NM_001367721.1(CASK):c.1466G>A (p.Arg489Gln) AND not provided

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Nov 13, 2024
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:: RCV000999405.29

Allele description [Variation Report for NM_001367721.1(CASK):c.1466G>A (p.Arg489Gln)]

NM_001367721.1(CASK):c.1466G>A (p.Arg489Gln)

Gene:

CASK:calcium/calmodulin dependent serine protein kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.4

Genomic location:

Preferred name:

NM_001367721.1(CASK):c.1466G>A (p.Arg489Gln)

HGVS:

NC_000023.11:g.41578377C>T
NG_016754.2:g.349658G>A
NM_001126054.3:c.1466G>A
NM_001126055.3:c.1448G>A
NM_001367721.1:c.1466G>AMANE SELECT
NM_001410745.1:c.1448G>A
NM_003688.4:c.1466G>A
NP_001119526.1:p.Arg489Gln
NP_001119526.1:p.Arg489Gln
NP_001119527.1:p.Arg483Gln
NP_001119527.1:p.Arg483Gln
NP_001354650.1:p.Arg489Gln
NP_001397674.1:p.Arg483Gln
NP_003679.2:p.Arg489Gln
NP_003679.2:p.Arg489Gln
NC_000023.10:g.41437630C>T
NC_000023.10:g.41437630C>T
NM_001126054.2:c.1466G>A
NM_001126055.2:c.1448G>A
NM_003688.3:c.1466G>A

Protein change:

R483Q

Links:

dbSNP: rs1602292076

NCBI 1000 Genomes Browser:

rs1602292076

Molecular consequence:

NM_001126054.3:c.1466G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126055.3:c.1448G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001367721.1:c.1466G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001410745.1:c.1448G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_003688.4:c.1466G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001156006	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely pathogenic (Mar 1, 2019)	germline	clinical testing	Citation Link,
SCV001988443	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Nov 13, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001156006

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely pathogenic
(Mar 1, 2019)

germline

clinical testing

Citation Link,

SCV001988443

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Nov 13, 2024)

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

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001156006.28

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

#	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, SCV001988443.4

#	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: 33090494, 30525188)

#	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: Jan 4, 2025

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