ClinVar Miner

Submissions for variant NM_001347721.2(DYRK1A):c.896T>C (p.Phe299Ser)

dbSNP: rs1569376809
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000730365 SCV000858095 likely pathogenic not provided 2017-12-11 criteria provided, single submitter clinical testing
Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn RCV001175155 SCV001245458 likely pathogenic DYRK1A-related intellectual disability syndrome criteria provided, single submitter clinical testing A likely disease-causing missense variant was detected in the DYRK1A gene. The sequencing of exon 6 (NM_001396.3) revealed a heterozygous base exchange at nucleotide position 923 of the cDNA. The designation of the variant is: c.923T> C; p.(Phe308Ser). This replaces the codon for the amino acid phenylalanine (TTT) with the codon for the amino acid serine (TCT). This variant could not be demonstrated in the parents. The missense variant is not recorded in population-related databases. In the phenotype-related database ClinVar it is listed as likely to be pathogenic, in LOVD and HGMD it is not recorded. The mutation prediction programs MutationTaster, SIFT and PolyPhen-2 assess the variant as pathogenic, the CADD score is 32. It is a highly conserved amino acid, which is located in a tyrosine kinase domain. The ACMG classification of the variant is: probably pathogenic (class 4: PS2, PM1, PM2, PP3). As an enzyme (protein kinase), the DYRK1A protein plays an important role in the differentiation, proliferation and survival of cells. Certain variants in the DYRK1A gene have been associated with autosomal dominant mental retardation 7 (OMIM # 614104). This syndrome is characterized by a delay in development or a decrease in intelligence, autistic behavioral traits, microcephaly, seizures, and dysmorphia of the face and ears. Various missense, splice, nonsense and frame shift variants have already been described as causing the disease. Functional studies have shown that a different exchange of the same amino acid (p. (Phe308Val)) in the DYRK1A protein leads to a functional failure (Widowati, et al., 2018, PMID: 29700199).

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