NM_001347721.2(DYRK1A):c.820A>G (p.Ile274Val) AND DYRK1A-related intellectual disability syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 19, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003640851.2

Allele description [Variation Report for NM_001347721.2(DYRK1A):c.820A>G (p.Ile274Val)]

NM_001347721.2(DYRK1A):c.820A>G (p.Ile274Val)

Gene:

DYRK1A:dual specificity tyrosine phosphorylation regulated kinase 1A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

21q22.13

Genomic location:

Preferred name:

NM_001347721.2(DYRK1A):c.820A>G (p.Ile274Val)

HGVS:

NC_000021.9:g.37490357A>G
NG_009366.1:g.127801A>G
NG_009366.2:g.129786A>G
NM_001347721.2:c.820A>GMANE SELECT
NM_001347722.2:c.820A>G
NM_001347723.2:c.733A>G
NM_001396.5:c.847A>G
NM_101395.2:c.847A>G
NM_130436.2:c.820A>G
NM_130438.2:c.847A>G
NP_001334650.1:p.Ile274Val
NP_001334651.1:p.Ile274Val
NP_001334652.1:p.Ile245Val
NP_001387.2:p.Ile283Val
NP_567824.1:p.Ile283Val
NP_569120.1:p.Ile274Val
NP_569122.1:p.Ile283Val
NC_000021.8:g.38862659A>G

Protein change:

I245V

Molecular consequence:

NM_001347721.2:c.820A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347722.2:c.820A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347723.2:c.733A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001396.5:c.847A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_101395.2:c.847A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_130436.2:c.820A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_130438.2:c.847A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: DYRK1A-related intellectual disability syndrome (MRD7)
Synonyms:: INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 7
Identifiers:: MONDO: MONDO:0013578; MedGen: C5568143; OMIM: 614104

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004511856	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 19, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004511856

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 19, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004511856.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 283 of the DYRK1A protein (p.Ile283Val). This variant is present in population databases (rs780310443, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with DYRK1A-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt DYRK1A protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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