Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001128918.3(MARK3):c.296A>G(p.Lys99Arg) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000597 in 1,508,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
MARK3 (HGNC:6897): (microtubule affinity regulating kinase 3) The protein encoded by this gene is activated by phosphorylation and in turn is involved in the phosphorylation of tau proteins MAP2 and MAP4. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
BP4
?
BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (MetaRNN=0.29328087).
Uncertain significance, criteria provided, single submitter
clinical testing
Ambry Genetics
Mar 20, 2023
The c.296A>G (p.K99R) alteration is located in exon 3 (coding exon 3) of the MARK3 gene. This alteration results from a A to G substitution at nucleotide position 296, causing the lysine (K) at amino acid position 99 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Gain of catalytic residue at R102 (P = 0.0155);Gain of catalytic residue at R102 (P = 0.0155);Gain of catalytic residue at R102 (P = 0.0155);Gain of catalytic residue at R102 (P = 0.0155);Gain of catalytic residue at R102 (P = 0.0155);Gain of catalytic residue at R102 (P = 0.0155);Gain of catalytic residue at R102 (P = 0.0155);.;