NM_177559.3(CSNK2A1):c.583C>T (p.Arg195Ter) AND not provided

Germline classification:: Conflicting classifications of pathogenicity (2 submissions)
Last evaluated:: Dec 18, 2025
Review status:: criteria provided, conflicting classifications

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:: RCV001269781.9

Allele description [Variation Report for NM_177559.3(CSNK2A1):c.583C>T (p.Arg195Ter)]

NM_177559.3(CSNK2A1):c.583C>T (p.Arg195Ter)

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.583C>T (p.Arg195Ter)

HGVS:

NC_000020.11:g.492292G>A
NG_011970.2:g.56547C>T
NM_001362770.2:c.583C>T
NM_001362771.2:c.583C>T
NM_001895.4:c.583C>T
NM_177559.3:c.583C>TMANE SELECT
NM_177560.2:c.175C>T
NM_177560.3:c.175C>T
NP_001349699.1:p.Arg195Ter
NP_001349700.1:p.Arg195Ter
NP_001886.1:p.Arg195Ter
NP_808227.1:p.Arg195Ter
NP_808228.1:p.Arg59Ter
NC_000020.10:g.472936G>A
NG_011970.1:g.56547C>T
NM_001895.3:c.583C>T

Protein change:

R195*

Links:

dbSNP: rs1034583315

Molecular consequence:

NM_001362770.2:c.583C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001362771.2:c.583C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001895.4:c.583C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_177559.3:c.583C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_177560.3:c.175C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

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
SCV001450036	Clinical Genetics and Genomics, Karolinska University Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 7, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001817911	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Dec 18, 2025)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001450036

Clinical Genetics and Genomics, Karolinska University Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 7, 2018)

germline

clinical testing

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

SCV001817911

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Dec 18, 2025)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Clinical Genetics and Genomics, Karolinska University Hospital, SCV001450036.1

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

#	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		1	not provided	not provided	not provided

From GeneDx, SCV001817911.3

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

Description

Identified in an individual with a neurodevelopmental disorder, but segregation was unknown and detailed clinical information was not provided (PMID: 33004838); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 33004838)

#	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

Last Updated: Dec 27, 2025

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