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NM_000310.3(PPT1):c.490C>T (p.Arg164Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Dec 18, 2017)
Last evaluated:
Dec 18, 2017
Accession:
VCV000056197.1
Variation ID:
56197
Description:
single nucleotide variant
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NM_000310.3(PPT1):c.490C>T (p.Arg164Ter)

Allele ID
70836
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p34.2
Genomic location
1: 40089456 (GRCh38) GRCh38 UCSC
1: 40555128 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.40555128G>A
NC_000001.11:g.40089456G>A
NM_000310.3:c.490C>T NP_000301.1:p.Arg164Ter
... more HGVS
Protein change
R164*
Other names
-
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
Links
dbSNP: rs386833649
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Dec 18, 2017 RCV000049608.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PPT1 - - GRCh38
GRCh37
263 274

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Aug 26, 2014)
criteria provided, single submitter
Method: literature only
Ceroid lipofuscinosis neuronal 1
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000220640.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (4)
Pathogenic
(Dec 18, 2017)
criteria provided, single submitter
Method: clinical testing
Ceroid lipofuscinosis neuronal 1
Allele origin: inherited
Genomic Research Center,Shahid Beheshti University of Medical Sciences
Accession: SCV000746400.1
Submitted: (Dec 18, 2017)
Evidence details
probable-pathogenic
(-)
no assertion criteria provided
Method: not provided
Ceroid lipofuscinosis neuronal 1
Allele origin: not provided
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)
Accession: SCV000082015.1
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
Evidence details
Comment:
Converted during submission to Likely pathogenic.

Citations for this variant

Title Author Journal Year Link
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
Neuronal ceroid lipofuscinoses: research update. Wisniewski KE Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology 2000 PMID: 11073228
Identification of three novel mutations of the palmitoyl-protein thioesterase-1 (PPT1) gene in children with neuronal ceroid-lipofuscinosis. Waliany S Human mutation 2000 PMID: 10649502
Molecular genetics of palmitoyl-protein thioesterase deficiency in the U.S. Das AK The Journal of clinical investigation 1998 PMID: 9664077

Record last updated Aug 25, 2019