ClinVar Miner

Submissions for variant NM_001347721.2(DYRK1A):c.542_545del (p.Ile181fs)

dbSNP: rs1555982601
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000593226 SCV000708617 pathogenic not provided 2017-06-07 criteria provided, single submitter clinical testing
GeneDx RCV000593226 SCV001168798 pathogenic not provided 2018-08-29 criteria provided, single submitter clinical testing The c.569_572delTAAA variant in the DYRK1A gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.569_572delTAAA variant causes a frameshift starting with codon Isoleucine 190, changes this amino acid to an Arginine residue, and creates a premature Stop codon at position 7 of the new reading frame, denoted p.Ile190ArgfsX7. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.569_572delTAAA variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.569_572delTAAA as a pathogenic variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV001867985 SCV002131922 pathogenic DYRK1A-related intellectual disability syndrome 2020-11-10 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ile190Argfs*7) in the DYRK1A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DYRK1A are known to be pathogenic (PMID: 25944381). This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with DYRK1A-related conditions. ClinVar contains an entry for this variant (Variation ID: 502025). For these reasons, this variant has been classified as Pathogenic.
Neuberg Centre For Genomic Medicine, NCGM RCV001867985 SCV004047129 pathogenic DYRK1A-related intellectual disability syndrome criteria provided, single submitter clinical testing The frameshift deletion p.I181Rfs*7 in DYRK1A (NM_001347721.2) has been previously reported in individuals affected with Mental retardation 7 disorder (Méjécase et al, 2021). The p.I181Rfs*7 variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. This variant causes a frameshift starting with codon Isoleucine 190, changes this amino acid to Arginine residue, and creates a premature Stop codon at position 7 of the new reading frame, denoted p.Ile190ArgfsTer7. For these reasons, this variant has been classified as Pathogenic.

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