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Aliases for GDF3 Gene

Aliases for GDF3 Gene

  • Growth Differentiation Factor 3 2 3 5
  • Growth/Differentiation Factor 3 3
  • MCOPCB6 3
  • MCOP7 3
  • GDF-3 4
  • KFS3 3

External Ids for GDF3 Gene

Previous GeneCards Identifiers for GDF3 Gene

  • GC12P007400
  • GC12M007892
  • GC12M007742
  • GC12M007733
  • GC12M007842

Summaries for GDF3 Gene

Entrez Gene Summary for GDF3 Gene

  • 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]

GeneCards Summary for GDF3 Gene

GDF3 (Growth Differentiation Factor 3) is a Protein Coding gene. Diseases associated with GDF3 include Klippel-Feil Syndrome 3, Autosomal Dominant and Microphthalmia, Isolated 7. GO annotations related to this gene include protein kinase binding and growth factor activity. An important paralog of this gene is GDF1.

UniProtKB/Swiss-Prot for GDF3 Gene

  • Growth factor involved in early embryonic development and adipose-tissue homeostasis. During embryogenesis controls formation of anterior visceral endoderm and mesoderm and the establishment of anterior-posterior identity through a receptor complex comprising the receptor ACVR1B and the coreceptor TDGF1/Cripto (By similarity). Regulates adipose-tissue homeostasis and energy balance under nutrient overload in part by signaling through the receptor complex based on ACVR1C and TDGF1/Cripto (PubMed:21805089).

Gene Wiki entry for GDF3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GDF3 Gene

Genomics for GDF3 Gene

Regulatory Elements for GDF3 Gene

Enhancers for GDF3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12F006762 1.4 FANTOM5 ENCODE 19.7 +929.4 929372 7.2 HDGF PKNOX1 ARNT MLX CREB3L1 ZFP64 ARID4B SIN3A FEZF1 ZNF2 ENSG00000219410 ENSG00000247853 NCAPD2 SPSB2 NOP2 ENSG00000256967 C1RL-AS1 GDF3 SCARNA12 TNFRSF1A
GH12F006751 0.2 ENCODE 18.3 +942.6 942622 3.0 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF416 ENSG00000219410 ENSG00000247853 NOP2 SCARNA12 GDF3 NCAPD2 MLF2 SPSB2 ENSG00000256967 C1RL-AS1
GH12F007805 0.2 ENCODE 11.8 -109.4 -109424 0.2 DPPA3 GDF3 ENSG00000201549 NECAP1 NANOGP1 SLC2A14 ENSG00000255356 ENSG00000199912 GC12M007800 GC12P007808
GH12F007806 0.9 Ensembl 11.8 -109.7 -109725 0.2 DPPA3 GDF3 ENSG00000201549 NECAP1 NANOGP1 SLC2A14 ENSG00000255356 GC12P007808 ENSG00000199912 GC12M007800
GH12F007807 0.2 ENCODE 11.8 -111.3 -111274 0.2 ELF3 CTCF ZNF654 SP3 SP5 ZNF511 CEBPB REST RAD21 POLR2A DPPA3 GDF3 ENSG00000201549 NECAP1 NANOGP1 SLC2A14 ENSG00000255356 NANOG SLC2A3 GC12P007808
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around GDF3 on UCSC Golden Path with GeneCards custom track

Genomic Location for GDF3 Gene

Chromosome:
12
Start:
7,689,782 bp from pter
End:
7,695,776 bp from pter
Size:
5,995 bases
Orientation:
Minus strand

Genomic View for GDF3 Gene

Genes around GDF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GDF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GDF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GDF3 Gene

Proteins for GDF3 Gene

  • Protein details for GDF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NR23-GDF3_HUMAN
    Recommended name:
    Growth/differentiation factor 3
    Protein Accession:
    Q9NR23
    Secondary Accessions:
    • Q8NEJ4

    Protein attributes for GDF3 Gene

    Size:
    364 amino acids
    Molecular mass:
    41387 Da
    Quaternary structure:
    • Homodimer or heterodimer (Potential). But, in contrast to other members of this family, cannot be disulfide-linked.
    Miscellaneous:
    • In contrast to other members of this family, cannot be disulfide-linked due to an atypical cysteine knot configuration, where the fourth cysteine is missing. This fourth cysteine is involved in an inter-molecular bridge to stabilize the active form of homodimeric or heterodimeric signaling molecules.

neXtProt entry for GDF3 Gene

Post-translational modifications for GDF3 Gene

  • Synthesized as large precursor molecule that undergo proteolytic cleavage, releasing the pro-domain from the active, receptor binding, C-terminal region of the molecule.
  • Glycosylation at Asn 112 and Asn 306
  • Modification sites at PhosphoSitePlus

Other Protein References for GDF3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for GDF3 Gene

Domains & Families for GDF3 Gene

Gene Families for GDF3 Gene

Suggested Antigen Peptide Sequences for GDF3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NR23

UniProtKB/Swiss-Prot:

GDF3_HUMAN :
  • Belongs to the TGF-beta family.
Family:
  • Belongs to the TGF-beta family.
genes like me logo Genes that share domains with GDF3: view

Function for GDF3 Gene

Molecular function for GDF3 Gene

GENATLAS Biochemistry:
growth differentiation factor 3,TGF beta superfamily member,expressed in human embryonal carcinoma cell lines in a stem cell-specific fashion
UniProtKB/Swiss-Prot Function:
Growth factor involved in early embryonic development and adipose-tissue homeostasis. During embryogenesis controls formation of anterior visceral endoderm and mesoderm and the establishment of anterior-posterior identity through a receptor complex comprising the receptor ACVR1B and the coreceptor TDGF1/Cripto (By similarity). Regulates adipose-tissue homeostasis and energy balance under nutrient overload in part by signaling through the receptor complex based on ACVR1C and TDGF1/Cripto (PubMed:21805089).

Gene Ontology (GO) - Molecular Function for GDF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005125 cytokine activity IEA,IBA --
GO:0005160 transforming growth factor beta receptor binding IBA --
GO:0008083 growth factor activity IEA --
GO:0019901 protein kinase binding IPI 21805089
genes like me logo Genes that share ontologies with GDF3: view
genes like me logo Genes that share phenotypes with GDF3: view

Human Phenotype Ontology for GDF3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for GDF3 Gene

MGI Knock Outs for GDF3:

Animal Model Products

  • Taconic Biosciences Mouse Models for GDF3

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for GDF3 Gene

Localization for GDF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GDF3 Gene

Secreted. Cytoplasm. Note=Mainly accumulated in the cytoplasm. {ECO:0000269 PubMed:21805089}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for GDF3 Gene COMPARTMENTS Subcellular localization image for GDF3 gene
Compartment Confidence
extracellular 5
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for GDF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IEA,IBA --
GO:0005737 cytoplasm IDA 21805089
genes like me logo Genes that share ontologies with GDF3: view

Pathways & Interactions for GDF3 Gene

SuperPathways for GDF3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for GDF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IMP 19864492
GO:0001654 eye development IMP 19864492
GO:0001701 in utero embryonic development IEA --
GO:0002021 response to dietary excess IEA --
GO:0007165 signal transduction IEA --
genes like me logo Genes that share ontologies with GDF3: view

No data available for Pathways by source and SIGNOR curated interactions for GDF3 Gene

Transcripts for GDF3 Gene

mRNA/cDNA for GDF3 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(36) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for GDF3 Gene

Growth differentiation factor 3:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for GDF3 Gene

No ASD Table

Relevant External Links for GDF3 Gene

GeneLoc Exon Structure for
GDF3
ECgene alternative splicing isoforms for
GDF3

Expression for GDF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GDF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GDF3 Gene

This gene is overexpressed in Kidney - Cortex (x12.8) and Spleen (x6.5).

NURSA nuclear receptor signaling pathways regulating expression of GDF3 Gene:

GDF3

SOURCE GeneReport for Unigene cluster for GDF3 Gene:

Hs.86232
genes like me logo Genes that share expression patterns with GDF3: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for GDF3 Gene

Orthologs for GDF3 Gene

This gene was present in the common ancestor of animals.

Orthologs for GDF3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GDF3 34 35
  • 99.54 (n)
dog
(Canis familiaris)
Mammalia GDF3 34 35
  • 86.55 (n)
cow
(Bos Taurus)
Mammalia GDF3 34
  • 83.62 (n)
-- 35
  • 78 (a)
OneToMany
-- 35
  • 78 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Gdf3 34 16 35
  • 77.5 (n)
rat
(Rattus norvegicus)
Mammalia Gdf3 34
  • 77.12 (n)
oppossum
(Monodelphis domestica)
Mammalia GDF3 35
  • 53 (a)
OneToOne
chicken
(Gallus gallus)
Aves GDF3 34
  • 57.95 (n)
CVG1 35
  • 43 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia gdf3 34
  • 56.09 (n)
Str.16175 34
African clawed frog
(Xenopus laevis)
Amphibia gdf3-A-prov 34
zebrafish
(Danio rerio)
Actinopterygii dvr1 34 35
  • 53.07 (n)
-- 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1497 34
fruit fly
(Drosophila melanogaster)
Insecta dpp 35
  • 15 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 20 (a)
OneToMany
Species where no ortholog for GDF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for GDF3 Gene

ENSEMBL:
Gene Tree for GDF3 (if available)
TreeFam:
Gene Tree for GDF3 (if available)

Paralogs for GDF3 Gene

Paralogs for GDF3 Gene

(3) SIMAP similar genes for GDF3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with GDF3: view

Variants for GDF3 Gene

Sequence variations from dbSNP and Humsavar for GDF3 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs140926412 Klippel-Feil syndrome 3, autosomal dominant (KFS3) [MIM:613702], Microphthalmia, isolated, with coloboma, 6 (MCOPCB6) [MIM:613703], Pathogenic 7,690,177(+) GTGAC(A/G/T)GTGGC reference, missense
rs146973734 Microphthalmia, isolated, 7 (MCOP7) [MIM:613704], Pathogenic 7,690,389(+) TTTTC(C/T)GGGGG reference, missense
rs387906945 Microphthalmia, isolated, 7 (MCOP7) [MIM:613704], Pathogenic 7,690,059(-) CTCTC(C/T)CAACA reference, missense
rs387906946 Microphthalmia, isolated, with coloboma, 6 (MCOPCB6) [MIM:613703], Pathogenic 7,690,153(-) ACTTC(C/T)GGGAC reference, missense
rs780787386 Likely pathogenic 7,695,497(+) GCGGA(C/G/T)GCCCA reference, missense

Structural Variations from Database of Genomic Variants (DGV) for GDF3 Gene

Variant ID Type Subtype PubMed ID
dgv5e196 CNV duplication 17116639
dgv6e196 CNV duplication 17116639
esv2422393 CNV duplication 17116639
esv2666104 CNV deletion 23128226
esv3580438 CNV gain 25503493
esv3628435 CNV loss 21293372
nsv557273 CNV loss 21841781
nsv557274 CNV gain 21841781

Variation tolerance for GDF3 Gene

Residual Variation Intolerance Score: 66.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.54; 77.81% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for GDF3 Gene

Human Gene Mutation Database (HGMD)
GDF3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GDF3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GDF3 Gene

Disorders for GDF3 Gene

MalaCards: The human disease database

(14) MalaCards diseases for GDF3 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
klippel-feil syndrome 3, autosomal dominant
  • kfs3
microphthalmia, isolated 7
  • isolated microphthalmia 7
microphthalmia with coloboma 6, digenic
  • microphthalmia with coloboma 6
klippel-feil syndrome 3
  • klippel-feil syndrome 3, autosomal dominant
mental retardation-hypotonic facies syndrome, x-linked
  • mental retardation-hypotonic facies syndrome, x-linked, 1
- elite association - COSMIC cancer census association via MalaCards
Search GDF3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

GDF3_HUMAN
  • Klippel-Feil syndrome 3, autosomal dominant (KFS3) [MIM:613702]: A skeletal disorder characterized by congenital fusion of cervical vertebrae. It is due to a failure in the normal segmentation of vertebrae during the early weeks of fetal development. The clinical triad consists of short neck, low posterior hairline, and limited neck movement. {ECO:0000269 PubMed:19864492}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Microphthalmia, isolated, 7 (MCOP7) [MIM:613704]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. {ECO:0000269 PubMed:19864492}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Microphthalmia, isolated, with coloboma, 6 (MCOPCB6) [MIM:613703]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. Ocular colobomas are a set of malformations resulting from abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure). {ECO:0000269 PubMed:19864492}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for GDF3

Genetic Association Database (GAD)
GDF3
Human Genome Epidemiology (HuGE) Navigator
GDF3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
GDF3
genes like me logo Genes that share disorders with GDF3: view

No data available for Genatlas for GDF3 Gene

Publications for GDF3 Gene

  1. Mutation of the bone morphogenetic protein GDF3 causes ocular and skeletal anomalies. (PMID: 19864492) Ye M. … Lehmann O.J. (Hum. Mol. Genet. 2010) 3 4 22 64
  2. Human growth-differentiation factor 3 (hGDF3): developmental regulation in human teratocarcinoma cell lines and expression in primary testicular germ cell tumours. (PMID: 9467948) Caricasole A.A. … van den Eijnden-van Raaij A.J. (Oncogene 1998) 2 3 22 64
  3. The conditioned medium from a stable human GDF3-expressing CHO cell line, induces the differentiation of PC12 cells. (PMID: 21805089) Li Q. … Yu L. (Mol. Cell. Biochem. 2012) 3 4 64
  4. A large-scale candidate gene association study of age at menarche and age at natural menopause. (PMID: 20734064) He C. … Hunter D.J. (Hum. Genet. 2010) 3 46 64
  5. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F. … Nebel A. (Mutat. Res. 2010) 3 46 64

Products for GDF3 Gene

Sources for GDF3 Gene

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