rs80338933
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Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_024577.4(SH3TC2):c.2860C>T(p.Arg954Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00104 in 1,614,014 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.00064 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 1 hom. )
Consequence
SH3TC2
NM_024577.4 stop_gained
NM_024577.4 stop_gained
Scores
2
3
2
Clinical Significance
Conservation
PhyloP100: 2.63
Genes affected
SH3TC2 (HGNC:29427): (SH3 domain and tetratricopeptide repeats 2) This gene encodes a protein with two N-terminal Src homology 3 (SH3) domains and 10 tetratricopeptide repeat (TPR) motifs, and is a member of a small gene family. The gene product has been proposed to be an adapter or docking molecule. Mutations in this gene result in autosomal recessive Charcot-Marie-Tooth disease type 4C, a childhood-onset neurodegenerative disease characterized by demyelination of motor and sensory neurons. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 5-149026872-G-A is Pathogenic according to our data. Variant chr5-149026872-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2482.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-149026872-G-A is described in Lovd as [Pathogenic]. Variant chr5-149026872-G-A is described in Lovd as [Likely_pathogenic]. Variant chr5-149026872-G-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SH3TC2 | NM_024577.4 | c.2860C>T | p.Arg954Ter | stop_gained | 11/17 | ENST00000515425.6 | NP_078853.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SH3TC2 | ENST00000515425.6 | c.2860C>T | p.Arg954Ter | stop_gained | 11/17 | 1 | NM_024577.4 | ENSP00000423660 | P2 |
Frequencies
GnomAD3 genomes 0.000644 AC: 98AN: 152176Hom.: 0 Cov.: 33
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GnomAD4 genome 0.000644 AC: 98AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.000511 AC XY: 38AN XY: 74346
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:37Other:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Pathogenic:15
| Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jul 21, 2021 | The SH3TC2 c.2860C>T; p.Arg954Ter variant (rs80338933) has been reported in the homozygous and compound heterozygous states in multiple families and individuals diagnosed with Charcot-Marie-Tooth disease type 4C (CMT4C) and was determined to be the most prevalent pathogenic variant in a cohort of CMT4C patients from the Czech Republic (Baets 2011, Høyer 2014, Laššuthová 2011, Lupski 2010, Senderek 2003, Varley 2015). This variant is listed in the Genome Aggregation Database (gnomAD) browser with an allele frequency of 0.12% in the non-Finnish European population (identified in 158 out of 126,576 chromosomes), and is classified as pathogenic in ClinVar (Variant ID: 2482). The p.Arg954Ter variant introduces a premature stop codon in exon 11 and is expected to result in a truncated or absent protein product. Therefore, based on the available evidence, the p.Arg954Ter variant is classified as pathogenic. Baets et al. Genetic spectrum of hereditary neuropathies with onset in the first year of life. Brain. 2011 Sep;134(Pt 9):2664-76. doi: 10.1093/brain/awr184. Epub 2011 Aug 11. Hoyer et al. Genetic diagnosis of Charcot-Marie-Tooth disease in a population by next-generation sequencing. Biomed Res Int. 2014;2014:210401. doi: 10.1155/2014/210401. Epub 2014 Jun 16. Lassuthova et al. High frequency of SH3TC2 mutations in Czech HMSN I patients. Clin Genet. 2011 Oct;80(4):334-45. doi: 10.1111/j.1399-0004.2011.01640.x. Epub 2011 Mar 1. Lupski et al. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med. 2010 Apr 1;362(13):1181-91. doi: 10.1056/NEJMoa0908094. Epub 2010 Mar 10. Senderek et al. Mutations in a gene encoding a novel SH3/TPR domain protein cause autosomal recessive Charcot-Marie-Tooth type 4C neuropathy. Am J Hum Genet. 2003 Nov;73(5):1106-19. Epub 2003 Oct 21. Varley et al. Phenotypic variability of CMT4C in a French-Canadian kindred. Muscle Nerve. 2015 Sep;52(3):444-9. doi: 10.1002/mus.24640. Epub 2015 May 14. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Sep 15, 2021 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 07, 2021 | This variant is expected to result in the loss of a functional protein. The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant has been identified in at least one individual with clinical features associated with this gene. In multiple individuals, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may also be pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Oct 23, 2020 | - - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Clinical Genetics and Genomics, Karolinska University Hospital | Dec 15, 2015 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 19, 2017 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Nov 30, 2023 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Sep 28, 2021 | Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 21840889, 18511281, 28981955, 29243538, 30001926, 28726809, 29653220, 30653784, 30373780, 16924012, 25737037, 23806086, 20220177, 25525159, 25025039, 27231023, 19272779, 27549087, 27296017, 14574644, 29321516, 21291453, 31028937, 31346473, 31634715, 31827005, 31980526, 33386210, 25736553, 34426522, 34169998, 32376792, 31589614, 33643188, 32909314, 33726816) - |
| Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | SH3TC2: PM3:Very Strong, PVS1, PM2, PP4 - |
| Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Clinical Genetics Laboratory, Skane University Hospital Lund | Jul 13, 2022 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 11, 2018 | DNA sequence analysis of the SH3TC2 gene demonstrated a sequence change, c.2860C>T, which results in the creation of a premature stop codon at amino acid position 954, p.Arg954*. This pathogenic sequence change is predicted to result in an abnormal transcript, which may be degraded, or may lead to the production of a truncated SH3TC2 protein with potentially abnormal function. This pathogenic sequence change has previously been described in the homozygous and compound heterozygous state in multiple patients with SH3TC2-related Charcot-Marie-Tooth disease type 4C (Senderek et al., 2003; Houlden et al., 2009.). - |
Charcot-Marie-Tooth disease type 4C Pathogenic:11Other:2
| not provided, no classification provided | literature only | GeneReviews | - | - - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | NeuroMeGen, Hospital Clinico Santiago de Compostela | Oct 08, 2018 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Oct 25, 2023 | Criteria applied: PVS1,PS4_MOD,PM3_SUP - |
| Pathogenic, criteria provided, single submitter | clinical testing | UCLA Clinical Genomics Center, UCLA | Apr 15, 2014 | - - |
| not provided, no classification provided | phenotyping only | GenomeConnect - Invitae Patient Insights Network | - | Variant interpreted as Pathogenic and reported on 07-19-2019 by 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 | Laboratory of Medical Genetics, National & Kapodistrian University of Athens | Feb 22, 2022 | PVS1, PM2, PM3, PP5 - |
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München | Jan 22, 2020 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Genomics England Pilot Project, Genomics England | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | MGZ Medical Genetics Center | Jul 19, 2022 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jun 07, 2023 | Variant summary: SH3TC2 c.2860C>T (p.Arg954X) results in a premature termination codon, predicted to cause absence of the protein due to nonsense mediated decay, which is a commonly known mechanism for disease. The variant allele was found at a frequency of 0.00075 in 251330 control chromosomes. c.2860C>T has been reported in the literature in many individuals affected with Charcot-Marie Disease Type 4C (e.g. Kontogeorgiou_2019), including individuals who were reported as compound heterozygous with another pathogenic variant. These report(s) suggest the variant is likely associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 30653784). 24 submitters have provided clinical-significance assessments for this variant to ClinVar after 2014, and classified it as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. - |
| Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2010 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | 3billion | Sep 01, 2022 | The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.073%). Stop-gained (nonsense) is predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000002482 / PMID: 14574644 / 3billion dataset). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Genetics and Molecular Pathology, SA Pathology | Feb 08, 2022 | The SH3TC2 c.2860C>T variant is classified as PATHOGENIC (PVS1, PS4, PM3, PP1) The SH3TC2 c.2860C>T variant is a single nucleotide change which is predicted to result in premature termination of the protein product at codon 954 (PVS1). This recurrent variant has been previously reported in both homozygous state or as compound heterozygotes with another pathogenic variant in SH3TC2 in patients with CMT4C (PMID:14574644, 20220177) (PS4, PM3). This variant has been reported to co-segregate with disease (PMID:25737037) (PP1). this variant has been reported in dbSNP (rs80338933) and has been reported in population databases (gnomAD 98/152176, no homozygotes). This variant has been reported in ClinVar as pathogenic for CMT4C by multiple other diagnostic laboratories (ClinVar Variation ID:2482) and is damaging in HGMD for CMT4C (CM033084). - |
Susceptibility to mononeuropathy of the median nerve, mild Pathogenic:3
| Pathogenic, criteria provided, single submitter | clinical testing | Knight Diagnostic Laboratories, Oregon Health and Sciences University | Feb 22, 2019 | - - |
| Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2010 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | DASA | Jan 05, 2022 | The c.2860C>T;p.(Arg954*) variant creates a premature translational stop signal in the SH3TC2 gene. It is expected to result in an absent or disrupted protein product -PVS1. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant(Clinvar ID: 2482; PMID: 31346473; 30653784; 27231023; 25737037; 25326637; 25025039; 23806086) - PS4. The p.(Arg954*) was detected in trans with a pathogenic variant (PMID: 31346473; 30653784; 27231023; PMID: 25737037; 25326637; 25025039; 23806086) - PM3_strong. The variant co-segregated with disease in multiple affected family members (PMID: 25737037; 23806086) - PP1_strong and is allele frequency is greater than expected for disorder - BS1. In summary, the currently available evidence indicates that the variant is pathogenic. - |
Charcot-Marie-Tooth disease Pathogenic:2
| Pathogenic, criteria provided, single submitter | clinical testing | Molecular Genetics Laboratory, London Health Sciences Centre | - | - - |
| Pathogenic, no assertion criteria provided | research | Dept. of Medical Genetics, Telemark Hospital Trust, Telemark Hospital Trust | Nov 01, 2013 | Observed in four sporadic individuals - |
SH3TC2-related disorder Pathogenic:2
| Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 26, 2023 | The SH3TC2 c.2860C>T variant is predicted to result in premature protein termination (p.Arg954*). This variant has been reported in the compound heterozygous and homozygous state to be causative for Charcot-Marie-Tooth disease (Baets et al. 2011. PubMed ID: 21840889; Høyer et al. 2014. PubMed ID: 25025039; Lupski et al. 2010. PubMed ID: 20220177). Although individuals heterozygous for the c.2860C>T (p.Arg954*) variant did not have Charcot-Marie-Tooth disease, they were reported to be at increased risk for developing neuropathy including carpal tunnel syndrome (Lupski et al. 2010. PubMed ID: 20220177). This variant is reported in 0.12% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Nonsense variants in SH3TC2 are expected to be pathogenic. This variant is interpreted as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 20, 2018 | The SH3TC2 c.2860C>T (p.Arg954Ter) variant is a stop-gained variant and is predicted to result in premature termination of the protein. The p.Arg954Ter variant is reported in at least nine studies associated with Charcot-Marie-Tooth, type 4, and found in a total of 39 unrelated patients including 26 homozygotes and 13 compound heterozygote (Senderek et al. 2003; Azzedine et al. 2006; Lupo et al. 2009; Gosselin et al. 2008; Houlden et al. 2009; Lupski et al. 2010; Baets et al. 2011; Hoyer et al. 2014; Varley et al. 2015). The p.Arg954Ter variant is reported once in association with mononeuropathy of the median nerve. Lupski et al. (2010) report a family affected with autosomal recessive Charcot-Marie-Tooth, type 4 which includes three family members who are heterozygous for the p.Arg954Ter variant and present with a subtle mild mononeuropathy of the median nerve. The p.Arg954Ter variant has been shown to segregate with disease in a recessive inheritance pattern in at least two families (Lupski et al. 2010; Varley et al. 2015). The variant was reported in five of 180 controls in a heterozygous state, consistent with carrier status, and at a frequency of 0.00141 in the European (non-Finnish) population of the Exome Aggregation Consortium. Based on the collective evidence and potential impact of stop-gained variants, the p.Arg954Ter variant is classified as pathogenic for SH3TC2-related disorders. It is most frequently described in association with autosomal recessive Charcot-Marie-Tooth, type 4, but has also been described in association with a mild presentation of dominantly inherited mononeuropathy of the median nerve. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. - |
Inborn genetic diseases Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2023 | The c.2860C>T (p.R954*) alteration, located in exon 11 (coding exon 11) of the SH3TC2 gene, consists of a C to T substitution at nucleotide position 2860. This changes the amino acid from a arginine (R) to a stop codon at amino acid position 954. Premature stop codons are typically deleterious in nature (Richards, 2015). Based on data from gnomAD, the T allele has an overall frequency of 0.073% (206/282718) total alleles studied. The highest observed frequency was 0.125% (9/7224) of Other alleles. This alteration has been reported either homozygous or compound heterozygous with another SH3TC2 variant in multiple individuals with Charcot-Marie-Tooth (CMT) disease and presenting with similar symptoms as the proband (Senderek, 2003; Lupski, 2010; Baets, 2011; Høyer, 2014; Laššuthová, 2016). This mutation is reported to cause CMT1 in several different populations (Høyer, 2014). Based on the available evidence, this alteration is classified as pathogenic. - |
Charcot-Marie-Tooth disease type 4C;C3150596:Susceptibility to mononeuropathy of the median nerve, mild Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 08, 2022 | - - |
Tip-toe gait Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Practice for Gait Abnormalities, David Pomarino, Competency Network Toe Walking c/o Practice Pomarino | Oct 26, 2021 | Hereditary motor sensory neuropathy (HMSN), also known as Charcot-Marie-Tooth Disease (CMT), is the most commonly inherited peripheral polyneuropathy. It constitutes a group of inherited, progressive, motor and sensory peripheral nerve disorders with properties of demyelination, axonal degeneration, or both. It is classified by clinical characteristics, modes of inheritance, electrophysiologic features, metabolic defects, and specific gene markers. Our patients all walk on tiptoe, so they show similar symptoms. When we genetically test them with our toe walking panel, we find that around 90 per cent of them have a genetic variant that explains their toe walking. These can be assigned, for example, to the area of myopathies (such as variants of the COL6A3 gene), the area of hereditary neuropathies (such as variants of the KMT2C gene) or the area of metabolic diseases (such as variants of the PYGM gene). In a smaller group of patients with almost identical symptoms, no abnormality is found in the genes of our panel, but spastic paraplegia can be detected. In another small group of our toe walkers, no abnormalities can be detected in the genes analysed in our toe walking panel, nor do they suffer from spastic paraplegia, as is also the case with healthy children. In contrast to these, however, they show a tiptoe gait. These patients suffer from infantile cerebral palsy, in which toe walking can also be observed. - |
Charcot-Marie-Tooth disease type 4 Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | This sequence change creates a premature translational stop signal (p.Arg954*) in the SH3TC2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SH3TC2 are known to be pathogenic (PMID: 20220177, 27068304). This variant is present in population databases (rs80338933, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This premature translational stop signal has been observed in individual(s) with Charcot-Marie-Tooth disease (PMID: 14574644, 16924012, 18511281, 19272779). It is commonly reported in individuals of French-Canadian ancestry (PMID: 18511281). ClinVar contains an entry for this variant (Variation ID: 2482). 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. - |
Computational scores
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BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
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Pathogenic
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Uncertain
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Uncertain
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Benign
D
MutationTaster
Benign
A;A;A;D
Vest4
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at