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    TECPR2 tectonin beta-propeller repeat containing 2 [ Homo sapiens (human) ]

    Gene ID: 9895, updated on 5-Mar-2024

    Summary

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    Official Symbol
    TECPR2provided by HGNC
    Official Full Name
    tectonin beta-propeller repeat containing 2provided by HGNC
    Primary source
    HGNC:HGNC:19957
    See related
    Ensembl:ENSG00000196663 MIM:615000; AllianceGenome:HGNC:19957
    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
    HSAN9; SPG49; KIAA0329
    Summary
    The protein encoded by this gene is a member of the tectonin beta-propeller repeat-containing (TECPR) family, and contains both TECPR and tryptophan-aspartic acid repeat (WD repeat) domains. This gene has been implicated in autophagy, as reduced expression levels of this gene have been associated with impaired autophagy. Recessive mutations in this gene have been associated with a hereditary form of spastic paraparesis (HSP). HSP is characterized by progressive spasticity and paralysis of the legs. There is also some evidence linking mutations in this gene with birdshot chorioretinopathy (BSCR), which results in inflammation of the choroid and retina. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]
    Expression
    Ubiquitous expression in brain (RPKM 5.6), testis (RPKM 5.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    14q32.31
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (102362941..102502477)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (96598536..96738379)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (102829278..102968814)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9070 Neighboring gene zinc finger protein 839 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6114 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6115 Neighboring gene uncharacterized LOC124903389 Neighboring gene cyclin dependent kinase 2 interacting protein Neighboring gene uncharacterized LOC124903440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9071 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9072 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:102877147-102878136 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6116 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:102906165-102906672 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:102974901-102975062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:102976187-102976830 Neighboring gene uncharacterized LOC105370679 Neighboring gene RNA, U6 small nuclear 244, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:102976831-102977476 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:102977477-102978120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6119 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6120 Neighboring gene uncharacterized LOC105370680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9073 Neighboring gene ankyrin repeat domain 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6121 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:102995075-102995576

    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. TECPR2-Related Hereditary Sensory and Autonomic Neuropathy with Intellectual Disability. Adam MP, et al. , 1993. PMID 36137062
    2. Multimodal bioinformatic analyses of the neurodegenerative disease-associated TECPR2 gene reveal its diverse roles. Shalev I, et al. J Med Genet, 2022 Oct. PMID 34933910
    3. Clinical, neuroimaging, and molecular spectrum of TECPR2-associated hereditary sensory and autonomic neuropathy with intellectual disability. Neuser S, et al. Hum Mutat, 2021 Jun. PMID 33847017
    4. Lysosomal targeting of autophagosomes by the TECPR domain of TECPR2. Fraiberg M, et al. Autophagy, 2021 Oct. PMID 33213269, Free PMC Article
    5. Neuropathology-driven Whole-genome Sequencing Study Points to Novel Candidate Genes for Healthy Brain Aging. Alexander J, et al. Alzheimer Dis Assoc Disord, 2019 Jan-Mar. PMID 30681437

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Multimodal bioinformatic analyses of the neurodegenerative disease-associated TECPR2 gene reveal its diverse roles.
      Title: Multimodal bioinformatic analyses of the neurodegenerative disease-associated TECPR2 gene reveal its diverse roles.
    2. Lysosomal targeting of autophagosomes by the TECPR domain of TECPR2.
      Title: Lysosomal targeting of autophagosomes by the TECPR domain of TECPR2.
    3. Clinical, neuroimaging, and molecular spectrum of TECPR2-associated hereditary sensory and autonomic neuropathy with intellectual disability.
      Title: Clinical, neuroimaging, and molecular spectrum of TECPR2-associated hereditary sensory and autonomic neuropathy with intellectual disability.
    4. The first was the Tectonin beta-propeller repeat containing 2 gene (TECPR2), with allele G on rs10149146 present in 15 controls and no AD cases. The Fisher exact test revealed statistically significant association to healthy brain aging with SNP rs10149146 on TECPR2 (P-value=4.055e-4).
      Title: Neuropathology-driven Whole-genome Sequencing Study Points to Novel Candidate Genes for Healthy Brain Aging.
    5. Whole exome sequencing in an Italian pedigree suggests involvement of TECPR2 in a complex form of progressive motor neuron disease.
      Title: WES in a family trio suggests involvement of TECPR2 in a complex form of progressive motor neuron disease.
    6. The discovery of additional TECPR2 utations in non-Bukharian patients implies that this disease might be more common than previously appreciated
      Title: TECPR2 mutations cause a new subtype of familial dysautonomia like hereditary sensory autonomic neuropathy with intellectual disability.
    7. Results show that TECPR2 associates with several trafficking components as SEC24D and cooperates with LC3C to regulate ER exit sites and ER export suggesting that TECPR2 functions as molecular scaffold linking early secretion pathway and autophagy.
      Title: TECPR2 Cooperates with LC3C to Regulate COPII-Dependent ER Export.
    8. The discovered TECPR2 mutation implicates autophagy, a central intracellular mechanism, in spastic paraparesis.
      Title: Mutation in TECPR2 reveals a role for autophagy in hereditary spastic paraparesis.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies a functional ERAP2 haplotype associated with birdshot chorioretinopathy.
    EBI GWAS Catalog

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0297, KIAA0329

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein exit from endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein exit from endoplasmic reticulum IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    tectonin beta-propeller repeat-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_042851.1 RefSeqGene

      Range
      5030..144566
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001172631.3 → NP_001166102.1  tectonin beta-propeller repeat-containing protein 2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents use of an alternate 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AB002327, AL137229, BC142667, BP365224
      Consensus CDS
      CCDS58337.1
      UniProtKB/Swiss-Prot
      O15040
      Related
      ENSP00000453671.1, ENST00000558678.1
      Conserved Domains (3) summary
      COG2319
      Location:36 → 365
      WD40; WD40 repeat [General function prediction only]
      pfam06462
      Location:996 → 1026
      Hyd_WA; Propeller
      sd00039
      Location:37 → 73
      7WD40; WD40 repeat [structural motif]

    2. NM_014844.5 → NP_055659.2  tectonin beta-propeller repeat-containing protein 2 isoform 1

      See identical proteins and their annotated locations for NP_055659.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB002327, AL136293, AL137229, BC136647, BP365224, BQ023338
      Consensus CDS
      CCDS32162.1
      UniProtKB/Swiss-Prot
      A5PKY3, A6NFY9, A7E2X3, H0YMM9, O15040, Q9UEG6
      Related
      ENSP00000352510.7, ENST00000359520.12
      Conserved Domains (4) summary
      smart00706
      Location:1347 → 1379
      TECPR; Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins
      COG2319
      Location:36 → 365
      WD40; WD40 repeat [General function prediction only]
      pfam06462
      Location:1324 → 1352
      Hyd_WA; Propeller
      sd00039
      Location:37 → 73
      7WD40; WD40 repeat [structural motif]

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      102362941..102502477
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      96598536..96738379
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O15040.4 GenPept UniProtKB/Swiss-Prot:O15040

    Gene LinkOut

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