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NM_177559.3(CSNK2A1):c.468T>A (p.Asp156Glu) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 4, 2016
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:
RCV000479609.1

Allele description [Variation Report for NM_177559.3(CSNK2A1):c.468T>A (p.Asp156Glu)]

NM_177559.3(CSNK2A1):c.468T>A (p.Asp156Glu)

Gene:
CSNK2A1:casein kinase 2 alpha 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20p13
Genomic location:
Preferred name:
NM_177559.3(CSNK2A1):c.468T>A (p.Asp156Glu)
HGVS:
  • NC_000020.11:g.495761A>T
  • NG_011970.2:g.53078T>A
  • NM_001362770.2:c.468T>A
  • NM_001362771.2:c.468T>A
  • NM_001895.4:c.468T>A
  • NM_177559.3:c.468T>AMANE SELECT
  • NM_177560.3:c.60T>A
  • NP_001349699.1:p.Asp156Glu
  • NP_001349700.1:p.Asp156Glu
  • NP_001886.1:p.Asp156Glu
  • NP_808227.1:p.Asp156Glu
  • NP_808228.1:p.Asp20Glu
  • NC_000020.10:g.476405A>T
  • NG_011970.1:g.53078T>A
  • NM_001895.3:c.468T>A
  • NM_177559.2:c.468T>A
Protein change:
D156E
Links:
dbSNP: rs1064795110
NCBI 1000 Genomes Browser:
rs1064795110
Molecular consequence:
  • NM_001362770.2:c.468T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001362771.2:c.468T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001895.4:c.468T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_177559.3:c.468T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_177560.3:c.60T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000570585GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Jun 4, 2016) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000570585.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The D156E variant in the CSNK2A1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The D156E variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The D156E variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. However, this substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. The D156E variant is a strong candidate for a pathogenic variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 17, 2023