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    THSD4 thrombospondin type 1 domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 79875, updated on 2-Nov-2024

    Summary

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    Official Symbol
    THSD4provided by HGNC
    Official Full Name
    thrombospondin type 1 domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:25835
    See related
    Ensembl:ENSG00000187720 MIM:614476; AllianceGenome:HGNC:25835
    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
    AAT12; ADAMTSL6; FVSY9334; PRO34005; ADAMTSL-6
    Summary
    Predicted to enable hydrolase activity. Predicted to be an extracellular matrix structural constituent. Involved in microfibril assembly. Located in microfibril. Implicated in thoracic aortic aneurysm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in esophagus (RPKM 9.7), prostate (RPKM 9.0) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See THSD4 in Genome Data Viewer
    Location:
    15q23
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (71096894..71783383)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (68920176..69602307)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (71389233..72075722)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:71364462-71365661 Neighboring gene uncharacterized LOC105370886 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:71377897-71378512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9703 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9704 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6613 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:71407710-71407887 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:71412420-71412936 Neighboring gene ribosomal protein L5 pseudogene 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:71446356-71447555 Neighboring gene Sharpr-MPRA regulatory region 1499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:71491544-71492044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:71492045-71492545 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:71494990-71495834 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:71495835-71496677 Neighboring gene THSD4 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:71515768-71516268 Neighboring gene cancer/testis associated 62 Neighboring gene high mobility group box 1 pseudogene 6 Neighboring gene uncharacterized LOC105370884 Neighboring gene uncharacterized LOC124903521 Neighboring gene uncharacterized LOC124903520 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:71587200-71588399 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:71655547-71656054 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:71656055-71656562 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:71656563-71657070 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:71678327-71678861 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:71678925-71679818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:71684826-71685326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:71685327-71685827 Neighboring gene ribosomal protein L17 pseudogene 39 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:71757823-71758514 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6614 Neighboring gene uncharacterized LOC107984716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6615 Neighboring gene Sharpr-MPRA regulatory region 7020 Neighboring gene Sharpr-MPRA regulatory region 14876 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:71947880-71949079 Neighboring gene THSD4 antisense RNA 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:72053567-72054766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9705 Neighboring gene Sharpr-MPRA regulatory region 1602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9706 Neighboring gene RNA, 5S ribosomal pseudogene 399 Neighboring gene nuclear receptor subfamily 2 group E member 3 Neighboring gene myosin IXA

    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. Pathogenic variants in THSD4, encoding the ADAMTS-like 6 protein, predispose to inherited thoracic aortic aneurysm. Elbitar S, et al. Genet Med, 2021 Jan. PMID 32855533, Free PMC Article
    2. Association of genetic variations of genes encoding thrombospondin, type 1, domain-containing 4 and 7A with low bone mineral density in Japanese women with osteoporosis. Mori S, et al. J Hum Genet, 2008. PMID 18488137
    3. A disintegrin-like and metalloprotease (reprolysin-type) with thrombospondin type 1 motif (ADAMTS) superfamily: functions and mechanisms. Apte SS. J Biol Chem, 2009 Nov 13. PMID 19734141, Free PMC Article
    4. ZNF37A promotes tumor metastasis through transcriptional control of THSD4/TGF-β axis in colorectal cancer. Liu J, et al. Oncogene, 2021 May. PMID 33875786
    5. ADAMTSL-6 is a novel extracellular matrix protein that binds to fibrillin-1 and promotes fibrillin-1 fibril formation. Tsutsui K, et al. J Biol Chem, 2010 Feb 12. PMID 19940141, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ZNF37A promotes tumor metastasis through transcriptional control of THSD4/TGF-beta axis in colorectal cancer.
      Title: ZNF37A promotes tumor metastasis through transcriptional control of THSD4/TGF-β axis in colorectal cancer.
    2. In breast cancer, some GATA3 effects shift from tumor suppressing to tumor promoting during tumorigenesis, with deregulation of three genes, BCL2, DACH1, THSD4, representing major GATA3-controlled processes in cancer progression.
      Title: Shift in GATA3 functions, and GATA3 mutations, control progression and clinical presentation in breast cancer.
    3. ADAMTSL6beta has a role in fibrillin-1 microfibril formation
      Title: ADAMTSL6β protein rescues fibrillin-1 microfibril disorder in a Marfan syndrome mouse model through the promotion of fibrillin-1 assembly.
    4. THSD4 polymorphism was not found to be associated with COPD risk
      Title: Effect of five genetic variants associated with lung function on the risk of chronic obstructive lung disease, and their joint effects on lung function.
    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. Data show expression of TNS1, GSTCD, AGER, HTR4 and THSD4 in lung tissue and indicate potential targets for interventions to alleviate respiratory disease.
      Title: Genome-wide association study identifies five loci associated with lung function.
    7. Meta-analysis and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association study identifies five loci associated with lung function.
    8. Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
    9. Variations may be important determinants of osteoporosis in Japanese women.
      Title: Association of genetic variations of genes encoding thrombospondin, type 1, domain-containing 4 and 7A with low bone mineral density in Japanese women with osteoporosis.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
    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

    Associated conditions

    Description Tests
    Aortic aneurysm, familial thoracic 12
    MedGen: C5676959 OMIM: 619825 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    EBI GWAS Catalog
    Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
    EBI GWAS Catalog
    Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction.
    EBI GWAS Catalog
    Genome-wide association study identifies five loci associated with lung function.
    EBI GWAS Catalog
    Genome-wide association study of chronic periodontitis in a general German population.
    EBI GWAS Catalog
    Genome-wide association study of lung function phenotypes in a founder population.
    EBI GWAS Catalog
    Genome-wide association study on dimethylarginines reveals novel AGXT2 variants associated with heart rate variability but not with overall mortality.
    EBI GWAS Catalog
    Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
    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

    • FLJ13710, FLJ16791, FLJ20575, FLJ27224, FLJ53165, FLJ54862, MGC176545, DKFZp586J1522, DKFZp686A1457, DKFZp686K0468, DKFZp686I18125

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in elastic fiber assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in microfibril assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in microfibril IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    thrombospondin type-1 domain-containing protein 4
    Names
    A disintegrin and metalloproteinase with thrombospondin motifs-like protein 6
    ADAMTS-like protein 6
    thrombospondin, type I, domain containing 4

    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_001286429.2 → NP_001273358.1  thrombospondin type-1 domain-containing protein 4 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001273358.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks multiple 5' coding exons, compared to variant 1. It represents use of an alternate promoter and initiates translation from an alternate start codon. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC104938, AK299056
      Consensus CDS
      CCDS66817.1
      UniProtKB/Swiss-Prot
      Q6ZMP0
      Related
      ENSP00000350413.4, ENST00000357769.4
      Conserved Domains (4) summary
      smart00209
      Location:376 → 433
      TSP1; Thrombospondin type 1 repeats
      pfam05986
      Location:52 → 168
      ADAM_spacer1; ADAM-TS Spacer 1
      pfam08686
      Location:615 → 645
      PLAC; PLAC (protease and lacunin) domain
      pfam16885
      Location:179 → 255
      CAC1F_C; Voltage-gated calcium channel subunit alpha, C-term

    2. NM_001394532.1 → NP_001381461.1  thrombospondin type-1 domain-containing protein 4 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      AC015711, AC026636, AC068181, AC104938, AC104943, AC105132
      Consensus CDS
      CCDS10238.2
      UniProtKB/Swiss-Prot
      B2RTY3, B4DR13, Q6MZI3, Q6UXZ8, Q6ZMP0, Q9H8E4
      Related
      ENSP00000347484.3, ENST00000355327.7
      Conserved Domains (4) summary
      smart00209
      Location:58 → 95
      TSP1; Thrombospondin type 1 repeats
      pfam05986
      Location:412 → 528
      ADAM_spacer1; ADAM-TS Spacer 1
      pfam08686
      Location:975 → 1005
      PLAC; PLAC (protease and lacunin) domain
      pfam19030
      Location:856 → 912
      TSP1_ADAMTS; Thrombospondin type 1 domain

    3. NM_024817.3 → NP_079093.2  thrombospondin type-1 domain-containing protein 4 isoform 1 precursor

      See identical proteins and their annotated locations for NP_079093.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC015711, AC026636, AC068181, AC104938, AC104943, AC105132
      Consensus CDS
      CCDS10238.2
      UniProtKB/Swiss-Prot
      B2RTY3, B4DR13, Q6MZI3, Q6UXZ8, Q6ZMP0, Q9H8E4
      Related
      ENSP00000261862.8, ENST00000261862.8
      Conserved Domains (4) summary
      smart00209
      Location:58 → 95
      TSP1; Thrombospondin type 1 repeats
      pfam05986
      Location:412 → 528
      ADAM_spacer1; ADAM-TS Spacer 1
      pfam08686
      Location:975 → 1005
      PLAC; PLAC (protease and lacunin) domain
      pfam19030
      Location:856 → 912
      TSP1_ADAMTS; Thrombospondin type 1 domain

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      71096894..71783383
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047433080.1 → XP_047289036.1  thrombospondin type-1 domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B2RTY3, B4DR13, Q6MZI3, Q6UXZ8, Q6ZMP0, Q9H8E4

    2. XM_017022582.3 → XP_016878071.1  thrombospondin type-1 domain-containing protein 4 isoform X2

    3. XM_017022585.2 → XP_016878074.1  thrombospondin type-1 domain-containing protein 4 isoform X6

    4. XM_011522044.3 → XP_011520346.1  thrombospondin type-1 domain-containing protein 4 isoform X4

      Conserved Domains (4) summary
      smart00209
      Location:400 → 457
      TSP1; Thrombospondin type 1 repeats
      pfam05986
      Location:76 → 192
      ADAM_spacer1; ADAM-TS Spacer 1
      pfam08686
      Location:639 → 669
      PLAC; PLAC (protease and lacunin) domain
      pfam16885
      Location:203 → 279
      CAC1F_C; Voltage-gated calcium channel subunit alpha, C-term

    5. XM_017022586.2 → XP_016878075.1  thrombospondin type-1 domain-containing protein 4 isoform X7

    6. XM_017022584.2 → XP_016878073.1  thrombospondin type-1 domain-containing protein 4 isoform X5

    7. XM_011522043.4 → XP_011520345.1  thrombospondin type-1 domain-containing protein 4 isoform X3

      Conserved Domains (4) summary
      smart00209
      Location:414 → 471
      TSP1; Thrombospondin type 1 repeats
      pfam05986
      Location:90 → 206
      ADAM_spacer1; ADAM-TS Spacer 1
      pfam08686
      Location:653 → 683
      PLAC; PLAC (protease and lacunin) domain
      pfam16885
      Location:217 → 293
      CAC1F_C; Voltage-gated calcium channel subunit alpha, C-term

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      68920176..69602307
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378846.1 → XP_054234821.1  thrombospondin type-1 domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B2RTY3, B4DR13, Q6MZI3, Q6UXZ8, Q6ZMP0, Q9H8E4

    2. XM_054378847.1 → XP_054234822.1  thrombospondin type-1 domain-containing protein 4 isoform X2

    3. XM_054378851.1 → XP_054234826.1  thrombospondin type-1 domain-containing protein 4 isoform X6

    4. XM_054378849.1 → XP_054234824.1  thrombospondin type-1 domain-containing protein 4 isoform X4

    5. XM_054378852.1 → XP_054234827.1  thrombospondin type-1 domain-containing protein 4 isoform X7

    6. XM_054378850.1 → XP_054234825.1  thrombospondin type-1 domain-containing protein 4 isoform X5

    7. XM_054378848.1 → XP_054234823.1  thrombospondin type-1 domain-containing protein 4 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZMP0.2 GenPept UniProtKB/Swiss-Prot:Q6ZMP0

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