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_006493.4(CLN5):c.188G>C (p.Arg63Pro)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Oct 12, 2021)
Last evaluated:
Aug 10, 2021
Accession:
VCV000056533.4
Variation ID:
56533
Description:
single nucleotide variant
Help

NM_006493.4(CLN5):c.188G>C (p.Arg63Pro)

Allele ID
71172
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q22.3
Genomic location
13: 76995077 (GRCh38) GRCh38 UCSC
13: 77569212 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_692:g.8154G>C
LRG_692t1:c.335G>C
NC_000013.10:g.77569212G>C
... more HGVS
Protein change
R63P
Other names
-
Canonical SPDI
NC_000013.11:76995076:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA263884
dbSNP: rs104894386
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 2 criteria provided, single submitter Aug 10, 2021 RCV000049946.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Aug 15, 2020 RCV000989149.2
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CLN5 - - GRCh38
GRCh37
145 450
FBXL3 - - GRCh38
GRCh37
5 310

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Pathogenic
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 1
Affected status: unknown
Allele origin: unknown
Mendelics
Accession: SCV001139365.1
Submitted: (Oct 22, 2019)
Uncertain significance
(Aug 15, 2020)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV001494463.1
Submitted: (Jan 07, 2021)
Publications:
PubMed (4)
PubMed: 16814585200527651572830730078242
Comment:
This sequence change replaces arginine with proline at codon 112 of the CLN5 protein (p.Arg112Pro). The arginine residue is highly conserved and there is a … (more)
Likely pathogenic
(Aug 10, 2021)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 5
Affected status: no
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001977458.1
Submitted: (Oct 12, 2021)
probable-pathogenic
(-)
no assertion criteria provided
Method: not provided
Ceroid lipofuscinosis neuronal 5
Affected status: not provided
Allele origin: not provided
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)
Accession: SCV000082355.1
Submitted: (May 19, 2013)
Comment:
FinDis database variant: This variant was not found or characterized by our laboratory, data were collected from public sources: see reference
Comment:
Converted during submission to Likely pathogenic.

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
[Clinical features and genetics studies of Finnish variant late infantile neuronal ceroid lipofuscinosis in two families]. Zhou ZZ Zhonghua er ke za zhi = Chinese journal of pediatrics 2018 PMID: 30078242
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
The neuronal ceroid lipofuscinosis protein CLN5: new insights into cellular maturation, transport, and consequences of mutations. Schmiedt ML Human mutation 2010 PMID: 20052765
Two novel CLN5 mutations in a Portuguese patient with vLINCL: insights into molecular mechanisms of CLN5 deficiency. Bessa C Molecular genetics and metabolism 2006 PMID: 16814585
A CLN5 mutation causing an atypical neuronal ceroid lipofuscinosis of juvenile onset. Pineda-Trujillo N Neurology 2005 PMID: 15728307

Text-mined citations for rs104894386...

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 Jan 12, 2022