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NM_000310.4(PPT1):c.665T>C (p.Leu222Pro)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Jul 27, 2021)
Last evaluated:
Jul 12, 2021
Accession:
VCV000056210.5
Variation ID:
56210
Description:
single nucleotide variant
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NM_000310.4(PPT1):c.665T>C (p.Leu222Pro)

Allele ID
70849
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p34.2
Genomic location
1: 40078621 (GRCh38) GRCh38 UCSC
1: 40544293 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P50897:p.Leu222Pro
LRG_690:g.23850T>C
LRG_690t1:c.665T>C LRG_690p1:p.Leu222Pro
... more HGVS
Protein change
L119P, L222P
Other names
-
Canonical SPDI
NC_000001.11:40078620:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00000
Exome Aggregation Consortium (ExAC) 0.00001
The Genome Aggregation Database (gnomAD) 0.00001
The Genome Aggregation Database (gnomAD) 0.00003
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
ClinGen: CA263538
UniProtKB: P50897#VAR_066879
dbSNP: rs386833661
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Nov 1, 2019 RCV001192781.1
Likely pathogenic 1 criteria provided, single submitter Jul 12, 2021 RCV001646987.1
Likely pathogenic 1 no assertion criteria provided - RCV000049621.1
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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
406 419

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Pathogenic
(Nov 01, 2019)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Affected status: unknown
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001361119.1
Submitted: (Mar 06, 2020)
Publications:
PubMed (5)
Comment:
Variant summary: PPT1 c.665T>C (p.Leu222Pro) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging … (more)
Likely pathogenic
(Jul 12, 2021)
criteria provided, single submitter
Method: research
Spastic ataxia
Affected status: yes
Allele origin: unknown
Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit,IRCCS Fondazione Stella Maris
Accession: SCV001519267.1
Submitted: (Jul 27, 2021)
probable-pathogenic
(-)
no assertion criteria provided
Method: not provided
Ceroid lipofuscinosis neuronal 1
Affected status: not provided
Allele origin: not provided
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)
Accession: SCV000082028.1
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

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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
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
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
Variant late infantile neuronal ceroid lipofuscinosis because of CLN1 mutations. Simonati A Pediatric neurology 2009 PMID: 19302939
Novel CLN1 mutation in two Italian sibs with late infantile neuronal ceroid lipofuscinosis. Bonsignore M European journal of paediatric neurology : EJPN : official journal of the European Paediatric Neurology Society 2006 PMID: 16759889
A novel mutation in the CLN1 gene in a patient with juvenile neuronal ceroid lipofuscinosis. Mazzei R Journal of neurology 2002 PMID: 12382155

Text-mined citations for rs386833661...

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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 Jan 12, 2022