Aliases for TTC39B Gene

Aliases for TTC39B Gene

  • Tetratricopeptide Repeat Domain 39B 2 3 5
  • Tetratricopeptide Repeat Protein 39B 3 4
  • TPR Repeat Protein 39B 3 4
  • C9orf52 3 4
  • Chromosome 9 Open Reading Frame 52 2
  • FLJ33868 2
  • TTC39B 5

External Ids for TTC39B Gene

Previous HGNC Symbols for TTC39B Gene

  • C9orf52

Previous GeneCards Identifiers for TTC39B Gene

  • GC09M015162

Summaries for TTC39B Gene

GeneCards Summary for TTC39B Gene

TTC39B (Tetratricopeptide Repeat Domain 39B) is a Protein Coding gene. Diseases associated with TTC39B include Gallbladder Disease. An important paralog of this gene is TTC39A.

UniProtKB/Swiss-Prot Summary for TTC39B Gene

  • Regulates high density lipoprotein (HDL) cholesterol metabolism by promoting the ubiquitination and degradation of the oxysterols receptors LXR (NR1H2 and NR1H3).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TTC39B Gene

Genomics for TTC39B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TTC39B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J015304 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 279.2 +0.8 759 5.2 JUND ZMYM3 KLF9 CEBPA POLR2A NFIC ZIC2 YY1 MXD4 ZNF341 TTC39B HSALNG0070150 HSALNG0070151 FREM1
GH09J015293 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 22.1 +10.2 10186 8.2 ATF2 CEBPA ATF3 ZSCAN16 YY1 KMT2B IRF2 FOXA2 RXRA ZBTB33 TTC39B PSIP1 piR-50437-648 piR-32214-666 FREM1
GH09J015285 Enhancer 0.9 Ensembl ENCODE dbSUPER 16.5 +20.6 20591 1.9 ATF1 ZNF217 RAD51 FOXA1 L3MBTL2 MEIS2 FOS SOX6 CBFA2T3 TTC39B piR-32214-666 piR-50437-648 FREM1
GH09J015275 Enhancer 1 Ensembl ENCODE dbSUPER 11.7 +29.9 29948 3.2 ZMYM3 CHD4 REST CTCF ZNF217 ELF1 CTBP1 RAD21 SMC3 ETV4 piR-32214-666 TTC39B PSIP1 piR-50437-648 FREM1
GH09J015331 Enhancer 1 Ensembl ENCODE 11.2 -25.7 -25681 3.1 CEBPA THAP11 KDM6A FOXA2 RXRA SMAD4 ZNF511 SAP130 ETV4 RARA hsa-miR-5096-139 TTC39B piR-60146-192 SNAPC3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TTC39B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TTC39B

Top Transcription factor binding sites by QIAGEN in the TTC39B gene promoter:
  • AP-1
  • Bach2
  • c-Fos
  • c-Jun
  • C/EBPbeta
  • FOXF2
  • Hlf
  • IRF-7A
  • POU6F1 (c2)
  • YY1

Genomic Locations for TTC39B Gene

Latest Assembly
chr9:15,163,622-15,307,360
(GRCh38/hg38)
Size:
143,739 bases
Orientation:
Minus strand

Previous Assembly
chr9:15,163,620-15,307,358
(GRCh37/hg19 by Entrez Gene)
Size:
143,739 bases
Orientation:
Minus strand

chr9:15,163,620-15,307,358
(GRCh37/hg19 by Ensembl)
Size:
143,739 bases
Orientation:
Minus strand

Genomic View for TTC39B Gene

Genes around TTC39B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TTC39B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TTC39B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TTC39B Gene

Proteins for TTC39B Gene

  • Protein details for TTC39B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5VTQ0-TT39B_HUMAN
    Recommended name:
    Tetratricopeptide repeat protein 39B
    Protein Accession:
    Q5VTQ0
    Secondary Accessions:
    • A5PLN1
    • B4DQ10
    • B4DQX4
    • B4DW93
    • Q8IVR7
    • Q8IXZ6
    • Q8N267

    Protein attributes for TTC39B Gene

    Size:
    682 amino acids
    Molecular mass:
    76956 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH42417.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=AAI42986.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAC03603.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAG60772.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for TTC39B Gene

neXtProt entry for TTC39B Gene

Post-translational modifications for TTC39B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for TTC39B Gene

Domains & Families for TTC39B Gene

Gene Families for TTC39B Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for TTC39B Gene

Suggested Antigen Peptide Sequences for TTC39B Gene

GenScript: Design optimal peptide antigens:
  • TTC39B protein (A5PLN1_HUMAN)
  • cDNA FLJ60910 (B4DVQ6_HUMAN)
  • Tetratricopeptide repeat domain 39B (Q8IXZ6_HUMAN)
  • Tetratricopeptide repeat protein 39B (TT39B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5VTQ0

UniProtKB/Swiss-Prot:

TT39B_HUMAN :
  • Belongs to the TTC39 family.
Family:
  • Belongs to the TTC39 family.
genes like me logo Genes that share domains with TTC39B: view

Function for TTC39B Gene

Molecular function for TTC39B Gene

UniProtKB/Swiss-Prot Function:
Regulates high density lipoprotein (HDL) cholesterol metabolism by promoting the ubiquitination and degradation of the oxysterols receptors LXR (NR1H2 and NR1H3).

Phenotypes From GWAS Catalog for TTC39B Gene

Gene Ontology (GO) - Molecular Function for TTC39B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 32296183
genes like me logo Genes that share ontologies with TTC39B: view
genes like me logo Genes that share phenotypes with TTC39B: view

Animal Models for TTC39B Gene

MGI Knock Outs for TTC39B:
  • Ttc39b Ttc39b<tm1e(EUCOMM)Wtsi>

Animal Models for research

miRNA for TTC39B Gene

miRTarBase miRNAs that target TTC39B

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TTC39B

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TTC39B Gene

Localization for TTC39B Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TTC39B gene
Compartment Confidence
plasma membrane 1
extracellular 1
nucleus 1
cytosol 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for TTC39B Gene

Pathways & Interactions for TTC39B Gene

PathCards logo

SuperPathways for TTC39B Gene

No Data Available

Gene Ontology (GO) - Biological Process for TTC39B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0010874 regulation of cholesterol efflux IBA,ISS --
GO:0010887 negative regulation of cholesterol storage IBA,ISS --
GO:0042632 cholesterol homeostasis IBA,ISS --
GO:0090181 regulation of cholesterol metabolic process IBA,ISS --
genes like me logo Genes that share ontologies with TTC39B: view

No data available for Pathways by source and SIGNOR curated interactions for TTC39B Gene

Drugs & Compounds for TTC39B Gene

No Compound Related Data Available

Transcripts for TTC39B Gene

mRNA/cDNA for TTC39B Gene

5 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TTC39B

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for TTC39B Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^
SP1: - - - - -
SP2: -
SP3:
SP4:
SP5:

ExUns: 24a · 24b
SP1:
SP2:
SP3:
SP4:
SP5:

Relevant External Links for TTC39B Gene

GeneLoc Exon Structure for
TTC39B

Expression for TTC39B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TTC39B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TTC39B Gene

This gene is overexpressed in Urine (32.1), Peripheral blood mononuclear cells (22.6), and Heart (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TTC39B Gene



Protein tissue co-expression partners for TTC39B Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TTC39B

SOURCE GeneReport for Unigene cluster for TTC39B Gene:

Hs.563630

Evidence on tissue expression from TISSUES for TTC39B Gene

  • Nervous system(4.6)
  • Blood(4.3)
  • Liver(2.1)
genes like me logo Genes that share expression patterns with TTC39B: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TTC39B Gene

Orthologs for TTC39B Gene

This gene was present in the common ancestor of animals.

Orthologs for TTC39B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TTC39B 29 30
  • 99.27 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TTC39B 29 30
  • 90.49 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TTC39B 29 30
  • 87.94 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ttc39b 29
  • 85.31 (n)
Mouse
(Mus musculus)
Mammalia Ttc39b 29 16 30
  • 84.55 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TTC39B 30
  • 70 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia TTC39B 30
  • 69 (a)
OneToOne
Chicken
(Gallus gallus)
Aves TTC39B 29 30
  • 74.65 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TTC39B 30
  • 70 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ttc39b 29
  • 69.41 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.18685 29
Zebrafish
(Danio rerio)
Actinopterygii zgc:158403 30
  • 52 (a)
ManyToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010417 29
  • 50.4 (n)
Worm
(Caenorhabditis elegans)
Secernentea C32D5.6 29 30
  • 49.34 (n)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 42 (a)
OneToMany
Species where no ortholog for TTC39B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for TTC39B Gene

ENSEMBL:
Gene Tree for TTC39B (if available)
TreeFam:
Gene Tree for TTC39B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TTC39B: view image
Alliance of Genome Resources:
Additional Orthologs for TTC39B

Paralogs for TTC39B Gene

Paralogs for TTC39B Gene

(1) SIMAP similar genes for TTC39B Gene using alignment to 3 proteins:

  • TT39B_HUMAN
  • B4DVQ6_HUMAN
  • H0YAJ6_HUMAN

Pseudogenes.org Pseudogenes for TTC39B Gene

genes like me logo Genes that share paralogs with TTC39B: view

Variants for TTC39B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TTC39B Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs112186053 Benign: not provided 15,187,012(-) T/C
NM_152574.2(TTC39B):c.1419A>G (p.Ala473=)
SYNONYMOUS
rs74818741 Benign: not provided 15,191,211(-) A/G
NM_152574.2(TTC39B):c.975T>C (p.Phe325=)
SYNONYMOUS
rs75681700 Benign: not provided 15,225,949(-) C/T
NM_152574.2(TTC39B):c.339G>A (p.Ala113=)
SYNONYMOUS_VARIANT,INTRON
rs77494837 Benign: not provided 15,177,720(-) T/C
NM_152574.2(TTC39B):c.1818A>G (p.Leu606=)
SYNONYMOUS
rs80193490 Benign: not provided 15,189,721(-) G/A
NM_152574.2(TTC39B):c.1173+4C>T
MISSENSE_VARIANT,INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TTC39B Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for TTC39B Gene

Variant ID Type Subtype PubMed ID
dgv12573n54 CNV loss 21841781
esv2677212 CNV deletion 23128226
esv2761504 CNV loss 21179565
esv2761505 CNV gain 21179565
esv2762797 CNV loss 21179565
esv3619762 CNV loss 21293372
esv3619763 CNV gain 21293372
esv3619765 CNV loss 21293372
esv3619766 CNV gain 21293372
esv3619768 CNV loss 21293372
esv3619769 CNV gain 21293372
esv3619771 CNV loss 21293372
esv3619772 CNV loss 21293372
esv3619774 CNV loss 21293372
esv3619775 CNV loss 21293372
nsv1015960 CNV loss 25217958
nsv436610 CNV deletion 17901297
nsv517975 CNV loss 19592680
nsv521191 CNV loss 19592680
nsv524381 CNV gain 19592680
nsv524849 CNV loss 19592680
nsv831519 CNV loss 17160897

Variation tolerance for TTC39B Gene

Residual Variation Intolerance Score: 35.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.08; 50.74% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TTC39B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TTC39B
Leiden Open Variation Database (LOVD)
TTC39B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TTC39B Gene

Disorders for TTC39B Gene

MalaCards: The human disease database

(1) MalaCards diseases for TTC39B Gene - From: COP and GCD

Disorder Aliases PubMed IDs
gallbladder disease
  • gall bladder
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TTC39B

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with TTC39B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TTC39B Gene

Publications for TTC39B Gene

  1. Biological, clinical and population relevance of 95 loci for blood lipids. (PMID: 20686565) Teslovich TM … Kathiresan S (Nature 2010) 3 40
  2. Evaluating the discriminative power of multi-trait genetic risk scores for type 2 diabetes in a northern Swedish population. (PMID: 20571754) Fontaine-Bisson B … Franks PW (Diabetologia 2010) 3 40
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40
  4. Genetic variants influencing circulating lipid levels and risk of coronary artery disease. (PMID: 20864672) Waterworth DM … Sandhu MS (Arteriosclerosis, thrombosis, and vascular biology 2010) 3 40
  5. Common variants at 30 loci contribute to polygenic dyslipidemia. (PMID: 19060906) Kathiresan S … Cupples LA (Nature genetics 2009) 3 40

Products for TTC39B Gene

Sources for TTC39B Gene