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NM_000310.4(PPT1):c.541G>A

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Apr 13, 2021)
Last evaluated:
Apr 12, 2021
Accession:
VCV000188857.7
Variation ID:
188857
Description:
single nucleotide variant
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NM_000310.4(PPT1):c.541G>A

Allele ID
186623
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p34.2
Genomic location
1: 40080483 (GRCh38) GRCh38 UCSC
1: 40546155 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P50897:p.Val181Met
LRG_690:g.21988G>A
NC_000001.10:g.40546155C>T
... more HGVS
Protein change
V181M, V78M
Other names
-
Canonical SPDI
NC_000001.11:40080482:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00006
Trans-Omics for Precision Medicine (TOPMed) 0.00002
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
ClinGen: CA274047
UniProtKB: P50897#VAR_005557
dbSNP: rs148412181
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 5 criteria provided, multiple submitters, no conflicts Apr 12, 2021 RCV000169209.7
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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
405 417

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jun 27, 2014)
criteria provided, single submitter
Method: literature only
Ceroid lipofuscinosis neuronal 1
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000220464.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (6)
Pathogenic
(Mar 11, 2019)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 1
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001361117.1
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: PPT1 c.541G>A (p.Val181Met) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging … (more)
Pathogenic
(Apr 12, 2021)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 1
(Autosomal recessive inheritance)
Allele origin: germline
Centre for Inherited Metabolic Diseases, Karolinska University Hospital
Accession: SCV001571358.1
Submitted: (Apr 13, 2021)
Evidence details
Pathogenic
(Jan 04, 2016)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 1
Allele origin: inherited
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
Accession: SCV000965817.1
Submitted: (Apr 26, 2017)
Evidence details
Pathogenic
(Oct 14, 2020)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 1
Allele origin: germline
Invitae
Accession: SCV000958226.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (11)
Comment:
This sequence change replaces valine with methionine at codon 181 of the PPT1 protein (p.Val181Met). The valine 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
Batten disease: biochemical and molecular characterization revealing novel PPT1 and TPP1 gene mutations in Indian patients. Sheth J BMC neurology 2018 PMID: 30541466
The Networks of Genes Encoding Palmitoylated Proteins in Axonal and Synaptic Compartments Are Affected in PPT1 Overexpressing Neuronal-Like Cells. Pezzini F Frontiers in molecular neuroscience 2017 PMID: 28878621
Molecular epidemiology of childhood neuronal ceroid-lipofuscinosis in Italy. Santorelli FM Orphanet journal of rare diseases 2013 PMID: 23374165
Infantile neuronal ceroid lipofuscinosis: follow-up on a Spanish series. Pérez Poyato MS Gene 2012 PMID: 22387303
Juvenile neuronal ceroid lipofuscinosis: clinical course and genetic studies in Spanish patients. Pérez-Poyato MS Journal of inherited metabolic disease 2011 PMID: 21499717
Variant late infantile neuronal ceroid lipofuscinosis because of CLN1 mutations. Simonati A Pediatric neurology 2009 PMID: 19302939
Electroretinographic and clinicopathologic correlations of retinal dysfunction in infantile neuronal ceroid lipofuscinosis (infantile Batten disease). Weleber RG Molecular genetics and metabolism 2004 PMID: 15464427
Clinicopathological and molecular characterization of neuronal ceroid lipofuscinosis in the Portuguese population. Teixeira C Journal of neurology 2003 PMID: 12796825
Biochemical analysis of mutations in palmitoyl-protein thioesterase causing infantile and late-onset forms of neuronal ceroid lipofuscinosis. Das AK Human molecular genetics 2001 PMID: 11440996
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
Genotype-phenotype correlations in neuronal ceroid lipofuscinosis due to palmitoyl-protein thioesterase deficiency. Hofmann SL Molecular genetics and metabolism 1999 PMID: 10191107
Molecular genetics of palmitoyl-protein thioesterase deficiency in the U.S. Das AK The Journal of clinical investigation 1998 PMID: 9664077

Text-mined citations for rs148412181...

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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 Jun 14, 2021