NM_001320.7(CSNK2B):c.94G>A (p.Asp32Asn) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Dec 16, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001860419.6

Allele description [Variation Report for NM_001320.7(CSNK2B):c.94G>A (p.Asp32Asn)]

NM_001320.7(CSNK2B):c.94G>A (p.Asp32Asn)

Gene:

CSNK2B:casein kinase 2 beta [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p21.33

Genomic location:

Preferred name:

NM_001320.7(CSNK2B):c.94G>A (p.Asp32Asn)

HGVS:

NC_000006.12:g.31667889G>A
NM_001282385.2:c.94G>A
NM_001320.7:c.94G>AMANE SELECT
NP_001269314.1:p.Asp32Asn
NP_001311.3:p.Asp32Asn
NP_001311.3:p.Asp32Asn
NC_000006.11:g.31635666G>A
NM_001320.5:c.94G>A
NM_001320.6:c.94G>A

Protein change:

D32N

Links:

dbSNP: rs1554169984

NCBI 1000 Genomes Browser:

rs1554169984

Molecular consequence:

NM_001282385.2:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001320.7:c.94G>A - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

dominant_negative_variant [Sequence Ontology: SO:0002052]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002107327	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Dec 16, 2021)	germline	clinical testing	Citation Link,
SCV002208921	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 15, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 33644862, 34041744, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002107327

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Dec 16, 2021)

germline

clinical testing

Citation Link,

SCV002208921

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 15, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Genetic and phenotypic analysis of 101 patients with developmental delay or intellectual disability using whole-exome sequencing.

Hiraide T, Yamoto K, Masunaga Y, Asahina M, Endoh Y, Ohkubo Y, Matsubayashi T, Tsurui S, Yamada H, Yanagi K, Nakashima M, Hirano K, Sugimura H, Fukuda T, Ogata T, Saitsu H.

Clin Genet. 2021 Jul;100(1):40-50. doi: 10.1111/cge.13951. Epub 2021 Mar 8.

PubMed [citation]

PMID:: 33644862

CSNK2B: A broad spectrum of neurodevelopmental disability and epilepsy severity.

Ernst ME, Baugh EH, Thomas A, Bier L, Lippa N, Stong N, Mulhern MS, Kushary S, Akman CI, Heinzen EL, Yeh R, Bi W, Hanchard NA, Burrage LC, Leduc MS, Chong JSC, Bend R, Lyons MJ, Lee JA, Suwannarat P, Brilstra E, Simon M, et al.

Epilepsia. 2021 Jul;62(7):e103-e109. doi: 10.1111/epi.16931. Epub 2021 May 26.

PubMed [citation]

PMID:: 34041744
PMCID:: PMC9189716

See all PubMed Citations (3)

Details of each submission

From GeneDx, SCV002107327.2

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 33644862, 34041744)

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002208921.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 520596). This missense change has been observed in individual(s) with CSNK2B-related conditions (PMID: 33644862, 34041744; Invitae). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (ExAC no frequency). This sequence change replaces aspartic acid with asparagine at codon 32 of the CSNK2B protein (p.Asp32Asn). The aspartic acid residue is highly conserved and there is a small physicochemical difference between aspartic acid and asparagine.

#	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: Nov 3, 2024

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