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    TTC39B tetratricopeptide repeat domain 39B [ Homo sapiens (human) ]

    Gene ID: 158219, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TTC39Bprovided by HGNC
    Official Full Name
    tetratricopeptide repeat domain 39Bprovided by HGNC
    Primary source
    HGNC:HGNC:23704
    See related
    Ensembl:ENSG00000155158 MIM:613574; AllianceGenome:HGNC:23704
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    C9orf52
    Summary
    Predicted to be involved in several processes, including cholesterol homeostasis; negative regulation of cholesterol storage; and regulation of cholesterol efflux. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 3.7), gall bladder (RPKM 3.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TTC39B in Genome Data Viewer
    Location:
    9p22.3
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (15163622..15307216, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (15175161..15318914, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (15163620..15307214, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902123 Neighboring gene RNA, U6 small nuclear 559, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr9:15175934-15176435 Neighboring gene Sharpr-MPRA regulatory region 7105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19777 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:15305852-15306415 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:15306979-15307541 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:15354881-15355722 Neighboring gene ribosomal protein L7 pseudogene 33 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:15418920-15419420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28214 Neighboring gene RNA, U6 small nuclear 319, pseudogene Neighboring gene small nuclear RNA activating complex polypeptide 3

    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 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. Common variants upstream of KDR encoding VEGFR2 and in TTC39B associate with endometriosis. Steinthorsdottir V, et al. Nat Commun, 2016 Jul 25. PMID 27453397, Free PMC Article
    2. Lipids, obesity and gallbladder disease in women: insights from genetic studies using the cardiovascular gene-centric 50K SNP array. Rodriguez S, et al. Eur J Hum Genet, 2016 Jan. PMID 25920552, Free PMC Article
    3. A genome-wide association study of seasonal pattern mania identifies NF1A as a possible susceptibility gene for bipolar disorder. Lee HJ, et al. J Affect Disord, 2013 Feb 20. PMID 22925353, Free PMC Article
    4. Common variants in the calcium-sensing receptor gene are associated with total serum calcium levels. O'Seaghdha CM, et al. Hum Mol Genet, 2010 Nov 1. PMID 20705733, Free PMC Article
    5. Genetic loci associated with lipid concentrations and cardiovascular risk factors in the Korean population. Park MH, et al. J Med Genet, 2011 Jan. PMID 20972250

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. association of rs519664[T] in TTC39B on 9p22 with endometriosis, is reported.
      Title: Common variants upstream of KDR encoding VEGFR2 and in TTC39B associate with endometriosis.
    2. Two new polymorphisms associated with gall bladder disease and obesity in women have been identified, GCKR rs1260326, and TTC39B rs686030.
      Title: Lipids, obesity and gallbladder disease in women: insights from genetic studies using the cardiovascular gene-centric 50K SNP array.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic loci associated with lipid concentrations and cardiovascular risk factors in the Korean population.
    4. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Evaluating the discriminative power of multi-trait genetic risk scores for type 2 diabetes in a northern Swedish population.
    5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    6. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Biological, clinical and population relevance of 95 loci for blood lipids.
    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 of seasonal pattern mania identifies NF1A as a possible susceptibility gene for bipolar disorder.
    EBI GWAS Catalog
    A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
    EBI GWAS Catalog
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog
    Common variants at 30 loci contribute to polygenic dyslipidemia.
    EBI GWAS Catalog
    Common variants in the calcium-sensing receptor gene are associated with total serum calcium levels.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog
    Genetic variants influencing circulating lipid levels and risk of coronary artery disease.
    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

    • FLJ33868

    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 cholesterol homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cholesterol homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cholesterol storage IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of cholesterol storage ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cholesterol efflux IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cholesterol efflux ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cholesterol metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cholesterol metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    tetratricopeptide repeat protein 39B
    Names
    TPR repeat protein 39B

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001168339.2 → NP_001161811.2  tetratricopeptide repeat protein 39B isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AL591393
      UniProtKB/Swiss-Prot
      A5PLN1, B4DQ10, B4DQX4, B4DW93, Q5VTQ0, Q8IVR7, Q8IXZ6, Q8N267
      Conserved Domains (1) summary
      pfam13424
      Location:526 → 590
      TPR_12; Tetratricopeptide repeat

    2. NM_001168340.2 → NP_001161812.2  tetratricopeptide repeat protein 39B isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has multiple differences in the central coding region but maintains the reading frame, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
      Source sequence(s)
      AL591393
      Consensus CDS
      CCDS55296.2
      UniProtKB/Swiss-Prot
      A5PLN1, B4DQ10, B4DQX4, B4DW93, Q5VTQ0, Q8IVR7, Q8IXZ6, Q8N267
      UniProtKB/TrEMBL
      A0A8V8NCV2
      Related
      ENSP00000370231.5, ENST00000380850.9
      Conserved Domains (1) summary
      pfam13424
      Location:515 → 579
      TPR_12; Tetratricopeptide repeat

    3. NM_001168341.2 → NP_001161813.2  tetratricopeptide repeat protein 39B isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 4, which is shorter than isoform 1.
      Source sequence(s)
      AL591393
      Consensus CDS
      CCDS55295.2
      UniProtKB/Swiss-Prot
      A5PLN1, B4DQ10, B4DQX4, B4DW93, Q5VTQ0, Q8IVR7, Q8IXZ6, Q8N267
      UniProtKB/TrEMBL
      A0A8V8N5K5
      Related
      ENSP00000297615.6, ENST00000297615.10
      Conserved Domains (1) summary
      pfam13424
      Location:459 → 523
      TPR_12; Tetratricopeptide repeat

    4. NM_001168342.2 → NP_001161814.1  tetratricopeptide repeat protein 39B isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at an in-frame downstream AUG and result an isoform (5) with a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AI473911, AK301427, AK310271, AL591393, BC142985, BX105862, DT217817
      Consensus CDS
      CCDS55294.1
      UniProtKB/Swiss-Prot
      Q5VTQ0
      Related
      ENSP00000423392.1, ENST00000507993.5
      Conserved Domains (2) summary
      pfam10300
      Location:1 → 433
      DUF3808; Protein of unknown function (DUF3808)
      pfam13424
      Location:429 → 493
      TPR_12; Tetratricopeptide repeat

    5. NM_152574.3 → NP_689787.3  tetratricopeptide repeat protein 39B isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL591393
      Consensus CDS
      CCDS6477.3
      UniProtKB/Swiss-Prot
      A5PLN1, B4DQ10, B4DQX4, B4DW93, Q5VTQ0, Q8IVR7, Q8IXZ6, Q8N267
      UniProtKB/TrEMBL
      A0A8V8PNE1
      Related
      ENSP00000422496.2, ENST00000512701.7
      Conserved Domains (2) summary
      pfam13424
      Location:528 → 592
      TPR_12; Tetratricopeptide repeat
      pfam10300
      Location:76 → 532
      DUF3808; Protein of unknown function (DUF3808)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      15163622..15307216 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422829.1 → XP_047278785.1  tetratricopeptide repeat protein 39B isoform X2

    2. XM_024447422.2 → XP_024303190.1  tetratricopeptide repeat protein 39B isoform X2

      UniProtKB/Swiss-Prot
      A5PLN1, B4DQ10, B4DQX4, B4DW93, Q5VTQ0, Q8IVR7, Q8IXZ6, Q8N267
      Conserved Domains (2) summary
      pfam13424
      Location:497 → 561
      TPR_12; Tetratricopeptide repeat
      pfam10300
      Location:45 → 501
      DUF3808; Protein of unknown function (DUF3808)

    3. XM_047422828.1 → XP_047278784.1  tetratricopeptide repeat protein 39B isoform X1

    4. XM_017014312.2 → XP_016869801.1  tetratricopeptide repeat protein 39B isoform X2

      UniProtKB/Swiss-Prot
      A5PLN1, B4DQ10, B4DQX4, B4DW93, Q5VTQ0, Q8IVR7, Q8IXZ6, Q8N267
      Conserved Domains (2) summary
      pfam13424
      Location:497 → 561
      TPR_12; Tetratricopeptide repeat
      pfam10300
      Location:45 → 501
      DUF3808; Protein of unknown function (DUF3808)

    5. XM_024447423.2 → XP_024303191.1  tetratricopeptide repeat protein 39B isoform X2

      UniProtKB/Swiss-Prot
      A5PLN1, B4DQ10, B4DQX4, B4DW93, Q5VTQ0, Q8IVR7, Q8IXZ6, Q8N267
      Conserved Domains (2) summary
      pfam13424
      Location:497 → 561
      TPR_12; Tetratricopeptide repeat
      pfam10300
      Location:45 → 501
      DUF3808; Protein of unknown function (DUF3808)

    6. XM_011517732.3 → XP_011516034.1  tetratricopeptide repeat protein 39B isoform X2

      UniProtKB/Swiss-Prot
      A5PLN1, B4DQ10, B4DQX4, B4DW93, Q5VTQ0, Q8IVR7, Q8IXZ6, Q8N267
      Conserved Domains (2) summary
      pfam13424
      Location:497 → 561
      TPR_12; Tetratricopeptide repeat
      pfam10300
      Location:45 → 501
      DUF3808; Protein of unknown function (DUF3808)

    7. XM_024447424.2 → XP_024303192.1  tetratricopeptide repeat protein 39B isoform X2

      UniProtKB/Swiss-Prot
      A5PLN1, B4DQ10, B4DQX4, B4DW93, Q5VTQ0, Q8IVR7, Q8IXZ6, Q8N267
      Conserved Domains (2) summary
      pfam13424
      Location:497 → 561
      TPR_12; Tetratricopeptide repeat
      pfam10300
      Location:45 → 501
      DUF3808; Protein of unknown function (DUF3808)

    8. XM_024447425.2 → XP_024303193.1  tetratricopeptide repeat protein 39B isoform X4

      Related
      ENSP00000426539.1, ENST00000507285.5
      Conserved Domains (2) summary
      pfam10300
      Location:1 → 433
      DUF3808; Protein of unknown function (DUF3808)
      pfam13424
      Location:429 → 493
      TPR_12; Tetratricopeptide repeat

    9. XM_047422831.1 → XP_047278787.1  tetratricopeptide repeat protein 39B isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      15175161..15318914 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362076.1 → XP_054218051.1  tetratricopeptide repeat protein 39B isoform X2

    2. XM_054362073.1 → XP_054218048.1  tetratricopeptide repeat protein 39B isoform X2

    3. XM_054362071.1 → XP_054218046.1  tetratricopeptide repeat protein 39B isoform X1

    4. XM_054362074.1 → XP_054218049.1  tetratricopeptide repeat protein 39B isoform X2

    5. XM_054362075.1 → XP_054218050.1  tetratricopeptide repeat protein 39B isoform X2

    6. XM_054362072.1 → XP_054218047.1  tetratricopeptide repeat protein 39B isoform X2

    7. XM_054362078.1 → XP_054218053.1  tetratricopeptide repeat protein 39B isoform X4

    8. XM_054362077.1 → XP_054218052.1  tetratricopeptide repeat protein 39B isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VTQ0.4 GenPept UniProtKB/Swiss-Prot:Q5VTQ0

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