Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP2PP3_ModeratePP5_Moderate
The NM_001161352.2(KCNMA1):c.1054A>G(p.Thr352Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. T352T) has been classified as Likely benign.
KCNMA1 (HGNC:6284): (potassium calcium-activated channel subfamily M alpha 1) This gene encodes the alpha subunit of calcium-activated BK channel. The encoded protein is involved in several physiological processes including smooth muscle contraction, neurotransmitter release and neuronal excitability. Mutations in this gene are associated with a spectrum of neurological disorders including Paroxysmal Nonkinesigenic Dyskinesia 3, Idiopathic Generalized Epilepsy 16 and Liang-Wang syndrome. [provided by RefSeq, Aug 2022]
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
PM1
?
PM1 - Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation
In a mutagenesis_site Activated at more negative voltages. Slower rate of inactivation. Impaired inhibition by HMIMP. No effect on channel inhibition by Iberiotoxin. (size 0) in uniprot entity KCMA1_HUMAN
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;
PP2
?
PP2 - Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease
Missense variant where missense usually causes diseases, KCNMA1
PP3
?
PP3 - Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)
MetaRNN computational evidence supports a deleterious effect, 0.933
PP5
?
PP5 - Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 10-77110250-T-C is Pathogenic according to our data. Variant chr10-77110250-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 216948.Status of the report is criteria_provided_single_submitter, 1 stars.
.;Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);.;Loss of glycosylation at T352 (P = 0.0615);.;Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);.;.;Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);.;.;.;.;.;.;Loss of glycosylation at T352 (P = 0.0615);.;Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);.;.;.;Loss of glycosylation at T352 (P = 0.0615);.;Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);.;Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);Loss of glycosylation at T352 (P = 0.0615);.;.;Loss of glycosylation at T352 (P = 0.0615);