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

Gene ID: 158219, updated on 7-Apr-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, Apr 2022]
Expression
Ubiquitous expression in kidney (RPKM 3.7), gall bladder (RPKM 3.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
9p22.3
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (15163622..15307216, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (15175161..15318914, complement)
105.20220307 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
  • 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 (27) 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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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_2023_10

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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