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NM_017882.3(CLN6):c.407G>A (p.Arg136His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 15, 2020
Accession:
VCV000402184.2
Variation ID:
402184
Description:
single nucleotide variant
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NM_017882.3(CLN6):c.407G>A (p.Arg136His)

Allele ID
389162
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q23
Genomic location
15: 68211754 (GRCh38) GRCh38 UCSC
15: 68504092 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.68211754C>T
NC_000015.9:g.68504092C>T
NG_008764.2:g.50458G>A
... more HGVS
Protein change
R136H
Other names
-
Canonical SPDI
NC_000015.10:68211753:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00005
The Genome Aggregation Database (gnomAD), exomes 0.00004
The Genome Aggregation Database (gnomAD) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
ClinGen: CA7630612
dbSNP: rs769701646
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 - RCV000454168.1
Uncertain significance 1 criteria provided, single submitter Oct 29, 2015 RCV000499595.1
Likely pathogenic 1 criteria provided, single submitter Sep 15, 2020 RCV001379796.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CLN6 - - GRCh38
GRCh37
443 458

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(-)
criteria provided, single submitter
Method: research
Abnormality of brain morphology
(Autosomal recessive inheritance)
Allele origin: inherited
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine
Accession: SCV000537961.1
Submitted: (Mar 29, 2017)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Oct 29, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000594156.1
Submitted: (Jul 05, 2017)
Evidence details
Likely pathogenic
(Sep 15, 2020)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Invitae
Accession: SCV001577667.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change replaces arginine with histidine at codon 136 of the CLN6 protein (p.Arg136His). The arginine residue is highly conserved and there is a … (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
Kufs disease due to mutation of CLN6: clinical, pathological and molecular genetic features. Berkovic SF Brain : a journal of neurology 2019 PMID: 30561534
[Clinical, genetic and pathological features of neuronal ceroid lipofuscinosis in 5 Chinese patients]. Ren SC Zhonghua yi xue za zhi 2016 PMID: 27903347
Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease. Karaca E Neuron 2015 PMID: 26539891
Lysoplex: An efficient toolkit to detect DNA sequence variations in the autophagy-lysosomal pathway. Di Fruscio G Autophagy 2015 PMID: 26075876
Variant late infantile ceroid lipofuscinoses associated with novel mutations in CLN6. Cannelli N Biochemical and biophysical research communications 2009 PMID: 19135028

Text-mined citations for rs769701646...

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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