11-6617154-C-G
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Variant summary
Our verdict is Pathogenic. Variant got 22 ACMG points: 22P and 0B. PVS1PM2PP3_StrongPP5_Very_Strong
The NM_000391.4(TPP1):c.509-1G>C variant causes a splice acceptor change. The variant allele was found at a frequency of 0.00126 in 1,613,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Genomes: 𝑓 0.00049 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 0 hom. )
Consequence
TPP1
NM_000391.4 splice_acceptor
NM_000391.4 splice_acceptor
Scores
5
1
1
Splicing: ADA: 1.000
2
Clinical Significance
Conservation
PhyloP100: 4.61
Genes affected
TPP1 (HGNC:2073): (tripeptidyl peptidase 1) This gene encodes a member of the sedolisin family of serine proteases. The protease functions in the lysosome to cleave N-terminal tripeptides from substrates, and has weaker endopeptidase activity. It is synthesized as a catalytically-inactive enzyme which is activated and auto-proteolyzed upon acidification. Mutations in this gene result in late-infantile neuronal ceroid lipofuscinosis, which is associated with the failure to degrade specific neuropeptides and a subunit of ATP synthase in the lysosome. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 22 ACMG points.
PVS1
Splicing variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
PM2
Very rare variant in population databases, with high coverage;
PP3
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
PP5
Variant 11-6617154-C-G is Pathogenic according to our data. Variant chr11-6617154-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 2644.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-6617154-C-G is described in Lovd as [Pathogenic]. Variant chr11-6617154-C-G is described in Lovd as [Pathogenic]. Variant chr11-6617154-C-G is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| TPP1 | NM_000391.4 | c.509-1G>C | splice_acceptor_variant | ENST00000299427.12 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TPP1 | ENST00000299427.12 | c.509-1G>C | splice_acceptor_variant | 1 | NM_000391.4 | P1 |
Frequencies
GnomAD3 genomes 0.000486 AC: 74AN: 152114Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000402 AC: 101AN: 251364Hom.: 0 AF XY: 0.000368 AC XY: 50AN XY: 135878
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GnomAD4 exome AF: 0.00134 AC: 1960AN: 1461866Hom.: 0 Cov.: 41 AF XY: 0.00127 AC XY: 927AN XY: 727242
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GnomAD4 genome 0.000486 AC: 74AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.000404 AC XY: 30AN XY: 74308
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:35Other:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Neuronal ceroid lipofuscinosis 2 Pathogenic:17Other:1
| Pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Nov 18, 2019 | 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 - |
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München | Nov 08, 2017 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | - | - - |
| not provided, no classification provided | phenotyping only | GenomeConnect - Invitae Patient Insights Network | - | 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. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Knight Diagnostic Laboratories, Oregon Health and Sciences University | Oct 23, 2015 | 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 - |
| Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Apr 05, 2019 | This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS1,PP3. - |
| Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 2013 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Courtagen Diagnostics Laboratory, Courtagen Life Sciences | Jan 13, 2014 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Aug 14, 2018 | 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. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | Oct 19, 2020 | 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 - |
| Pathogenic, criteria provided, single submitter | clinical testing | New York Genome Center | Feb 22, 2021 | - - |
| Pathogenic, criteria provided, single submitter | research | UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill | Jul 13, 2021 | - - |
| Pathogenic, no assertion criteria provided | curation | GeneReviews | Aug 01, 2013 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Sep 21, 2015 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 22, 2016 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
| Pathogenic, criteria provided, single submitter | research | HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology | Feb 10, 2015 | - - |
not provided Pathogenic:11
| Pathogenic, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Mar 13, 2018 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 16, 2017 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | This sequence change affects an acceptor splice site in intron 5 of the TPP1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in TPP1 are known to be pathogenic (PMID: 10330339). This variant is present in population databases (rs56144125, gnomAD 0.08%). Disruption of this splice site has been observed in individuals with late-infantile neuronal ceroid lipofuscinosis (PMID: 9295267, 9788728, 10330339, 12376936). This variant is also known as c.523-1G>C, c.3556G>C or IVS5-1G>C. ClinVar contains an entry for this variant (Variation ID: 2644). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 26, 2017 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | TPP1: PVS1, PP1, PS3:Supporting - |
| Pathogenic, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jan 28, 2022 | Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Different variant affecting the same splice site (c.509-1G>A) has been reported as pathogenic in the Human Gene Mutation Database and at GeneDx in association with NCL (Stenson et al., 2014); This variant is associated with the following publications: (PMID: 26026925, 26143525, 25976102, 26795593, 28335910, 10330339, 9788728, 26224725, 28554332, 9295267, 29056246, 29631617, 29655203, 30283815, 30548430, 31487502, 32631363, 31980526, 33845243, 12376936, 32298681, 31589614, 21990111, 23539563, 35054396, 34831035) - |
| Pathogenic, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Feb 16, 2023 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Nov 03, 2021 | - - |
Autosomal recessive spinocerebellar ataxia 7;C1876161:Neuronal ceroid lipofuscinosis 2 Pathogenic:2Other:1
| Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 26, 2022 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
| not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpreted as Pathogenic and reported on 07/28/2014 by Lab or GTR ID 1006. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Neuronal ceroid lipofuscinosis Pathogenic:2
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 10, 2017 | Variant summary: The TPP1 c.509-1G>C variant (also known as G3556C) involves the alteration of a highly conserved nucleotide at canonical splice acceptor site in intron 5. 5/5 splice prediction tools predict abrogation of the splice-site. This variant was found in 43/121262 control chromosomes from ExAC at a frequency of 0.0003546, which does not exceed the estimated maximal expected allele frequency of a pathogenic TPP1 variant (0.002958). This variant is one of the most common pathogenic variants associated with LINCL and is found in both the homozygous and compound heterozygous state, including evidence of cosegregation with disease (Sleat_ 1999; Ju_2002; Worgall_2007). Enzyme activity in the in patients carrying this variant was very low to absent, suggesting it leads to loss of protein function (Sleat_1999). In addition, several clinical diagnostic laboratories/reputable databases have classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. - |
| Pathogenic, no assertion criteria provided | clinical testing | Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital | May 03, 2012 | - - |
Autosomal recessive spinocerebellar ataxia 7 Pathogenic:1
| Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 2013 | - - |
Inborn genetic diseases Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 23, 2018 | The c.509-1G>C intronic pathogenic mutation results from a G to C substitution one nucleotide upstream from coding exon 6 of the TPP1 gene. This mutation has been well described as one of the most common mutations causing late infantile neuronal ceroid lipofuscinosis (CLN2), having been reported in the homozygous and compound heterozygous state in numerous affected individuals across various ethnic backgrounds (Williams RE et al. Pediatr. Neurol., 2017 Apr;69:102-112; Sleat DE et al. Am. J. Hum. Genet. 1999;64(6):1511-23, Zhong N et al. Clin. Genet. 1998;54(3):234-8). This mutation has also been reported in individuals with autosomal recessive spinocereballar ataxia (SCAR7) (Dy ME, et al. Neurology 2015;85(14):1259-61). In one RNA study, RT-PCR analysis revealed retention of intron 5, resulting in a frameshift and premature protein truncation. Furthermore, residual enzyme activity in probands was reduced to 9% in CLN2 and 15% in SCAR7 compared to unaffected family members (Miller JN et al. Hum. Mol. Genet. 2013;22(13):2723-34). Based on the available evidence, c.509-1G>C is classified as a pathogenic mutation. - |
TPP1-related disorder Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 28, 2024 | The TPP1 c.509-1G>C variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant (also known as G3556C) has been reported as causative for neuronal ceroid lipofuscinosis in the homozygous and compound heterozygous states (Sleat et al. 1997. PubMed ID: 9295267; Sleat et al. 1999. PubMed ID: 10330339; Miller et al. 2013. PubMed ID: 23539563). This variant is reported in 0.081% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Variants that disrupt the consensus splice acceptor site in TPP1 are expected to be pathogenic. This variant is interpreted as pathogenic. - |
Computational scores
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Name
Calibrated prediction
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BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
MutationTaster
Benign
D;D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
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DS_AL_spliceai
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at