chr17-62522213-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2
The NM_006852.6(TLK2):āc.163A>Gā(p.Lys55Glu) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,106 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006852.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250184Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135302
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461106Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726850
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Intellectual disability Uncertain:1
The homozygous p.Lys55Glu variant in TLK2 was identified by our study in an individual with intellectual disability (PMID: 31558842). The presence of this variant in an affected homozygote increases the likelihood that the p.Lys55Glu variant is pathogenic. This variant has been identified in 0.0009% (1/113274) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs774263147). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The number of missense variants reported in TLK2 in the general population is lower than expected, suggesting there is little benign variation in this gene and slightly increasing the possibility that a missense variant in this gene may not be tolerated. In summary, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PM2, PP3, PM3_Supporting, PP3 (Richards 2015). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at