NC_000023.10:g.(?_41193506)_(41646556_?)dup AND Intellectual disability, CASK-related, X-linked

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 17, 2022
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:: RCV004582131.2

Allele description [Variation Report for NC_000023.10:g.(?_41193506)_(41646556_?)dup]

NC_000023.10:g.(?_41193506)_(41646556_?)dup

Genes:: DDX3X:DEAD-box helicase 3 X-linked [Gene - OMIM - HGNC]
GPR34:G protein-coupled receptor 34 [Gene - OMIM - HGNC]
GPR82:G protein-coupled receptor 82 [Gene - OMIM - HGNC]
CASK:calcium/calmodulin dependent serine protein kinase [Gene - OMIM - HGNC]
NYX:nyctalopin [Gene - OMIM - HGNC]
Variant type:: Duplication
Cytogenetic location:: Xp11.4
Genomic location:: ChrX: 41193506 - 41646556 (on Assembly GRCh37)
Preferred name:: NC_000023.10:g.(?_41193506)_(41646556_?)dup
HGVS:: NC_000023.10:g.(?_41193506)_(41646556_?)dup
This HGVS expression did not pass validation

Condition(s)

Name:: Intellectual disability, CASK-related, X-linked
Identifiers:: MedGen: CN043158

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005062732	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 17, 2022)	unknown	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

SCV005062732

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 17, 2022)

unknown

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	unknown	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, SCV005062732.1

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

Description

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. This variant has not been reported in the literature in individuals affected with CASK-related conditions. This variant results in a copy number gain of the genomic region encompassing exon(s) 3-27 of the CASK gene. This region includes the termination codon of the gene. This copy number gain extends beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome.

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

Last Updated: Sep 29, 2024

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