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NM_017882.3(CLN6):c.755G>A (p.Arg252His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Sep 24, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000205176.7
Variation ID:
205176
Description:
single nucleotide variant
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NM_017882.3(CLN6):c.755G>A (p.Arg252His)

Allele ID
202869
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q23
Genomic location
15: 68208321 (GRCh38) GRCh38 UCSC
15: 68500659 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
Q9NWW5:p.Arg252His
LRG_832:g.53891G>A
LRG_832t1:c.755G>A LRG_832p1:p.Arg252His
... more HGVS
Protein change
R252H
Other names
p.R252H:CGC>CAC
Canonical SPDI
NC_000015.10:68208320:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00004
Trans-Omics for Precision Medicine (TOPMed) 0.00008
The Genome Aggregation Database (gnomAD), exomes 0.00020
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
Exome Aggregation Consortium (ExAC) 0.00017
Trans-Omics for Precision Medicine (TOPMed) 0.00009
Links
ClinGen: CA313980
UniProtKB: Q9NWW5#VAR_066912
dbSNP: rs374681194
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jun 4, 2019 RCV000187105.6
Uncertain significance 2 criteria provided, single submitter Dec 20, 2017 RCV000671648.3
Likely benign 1 criteria provided, single submitter Dec 7, 2020 RCV001083020.2
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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
447 462

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 20, 2017)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 6
Allele origin: unknown
Counsyl
Accession: SCV000796641.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (2)
Likely benign
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Invitae
Accession: SCV001003471.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Jun 04, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000240680.14
Submitted: (Sep 24, 2021)
Evidence details
Comment:
In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Previously reported two patients with suspected … (more)
Pathogenic
(-)
no assertion criteria provided
Method: research
Neuronal ceroid lipofuscinosis 6
Allele origin: inherited
Translational Research Program on Neuronal Ceroid Lipofuscinosis,Center for the Study of Inborn Errors of Metabolism
Accession: SCV000804310.1
Submitted: (Jul 01, 2018)
Evidence details
Comment:
Late Infantile NCL

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
GESPA: classifying nsSNPs to predict disease association. Khurana JK BMC bioinformatics 2015 PMID: 26206375
Update of the mutation spectrum and clinical correlations of over 360 mutations in eight genes that underlie the neuronal ceroid lipofuscinoses. Kousi M Human mutation 2012 PMID: 21990111

Text-mined citations for rs374681194...

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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