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NM_001367721.1(CASK):c.2040-9A>G

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000158068.5
Variation ID:
158068
Description:
single nucleotide variant
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NM_001367721.1(CASK):c.2040-9A>G

Allele ID
167915
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xp11.4
Genomic location
X: 41542815 (GRCh38) GRCh38 UCSC
X: 41402068 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.41402068T>C
NC_000023.11:g.41542815T>C
NG_016754.1:g.385220A>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000023.11:41542814:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00503 (C)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00595
Trans-Omics for Precision Medicine (TOPMed) 0.00640
1000 Genomes Project 0.00503
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00786
The Genome Aggregation Database (gnomAD) 0.00493
Trans-Omics for Precision Medicine (TOPMed) 0.00639
Links
ClinGen: CA171479
dbSNP: rs138290714
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Apr 14, 2017 RCV000145396.4
Benign 1 criteria provided, single submitter Dec 8, 2020 RCV000540540.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CASK Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
411 581

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jul 21, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
(X-linked inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000192484.1
Submitted: (Sep 11, 2014)
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Evidence details
Benign
(Apr 14, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000612649.1
Submitted: (Aug 17, 2017)
Evidence details
Benign
(Mar 22, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000522094.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Mental retardation, CASK-related, X-linked
Allele origin: germline
Invitae
Accession: SCV000647906.5
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs138290714...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021