- This record was updated by the submitter. Please see the current version.
NM_000391.4(TPP1):c.509-1G>C AND Neuronal ceroid lipofuscinosis 2
- Germline classification:
- Pathogenic (18 submissions)
- Last evaluated:
- Jul 13, 2021
- Review status:
- 2 stars out of maximum of 4 starscriteria provided, multiple submitters, no conflicts
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000002763.44
Allele description
NM_000391.4(TPP1):c.509-1G>C
- Gene:
- TPP1:tripeptidyl peptidase 1 [Gene - OMIM - HGNC]
- Variant type:
- single nucleotide variant
- Cytogenetic location:
- 11p15.4
- Genomic location:
- Preferred name:
- NM_000391.4(TPP1):c.509-1G>C
- HGVS:
- NC_000011.10:g.6617154C>G
- NG_008653.1:g.7308G>C
- NM_000391.4:c.509-1G>CMANE SELECT
- LRG_830t1:c.509-1G>C
- LRG_830:g.7308G>C
- NC_000011.9:g.6638385C>G
- NM_000391.3:c.509-1G>C
- NM_000391.3:c.509-1G>C(IVS5-1G>C)
This HGVS expression did not pass validation- Nucleotide change:
- IVS5AS, G-C, -1
- Links:
- Genetic Testing Registry (GTR): GTR000330881; OMIM: 607998.0004; dbSNP: rs56144125
- NCBI 1000 Genomes Browser:
- rs56144125
- Molecular consequence:
- NM_000391.4:c.509-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
- Observations:
- 4
Condition(s)
Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000022921 | OMIM | no assertion criteria provided | Pathogenic (May 1, 2013) | germline | literature only | |
SCV000086784 | GeneReviews | no assertion criteria provided | pathologic (Aug 1, 2013) | not provided | curation | |
SCV000236538 | Courtagen Diagnostics Laboratory, Courtagen Life Sciences | criteria provided, single submitter (Courtagen Life Sciences Classifications) | Pathogenic (Jan 13, 2014) | germline | clinical testing | |
SCV000265553 | HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-HudsonAlpha | criteria provided, single submitter (HA_assertions_20161101) | Pathogenic (Feb 10, 2015) | unknown | research | HA_assertions_20161101.pdf, |
SCV000538068 | Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Oct 23, 2015) | germline | clinical testing | |
SCV000597532 | Genetic Services Laboratory, University of Chicago | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 22, 2016) | germline | clinical testing | |
SCV000680415 | Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München | criteria provided, single submitter (Classification criteria August 2017) | Pathogenic (Nov 8, 2017) | paternal | clinical testing | |
SCV000733090 | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus | no assertion criteria provided | Pathogenic | germline | clinical testing | |
SCV000744910 | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus | criteria provided, single submitter (ACGS Guidelines, 2013) | Pathogenic (Sep 21, 2015) | germline | clinical testing | |
SCV000915544 | Illumina Laboratory Services, Illumina | criteria provided, single submitter (ICSL Variant Classification Criteria 09 May 2019) | Pathogenic (Aug 14, 2018) | germline | clinical testing | |
SCV001163321 | Baylor Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic | germline | clinical testing | |
SCV001194046 | Myriad Genetics, Inc. | criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019)) | Pathogenic (Nov 18, 2019) | unknown | clinical testing | |
SCV001366363 | Centre for Mendelian Genomics, University Medical Centre Ljubljana | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Apr 5, 2019) | unknown | clinical testing | |
SCV001459950 | Natera, Inc. | no assertion criteria provided | Pathogenic (Sep 16, 2020) | germline | clinical testing | |
SCV002097939 | New York Genome Center - CSER-NYCKidSeq | criteria provided, single submitter (NYGC Assertion Criteria 2020) | Pathogenic (Feb 22, 2021) | inherited | clinical testing | |
SCV002587053 | UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill - CSER_NCGENES_2 | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jul 13, 2021) | unknown | research | |
SCV002767822 | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
| criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Oct 19, 2020) | germline | clinical testing | |
SCV004228772 | GenomeConnect - Invitae Patient Insights Network | no classification provided | not provided | unknown | phenotyping only |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | germline | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | no | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
not provided | germline | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | inherited | unknown | 1 | not provided | not provided | 1 | not provided | clinical testing |
not provided | not provided | not provided | not provided | not provided | not provided | not provided | not provided | curation |
not provided | paternal | yes | 1 | not provided | not provided | 1 | not provided | clinical testing |
not provided | unknown | yes | not provided | not provided | not provided | not provided | not provided | clinical testing, research |
not provided | unknown | unknown | 2 | not provided | not provided | 2 | not provided | clinical testing, research, phenotyping only |
Citations
PubMed
Breedveld GJ, van Wetten B, te Raa GD, Brusse E, van Swieten JC, Oostra BA, Maat-Kievit JA.
J Med Genet. 2004 Nov;41(11):858-66. No abstract available.
- PMID:
- 15520412
- PMCID:
- PMC1735612
TPP1 deficiency: Rare cause of isolated childhood-onset progressive ataxia.
Dy ME, Sims KB, Friedman J.
Neurology. 2015 Oct 6;85(14):1259-61. doi: 10.1212/WNL.0000000000001876. Epub 2015 Jul 29. No abstract available.
- PMID:
- 26224725
Details of each submission
From OMIM, SCV000022921.5
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (4) |
Description
Sleat et al. (1997) described compound heterozygosity in 2 sibs with late-infantile onset of neuronal ceroid lipofuscinosis-2 (CLN2; 204500). One allele of the CLN2 gene carried the R208X nonsense mutation (607998.0003); the other allele showed a splice site mutation, a G-to-C transversion of the consensus AG 3-prime splice acceptor site immediately preceding 523T of the cDNA sequence.
In affected members of a Dutch family with autosomal recessive spinocerebellar ataxia-7 (SCAR7; 609270), originally reported by Breedveld et al. (2004), Sun et al. (2013) identified compound heterozygous mutations in the TPP1 gene: a G-to-C transversion in intron 5 (c.509-1G-C) resulting in a frameshift and premature termination (Val170GlyfsTer29), and V466G (607998.0010). The mutations, which were found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. An unrelated Dutch woman with the disorder was also found to be compound heterozygous for these 2 mutations, although a founder effect could not be confirmed. Residual TPP1 activity in patient lymphocytes was 10 to 15% that of controls, with 5% activity in patient fibroblasts.
In an 11-year-old girl with SCAR7, Dy et al. (2015) identified compound heterozygous mutations in the TPP1 gene: c.509-1G-C, and a missense mutation (E343D; 607998.0011).
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | not provided | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From GeneReviews, SCV000086784.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | curation | not provided |
Description
Converted during submission to Pathogenic.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | not provided | not provided | not provided | not provided | Assert pathogenicity | not provided | not provided | not provided | not provided |
From Courtagen Diagnostics Laboratory, Courtagen Life Sciences, SCV000236538.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-HudsonAlpha, SCV000265553.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | research | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen, SCV000538068.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
he c.509-1G>C variant is one of the most common pathogenic variants associated with LINCL and is found in both the homozygous or compound heterozygous state (Sleat DE et al., 1999; Zhong N et al., 1998; Kousi M et al., 2011). This variant was shown to segregate with disease in a non-consanguineous sib ship and in affected individuals who harbor this variant; enzyme activity in the leukocytes and fibroblasts was very low to almost absent respectively (Sun Y et al., 2013). Furthermore, the frequency of this variant is very low in the population database (1000 Genome, Exome Sequencing Project and ExAC). This locus is conserved across species and several computational algorithms predict the loss of splice-acceptor site in intron 5. Finally, several reputable clinical sources have classified this variant as pathogenic. In summary, the evidence meets our laboratory’s criteria for a Pathogenic classification
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | no | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Genetic Services Laboratory, University of Chicago, SCV000597532.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV000680415.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | paternal | yes | 1 | blood | not provided | 1 | not provided | not provided | not provided |
From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000733090.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000744910.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Illumina Laboratory Services, Illumina, SCV000915544.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (5) |
Description
The TPP1 c.509-1G>C variant occurs in a canonical splice site (acceptor) and is therefore predicted to disrupt or distort the normal gene product. The c.509-1G>C variant is described as one of the two most common pathogenic variants found in individuals with the classical late-infantile form of neuronal ceroid-lipofuscinosis (LINCL), often found in a compound heterozygous state with the other common variant, p.Arg508Ter. Together they account for up to 60% of pathogenic variants in the TPP1 gene (Zhong et al. 1998; Sleat et al. 1999; Steinfeld et al. 2002). Across a selection of the literature, the c.509-1G>C variant was detected in a total of 56 individuals affected with LINCL, including in ten individuals in a homozygous state, in 42 individuals in a compound heterozygous state (two of whom were related) and in four individuals in a heterozygous state in whom a second variant was not detected due to incomplete screening methods. The variant was also found in a heterozygous state in one unaffected family member (Sleat et al. 1997; Zhong et al. 1998; Sleat et al. 1999; Steinfeld et al. 2002). The variant was absent from 32 control chromosomes and is reported at a frequency of 0.001047 in the European American population of the Exome Sequencing Project. The variant results in a significant reduction in TPP1 protease activity to between 0 - 10% of wild type depending on the sample type (Sleat et al. 1999; Steinfeld et al. 2002; Miller et al. 2013). Based on the collective evidence and the potential impact of splice acceptor variants, the c.509-1G>C variant is classified as pathogenic for neuronal ceroid-lipofuscinosis. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Baylor Genetics, SCV001163321.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Myriad Genetics, Inc., SCV001194046.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (3) |
Description
NM_000391.3(TPP1):c.509-1G>C(aka IVS5-1G>C) is classified as pathogenic in the context of TPP1-related neuronal ceroid lipofuscinosis and is associated with the late-infantile form of the disease. Sources cited for classification include the following: PMID 9788728, 11339651 and 18684116. Classification of NM_000391.3(TPP1):c.509-1G>C(aka IVS5-1G>C) is based on the following criteria: The variant is located at a canonical splice site, is expected to disrupt gene function and is reported in individuals with the relevant phenotype. Please note: this variant was assessed in the context of healthy population screening.‚Äã
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001366363.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS1,PP3.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Natera, Inc., SCV001459950.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From New York Genome Center - CSER-NYCKidSeq, SCV002097939.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | inherited | unknown | 1 | not provided | not provided | 1 | not provided | not provided | not provided |
From UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill - CSER_NCGENES_2, SCV002587053.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | research | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | 1 | not provided | not provided | 1 | not provided | not provided | not provided |
From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767822.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (4) |
Description
Based on the classification scheme VCGS_Germline_v1.3.3, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with neuronal ceroid lipofuscinosis 2 (CLN2; MIM#204500). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0210 - Splice site variant proven to affect splicing of the transcript with a known effect on protein sequence. RT-PCR studies showed intron 5 retention, resulting in p.(Val170Glyfs*29) which is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction) (PMID: 23418007). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 113 heterozygotes, 0 homozygotes). (SP) 0701 - Other NMD predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity (ClinVar, Decipher). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It is one of the most commonly reported variants in homozygous and compound heterozygous patients with CLN2 (ClinVar; PMID: 31283065; PMID: 32329550). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. The father has not been tested and the mother (VCGS # 20G001560) has tested negative for this variant. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From GenomeConnect - Invitae Patient Insights Network, SCV004228772.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | phenotyping only | not provided |
Description
Variant interpreted as Pathogenic and reported on 06-16-2020 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | 1 | not provided | not provided | 1 | not provided | not provided | not provided |
Last Updated: May 1, 2024