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    SH3TC2 SH3 domain and tetratricopeptide repeats 2 [ Homo sapiens (human) ]

    Gene ID: 79628, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SH3TC2provided by HGNC
    Official Full Name
    SH3 domain and tetratricopeptide repeats 2provided by HGNC
    Primary source
    HGNC:HGNC:29427
    See related
    Ensembl:ENSG00000169247 MIM:608206; AllianceGenome:HGNC:29427
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MNMN; CMT4C
    Summary
    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]
    Expression
    Biased expression in testis (RPKM 1.4), brain (RPKM 0.6) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    5q32
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (148982150..149063062, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (149516997..149597907, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (148361713..148442625, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986462 Neighboring gene 5-hydroxytryptamine receptor 4 Neighboring gene NANOG hESC enhancer GRCh37_chr5:148099086-148099657 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23365 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23368 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148206489-148207074 Neighboring gene adrenoceptor beta 2 Neighboring gene MPRA-validated peak5531 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:148289701-148290900 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82030 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:148335980-148336552 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:148349629-148350210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148358305-148358824 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:148363540-148364739 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82036 Neighboring gene Sharpr-MPRA regulatory region 10809 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:148452563-148453762 Neighboring gene RNA, U6 small nuclear 732, pseudogene Neighboring gene SH3TC2 divergent transcript Neighboring gene microRNA 584 Neighboring gene RN7SK pseudogene 145

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Screening for SH3TC2 variants in Charcot-Marie-Tooth disease in a cohort of Chinese patients. Sun B, et al. Acta Neurol Belg, 2022 Oct. PMID 33587240
    2. Implication of the SH3TC2 gene in Charcot-Marie-Tooth disease associated with deafness and/or scoliosis: Illustration with four new pathogenic variants. Lerat J, et al. J Neurol Sci, 2019 Nov 15. PMID 31634715
    3. Compound heterozygous mutations of SH3TC2 in Charcot-Marie-Tooth disease type 4C patients. Lee AJ, et al. J Hum Genet, 2019 Sep. PMID 31227790
    4. Mutational screening of the SH3TC2 gene in Greek patients with suspected demyelinating recessive Charcot-Marie-Tooth disease reveals a varied and unusual phenotypic spectrum. Kontogeorgiou Z, et al. J Peripher Nerv Syst, 2019 Mar. PMID 30653784
    5. Charcot-Marie-Tooth Disease type 4C: Novel mutations, clinical presentations, and diagnostic challenges. Jerath NU, et al. Muscle Nerve, 2018 May. PMID 28981955, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Characterisation of Patients with SH3TC2 Associated Neuropathy in an Indian Cohort.
      Title: Characterisation of Patients with SH3TC2 Associated Neuropathy in an Indian Cohort.
    2. Evaluation of Pathogenicity and Causativity of Variants in the MPZ and SH3TC2 Genes in a Family Case of Hereditary Peripheral Neuropathy.
      Title: Evaluation of Pathogenicity and Causativity of Variants in the MPZ and SH3TC2 Genes in a Family Case of Hereditary Peripheral Neuropathy.
    3. Screening for SH3TC2 variants in Charcot-Marie-Tooth disease in a cohort of Chinese patients.
      Title: Screening for SH3TC2 variants in Charcot-Marie-Tooth disease in a cohort of Chinese patients.
    4. Implication of the SH3TC2 gene in Charcot-Marie-Tooth disease associated with deafness and/or scoliosis: Illustration with four new pathogenic variants.
      Title: Implication of the SH3TC2 gene in Charcot-Marie-Tooth disease associated with deafness and/or scoliosis: Illustration with four new pathogenic variants.
    5. Mutations in SH3TC2 are responsible for 26% of Greek patients with suspected CMT4C.
      Title: Mutational screening of the SH3TC2 gene in Greek patients with suspected demyelinating recessive Charcot-Marie-Tooth disease reveals a varied and unusual phenotypic spectrum.
    6. Compound heterozygous mutations of SH3TC2 in Charcot-Marie-Tooth disease type 4C patients.
      Title: Compound heterozygous mutations of SH3TC2 in Charcot-Marie-Tooth disease type 4C patients.
    7. This present clinical and physiologic features of 5 patients with CMT4C caused by biallelic private mutations of SH3TC2.
      Title: Charcot-Marie-Tooth Disease type 4C: Novel mutations, clinical presentations, and diagnostic challenges.
    8. SH3TC2, PMP2, and BSCL2 pathogenic variants might be rare in Chinese Charcot-Marie-Tooth (CMT) patients.
      Title: Screening for SH3TC2, PMP2, and BSCL2 Variants in a Cohort of Chinese Patients with Charcot-Marie-Tooth.
    9. In this series of undiagnosed CMT4 patients, SH3TC2 mutation frequency is 30%, confirming that CMT4C may be the most common AR-CMT type.
      Title: Screening for SH3TC2 gene mutations in a series of demyelinating recessive Charcot-Marie-Tooth disease (CMT4).
    10. Charcot-Marie-Tooth disease type 4C (CMT4C) is an autosomal recessive demyelinating form of CMT characterized clinically by early onset and severe spinal deformities, and is caused by mutations in SH3TC2.
      Title: Novel mutations in SH3TC2 in a young Japanese girl with Charcot-Marie-Tooth disease type 4C.
    Submit: New GeneRIF Correction See all GeneRIFs (27)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    General gene information

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    Markers

    Potential readthrough

    Included gene: HTR4

    Homology

    Clone Names

    • FLJ13605, KIAA1985

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in peripheral nervous system myelin maintenance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of ERBB signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    SH3 domain and tetratricopeptide repeat-containing protein 2
    Names
    SH3 domain and tetratricopeptide repeats-containing protein 2

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_007947.2 RefSeqGene

      Range
      5001..86025
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_269

    mRNA and Protein(s)

    1. NM_024577.4 → NP_078853.2  SH3 domain and tetratricopeptide repeat-containing protein 2

      See identical proteins and their annotated locations for NP_078853.2

      Status: REVIEWED

      Source sequence(s)
      AC011364, AC116312, AF086088, AY341075
      Consensus CDS
      CCDS4293.1
      UniProtKB/Swiss-Prot
      B3KWE5, Q14CC0, Q14CF5, Q8TF17, Q9H8I5
      UniProtKB/TrEMBL
      A0A514TP98, E9PDF1
      Related
      ENSP00000423660.1, ENST00000515425.6
      Conserved Domains (5) summary
      sd00006
      Location:1127 → 1154
      TPR; TPR repeat [structural motif]
      pfam13424
      Location:834 → 906
      TPR_12; Tetratricopeptide repeat
      pfam00515
      Location:1168 → 1197
      TPR_1; Tetratricopeptide repeat
      pfam17874
      Location:811 → 1048
      TPR_MalT; MalT-like TPR region
      cl17036
      Location:272 → 326
      SH3; Src Homology 3 domain superfamily

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      148982150..149063062 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      149516997..149597907 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TF17.2 GenPept UniProtKB/Swiss-Prot:Q8TF17

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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