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    GDF3 growth differentiation factor 3 [ Homo sapiens (human) ]

    Gene ID: 9573, updated on 2-Nov-2024

    Summary

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    Official Symbol
    GDF3provided by HGNC
    Official Full Name
    growth differentiation factor 3provided by HGNC
    Primary source
    HGNC:HGNC:4218
    See related
    Ensembl:ENSG00000184344 MIM:606522; AllianceGenome:HGNC:4218
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    KFS3; MCOP7; MCOPCB6
    Summary
    This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. This protein plays a role ocular and skeletal development. Mutations in this gene are associated with microphthalmia, coloboma, and skeletal abnormalities in human patients. [provided by RefSeq, Aug 2016]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See GDF3 in Genome Data Viewer
    Location:
    12p13.31
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (7689784..7695775, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (7704552..7710540, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (7842380..7848371, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene clathrin light chain A pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7761225-7761725 Neighboring gene MPRA-validated peak1559 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:7790442-7790976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4203 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 1 Neighboring gene Sharpr-MPRA regulatory region 10898 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:7824935-7825436 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:7825437-7825936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5919 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:7846215-7846852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7856907-7857580 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7860307-7860932 Neighboring gene developmental pluripotency associated 3 Neighboring gene MPRA-validated peak1561 silencer Neighboring gene C-type lectin domain family 4 member C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5921

    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. Increased Serum Levels of Growth-Differentiation Factor 3 (GDF3) and Inflammasome-Related Markers in Pregnant Women during Acute Zika Virus Infection. de Castro Alves CE, et al. Viruses, 2022 May 9. PMID 35632746, Free PMC Article
    2. [Expression and significance analysis of GDF3 in testicular cancer based on TCGA and GTEx databases]. Yan ZC, et al. Zhonghua Nan Ke Xue, 2023 Dec. PMID 38639949
    3. Functional and In Silico Assessment of GDF3 Gene Variants in a Chinese Congenital Scoliosis Population. Chen J, et al. Med Sci Monit, 2018 May 8. PMID 29735971, Free PMC Article
    4. Human growth-differentiation factor 3 (hGDF3): developmental regulation in human teratocarcinoma cell lines and expression in primary testicular germ cell tumours. Caricasole AA, et al. Oncogene, 1998 Jan 8. PMID 9467948
    5. Expression pattern of growth/differentiation factor 3 in human and murine cerebral cortex, hippocampus as well as cerebellum. Hexige S, et al. Neurosci Lett, 2005 Dec 2. PMID 16126341

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. [Expression and significance analysis of GDF3 in testicular cancer based on TCGA and GTEx databases].
      Title: [Expression and significance analysis of GDF3 in testicular cancer based on TCGA and GTEx databases].
    2. Novel Cardiokine GDF3 Predicts Adverse Fibrotic Remodeling After Myocardial Infarction.
      Title: Novel Cardiokine GDF3 Predicts Adverse Fibrotic Remodeling After Myocardial Infarction.
    3. Increased Serum Levels of Growth-Differentiation Factor 3 (GDF3) and Inflammasome-Related Markers in Pregnant Women during Acute Zika Virus Infection.
      Title: Increased Serum Levels of Growth-Differentiation Factor 3 (GDF3) and Inflammasome-Related Markers in Pregnant Women during Acute Zika Virus Infection.
    4. the 4 of the 5 variants in [i]GDF3[/i] gene contribute different pathogenicity in congenital scoliosis, which may provide molecular evidence for clinical genetic testing.
      Title: Functional and In Silico Assessment of GDF3 Gene Variants in a Chinese Congenital Scoliosis Population.
    5. OCT4 plays a role as a transcriptional activator for GDF3 transcription in pluripotent human embryonic carcinoma NCCIT cells and contributes to the understanding of the molecular networks of stem cell regulators in germ cell-derived pluripotency and tumorigenesis.
      Title: Growth and Differentiation Factor 3 Is Transcriptionally Regulated by OCT4 in Human Embryonic Carcinoma Cells.
    6. The results expand the spectrum of mutations associated with CHDs and first suggest the potentially disease-related GDF3 gene variant in the pathogenesis of CHDs.
      Title: A novel variation of GDF3 in Chinese Han children with a broad phenotypic spectrum of non-syndromic CHDs.
    7. first evidence that NANOG is a transcriptional activator of the expression of the oncogenic growth factor GDF3 in embryonic carcinoma cells
      Title: Regulation of human growth and differentiation factor 3 gene expression by NANOG in human embryonic carcinoma NCCIT cells.
    8. GDF3 expression level was significantly down-regulated in breast cancer tissues compared to the surrounding nontumorous tissues.
      Title: GDF3 inhibits the growth of breast cancer cells and promotes the apoptosis induced by Taxol.
    9. the conditioned medium from CHO-GDF3 could reduce PC12 cell growth and induce cell differentiation
      Title: The conditioned medium from a stable human GDF3-expressing CHO cell line, induces the differentiation of PC12 cells.
    10. Growth differentiation factor 3 is induced by bone morphogenetic protein 6 (BMP-6) and BMP-7 and increases luteinizing hormone receptor messenger RNA expression in human granulosa cells.
      Title: Growth differentiation factor 3 is induced by bone morphogenetic protein 6 (BMP-6) and BMP-7 and increases luteinizing hormone receptor messenger RNA expression in human granulosa cells.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    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
    Isolated microphthalmia 7
    MedGen: C3150969 OMIM: 613704 GeneReviews: Not available
    		Compare labs
    Klippel-Feil syndrome 3, autosomal dominant
    MedGen: C3150967 OMIM: 613702 GeneReviews: Not available
    		Compare labs
    Microphthalmia, isolated, with coloboma 6
    MedGen: C3150968 OMIM: 613703 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cytokine activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables growth factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endoderm development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in eye development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in formation of anatomical boundary IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mesoderm development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of BMP signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of epidermal cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of myoblast differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in notochord development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of fat cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in primitive streak formation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cell fate commitment IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to dietary excess IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in somite rostral/caudal axis specification IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    growth/differentiation factor 3

    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.

    Genomic

    1. NG_028167.1 RefSeqGene

      Range
      4990..10981
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_020634.3 → NP_065685.1  growth/differentiation factor 3 preproprotein

      See identical proteins and their annotated locations for NP_065685.1

      Status: REVIEWED

      Source sequence(s)
      AA926805, AF263538, AY358875
      Consensus CDS
      CCDS8581.1
      UniProtKB/Swiss-Prot
      Q8NEJ4, Q9NR23
      UniProtKB/TrEMBL
      Q8NI58
      Related
      ENSP00000331745.3, ENST00000329913.4
      Conserved Domains (2) summary
      smart00204
      Location:264 → 364
      TGFB; Transforming growth factor-beta (TGF-beta) family
      pfam00688
      Location:109 → 220
      TGFb_propeptide; TGF-beta propeptide

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      7689784..7695775 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      7704552..7710540 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NR23.3 GenPept UniProtKB/Swiss-Prot:Q9NR23

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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