Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_017882.3(CLN6):c.339G>A (p.Thr113=)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 13, 2021)
Last evaluated:
Mar 16, 2021
Accession:
VCV000136797.6
Variation ID:
136797
Description:
single nucleotide variant
Help

NM_017882.3(CLN6):c.339G>A (p.Thr113=)

Allele ID
140500
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q23
Genomic location
15: 68211822 (GRCh38) GRCh38 UCSC
15: 68504160 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_832:g.50390G>A
LRG_832t1:c.339G>A LRG_832p1:p.Thr113=
NC_000015.10:g.68211822C>T
... more HGVS
Protein change
-
Other names
p.T113T:ACG>ACA
Canonical SPDI
NC_000015.10:68211821:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00031
1000 Genomes Project 0.00040
The Genome Aggregation Database (gnomAD) 0.00118
Trans-Omics for Precision Medicine (TOPMed) 0.00148
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00154
The Genome Aggregation Database (gnomAD), exomes 0.00034
Links
ClinGen: CA290143
dbSNP: rs146135801
Varsome
Help

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 Mar 16, 2021 RCV000124339.5
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 4, 2020 RCV000465480.6
Help
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

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Mar 16, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV001880568.1
Submitted: (Sep 13, 2021)
Evidence details
Benign
(Feb 05, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000167768.12
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)
Likely benign
(Jul 08, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000332725.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Invitae
Accession: SCV000560150.6
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000393740.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)

Functional evidence

Help
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

Help
Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CLN6 - - - -

Text-mined citations for rs146135801...

Help
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 Sep 23, 2021