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

Gene ID: 79875, updated on 11-Apr-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. Predicted to act upstream of or within elastic fiber assembly. Located in collagen-containing extracellular matrix and extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in esophagus (RPKM 9.7), prostate (RPKM 9.0) and 20 other tissues See more
Orthologs
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Genomic context

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Location:
15q23
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (71096894..71783383)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (68920176..69602307)
105.20220307 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
  • 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. 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
  3. 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
  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. Shift in GATA3 functions, and GATA3 mutations, control progression and clinical presentation in breast cancer. Cohen H, et al. Breast Cancer Res, 2014 Nov 20. PMID 25410484, 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 
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_2023_10

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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