28217183, 29602790, 16908738, 33486010, 19265691, 18021809, 12873860, 1734306, 12391347, 23303857, 26925861, 27839525, 28812460, 29625556, 25948719, 31060578, 32140910, 31589614, 32161153, 15639197) -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Sep 01, 2023	TK2: PP4:Strong, PM1, PM2, PM3, PS3:Supporting -

Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 3 Pathogenic:1

Pathogenic, criteria provided, single submitter

research

DECIPHERD-UDD, Universidad del Desarrollo

Jul 01, 2023

- -

Mitochondrial DNA depletion syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Feb 23, 2024

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Pathogenic	0.25	D
BayesDel_noAF	Pathogenic	0.41
Cadd	Pathogenic	31
Dann	Uncertain	0.99
DEOGEN2	Pathogenic	0.96	D;.;D;.;.;.;.;D;.;.;.;D;D
Eigen	Uncertain	0.43
Eigen_PC	Uncertain	0.40
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Pathogenic	0.98	D;D;.;D;.;D;D;D;.;D;D;D;D
M_CAP	Pathogenic	0.50	D
MetaRNN	Pathogenic	0.80	D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.86	D
MutationAssessor	Pathogenic	3.0	M;.;M;.;.;.;.;.;.;.;.;.;.
MutationTaster	Benign	0.96	D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.60	T
REVEL	Pathogenic	0.85
Sift4G	Uncertain	0.028	D;D;D;D;T;D;D;D;T;D;T;.;.
Polyphen		1.0	D;.;D;.;.;P;.;.;.;.;.;.;.
Vest4		0.84
MVP		0.96
MPC		1.1
ClinPred		0.61	D
GERP RS		5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.47
gMVP		0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs137854431; hg19: chr16-66565335;