Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PM5PP2
The NM_001904.4(CTNNB1):c.109T>A(p.Ser37Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S37A) has been classified as Likely pathogenic.
CTNNB1 (HGNC:2514): (catenin beta 1) The protein encoded by this gene is part of a complex of proteins that constitute adherens junctions (AJs). AJs are necessary for the creation and maintenance of epithelial cell layers by regulating cell growth and adhesion between cells. The encoded protein also anchors the actin cytoskeleton and may be responsible for transmitting the contact inhibition signal that causes cells to stop dividing once the epithelial sheet is complete. Finally, this protein binds to the product of the APC gene, which is mutated in adenomatous polyposis of the colon. Mutations in this gene are a cause of colorectal cancer (CRC), pilomatrixoma (PTR), medulloblastoma (MDB), and ovarian cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2016]
Verdict is Likely_pathogenic. Variant got 7 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 hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 4 uncertain in NM_001904.4
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;
PM5
?
PM5 - Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before
Other missense variant is known to change same aminoacid residue: Variant chr3-41224621-T-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 376235.Status of the report is no_assertion_criteria_provided, 0 stars.
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, CTNNB1
Loss of glycosylation at S37 (P = 0.0182);.;Loss of glycosylation at S37 (P = 0.0182);.;Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);.;Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);.;.;Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);.;.;.;.;Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);.;Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);.;Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);.;Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);Loss of glycosylation at S37 (P = 0.0182);