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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 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no 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:
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)

Name:
Neuronal ceroid lipofuscinosis 2
Synonyms:
JANSKY-BIELSCHOWSKY DISEASE NEURONAL CEROID LIPOFUSCINOSIS, LATE INFANTILE; TPP1-Related Neuronal Ceroid-Lipofuscinosis
Identifiers:
MONDO: MONDO:0008769; MedGen: C1876161; Orphanet: 168491; Orphanet: 228349; Orphanet: 79264; OMIM: 204500

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000022921OMIM
no assertion criteria provided
Pathogenic
(May 1, 2013)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV000086784GeneReviews
no assertion criteria provided
pathologic
(Aug 1, 2013)
not providedcuration

SCV000236538Courtagen Diagnostics Laboratory, Courtagen Life Sciences
criteria provided, single submitter

(Courtagen Life Sciences Classifications)
Pathogenic
(Jan 13, 2014)
germlineclinical testing

Citation Link,

SCV000265553HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-HudsonAlpha
criteria provided, single submitter

(HA_assertions_20161101)
Pathogenic
(Feb 10, 2015)
unknownresearch

HA_assertions_20161101.pdf,

Citation Link,

SCV000538068Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 23, 2015)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000597532Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 22, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000680415Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
criteria provided, single submitter

(Classification criteria August 2017)
Pathogenic
(Nov 8, 2017)
paternalclinical testing

Citation Link,

SCV000733090Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus
no assertion criteria provided
Pathogenicgermlineclinical testing

SCV000744910Clinical 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)
germlineclinical testing

Citation Link,

SCV000915544Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)
Pathogenic
(Aug 14, 2018)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Citation Link,

SCV001163321Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001194046Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019))
Pathogenic
(Nov 18, 2019)
unknownclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV001366363Centre for Mendelian Genomics, University Medical Centre Ljubljana
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 5, 2019)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001459950Natera, Inc.
no assertion criteria provided
Pathogenic
(Sep 16, 2020)
germlineclinical testing

SCV002097939New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)
Pathogenic
(Feb 22, 2021)
inheritedclinical testing

Citation Link,

SCV002587053UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill - CSER_NCGENES_2
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 13, 2021)
unknownresearch

PubMed (1)
[See all records that cite this PMID]

SCV002767822Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 19, 2020)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV004228772GenomeConnect - Invitae Patient Insights Network
no classification provided
not providedunknownphenotyping only

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedinheritedunknown1not providednot provided1not providedclinical testing
not providednot providednot providednot providednot providednot providednot providednot providedcuration
not providedpaternalyes1not providednot provided1not providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing, research
not providedunknownunknown2not providednot provided2not providedclinical testing, research, phenotyping only

Citations

PubMed

A new locus for a childhood onset, slowly progressive autosomal recessive spinocerebellar ataxia maps to chromosome 11p15.

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.

PubMed [citation]
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.

PubMed [citation]
PMID:
26224725
See all PubMed Citations (13)

Details of each submission

From OMIM, SCV000022921.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature 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).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From GeneReviews, SCV000086784.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

Converted during submission to Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providednot providednot providednot providedAssert pathogenicitynot providednot providednot providednot provided

From Courtagen Diagnostics Laboratory, Courtagen Life Sciences, SCV000236538.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-HudsonAlpha, SCV000265553.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen, SCV000538068.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

From Genetic Services Laboratory, University of Chicago, SCV000597532.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV000680415.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1paternalyes1bloodnot provided1not providednot providednot provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000733090.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000744910.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV000915544.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV001163321.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Myriad Genetics, Inc., SCV001194046.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001366363.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS1,PP3.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001459950.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From New York Genome Center - CSER-NYCKidSeq, SCV002097939.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

From UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill - CSER_NCGENES_2, SCV002587053.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknown1not providednot provided1not providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767822.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GenomeConnect - Invitae Patient Insights Network, SCV004228772.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedphenotyping onlynot 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknown1not providednot provided1not providednot providednot provided

Last Updated: May 1, 2024