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NM_152393.4(KLHL40):c.1152+2T>A

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, single submitter
Submissions:
1 (Most recent: Mar 28, 2019)
Last evaluated:
Dec 12, 2018
Accession:
VCV000653053.1
Variation ID:
653053
Description:
single nucleotide variant
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NM_152393.4(KLHL40):c.1152+2T>A

Allele ID
651070
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p22.1
Genomic location
3: 42686772 (GRCh38) GRCh38 UCSC
3: 42728264 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.42728264T>A
NC_000003.12:g.42686772T>A
NG_033035.1:g.6254T>A
NM_152393.4:c.1152+2T>A MANE Select splice donor
Protein change
-
Other names
-
Canonical SPDI
NC_000003.12:42686771:T:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs1575219191
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Dec 12, 2018 RCV000808744.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KLHL40 - - GRCh38
GRCh37
257 265

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Dec 12, 2018)
criteria provided, single submitter
Method: clinical testing
Nemaline myopathy 8
Allele origin: germline
Invitae
Accession: SCV000948862.1
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change affects a donor splice site in intron 1 of the KLHL40 gene. It is expected to disrupt RNA splicing and likely results … (more)

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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Title Author Journal Year Link
Mutations in KLHL40 are a frequent cause of severe autosomal-recessive nemaline myopathy. Ravenscroft G American journal of human genetics 2013 PMID: 23746549

Text-mined citations for rs1575219191...

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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 Oct 08, 2021