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Aliases for DYM Gene

Aliases for DYM Gene

  • Dymeclin 2 3 3 5
  • Dyggve-Melchior-Clausen Syndrome Protein 3 4
  • DMC 3
  • SMC 3

External Ids for DYM Gene

Previous GeneCards Identifiers for DYM Gene

  • GC18M044825
  • GC18M046570
  • GC18M043422

Summaries for DYM Gene

Entrez Gene Summary for DYM Gene

  • This gene encodes a protein which regulates Golgi-associated secretory pathways that are essential to endochondral bone formation during early development. This gene is also believed to play a role in early brain development. This gene is widely expressed in embryos and is particularly abundant in chodrocytes and brain tissues. It encodes a peripheral membrane protein which shuttles between the cytosol and Golgi complex. Mutations in this gene are associated with two types of recessive osteochondrodysplasia: Dyggve-Melchior-Clausen (DMC) dysplasia and Smith-McCort (SMC) dysplasia. [provided by RefSeq, Jun 2017]

GeneCards Summary for DYM Gene

DYM (Dymeclin) is a Protein Coding gene. Diseases associated with DYM include Smith-Mccort Dysplasia and Dyggve-Melchior-Clausen Disease. GO annotations related to this gene include binding and enzyme binding.

UniProtKB/Swiss-Prot for DYM Gene

  • Necessary for correct organization of Golgi apparatus. Involved in bone development.

Gene Wiki entry for DYM Gene

Additional gene information for DYM Gene

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

Genomics for DYM Gene

Regulatory Elements for DYM Gene

Enhancers for DYM 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
GH18H049019 1.6 Ensembl ENCODE dbSUPER 12.9 +440.1 440149 3 HDGF ARID4B SIN3A YBX1 ZNF2 SLC30A9 ZNF416 ZNF207 ZNF143 FOS RPL17 ENSG00000264269 DYM ZBTB7C LOC105372109
GH18H049485 1.2 ENCODE 11.3 -28.5 -28519 8 HDGF PKNOX1 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF766 C18orf32 DYM CXXC1 ACAA2 ENSG00000252139 SCARNA17 LIPG MBD1 ENSG00000265496 GC18M049515
GH18H049810 1.3 ENCODE dbSUPER 10 -351.4 -351439 4 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF143 ZNF207 RPL17 ACAA2 CXXC1 DYM GC18M049798
GH18H049728 1.3 Ensembl ENCODE dbSUPER 9.9 -269.1 -269086 4 CTCF FOXA2 MAX ZIC2 ZNF2 RAD21 RARA SMC3 ZNF143 ZNF654 DYM ENSG00000267674 GC18M049670
GH18H049161 0.8 ENCODE 14.9 +299.2 299215 1 PKNOX1 TBL1XR1 BMI1 BATF RAD21 ATF7 ETV6 RUNX3 IKZF2 CREM DYM GC18P049202 ENSG00000265128
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around DYM on UCSC Golden Path with GeneCards custom track

Promoters for DYM Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000103212 847 1401 PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF302 ZNF207

Genomic Location for DYM Gene

Chromosome:
18
Start:
49,041,474 bp from pter
End:
49,461,347 bp from pter
Size:
419,874 bases
Orientation:
Minus strand

Genomic View for DYM Gene

Genes around DYM on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for DYM Gene

Proteins for DYM Gene

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

    Protein Symbol:
    Q7RTS9-DYM_HUMAN
    Recommended name:
    Dymeclin
    Protein Accession:
    Q7RTS9
    Secondary Accessions:
    • A8K5I8
    • B2RCF9
    • B4DKI7
    • Q3ZTS8
    • Q6P2P5
    • Q8N2M0
    • Q9BVE9
    • Q9NPU7

    Protein attributes for DYM Gene

    Size:
    669 amino acids
    Molecular mass:
    75935 Da
    Quaternary structure:
    • Interacts with GOLM1 and PPIB.

    Alternative splice isoforms for DYM Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DYM Gene

Post-translational modifications for DYM Gene

  • Myristoylated in vitro; myristoylation is not essential for protein targeting to Golgi compartment.
  • Ubiquitination at posLast=498498 and isoforms=2608
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for DYM Gene

Domains & Families for DYM Gene

Gene Families for DYM Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for DYM Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for DYM Gene

Graphical View of Domain Structure for InterPro Entry

Q7RTS9

UniProtKB/Swiss-Prot:

DYM_HUMAN :
  • Belongs to the dymeclin family.
Family:
  • Belongs to the dymeclin family.
genes like me logo Genes that share domains with DYM: view

Function for DYM Gene

Molecular function for DYM Gene

UniProtKB/Swiss-Prot Function:
Necessary for correct organization of Golgi apparatus. Involved in bone development.

Phenotypes From GWAS Catalog for DYM Gene

Gene Ontology (GO) - Molecular Function for DYM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21280149
GO:0019899 enzyme binding IPI 21280149
genes like me logo Genes that share ontologies with DYM: view
genes like me logo Genes that share phenotypes with DYM: view

Human Phenotype Ontology for DYM Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for DYM
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

Localization for DYM Gene

Subcellular locations from UniProtKB/Swiss-Prot for DYM Gene

Cytoplasm. Golgi apparatus. Membrane; Lipid-anchor. Note=Sequence analysis programs clearly predict 1 transmembrane region. However, PubMed:18996921 shows that it is not a stably anchored transmembrane protein but it weakly associates with the Golgi apparatus and shuttles between the Golgi and the cytosol.

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 DYM gene
Compartment Confidence
golgi apparatus 5
plasma membrane 3
cytosol 3
extracellular 2
mitochondrion 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DYM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA 21280149
GO:0005794 Golgi apparatus IEA,IDA 21280149
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with DYM: view

Pathways & Interactions for DYM Gene

No Data Available

Interacting Proteins for DYM Gene

Gene Ontology (GO) - Biological Process for DYM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007030 Golgi organization IMP 21280149
GO:0060348 bone development IMP 21280149
genes like me logo Genes that share ontologies with DYM: view

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

Drugs & Compounds for DYM Gene

No Compound Related Data Available

Transcripts for DYM Gene

Unigene Clusters for DYM Gene

Dymeclin:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for DYM
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

No ASD Table

Relevant External Links for DYM Gene

GeneLoc Exon Structure for
DYM
ECgene alternative splicing isoforms for
DYM

Expression for DYM Gene

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

Protein differential expression in normal tissues from HIPED for DYM Gene

This gene is overexpressed in Bone (55.6).

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



Protein tissue co-expression partners for DYM Gene

NURSA nuclear receptor signaling pathways regulating expression of DYM Gene:

DYM

SOURCE GeneReport for Unigene cluster for DYM Gene:

Hs.162996

mRNA Expression by UniProt/SwissProt for DYM Gene:

Q7RTS9-DYM_HUMAN
Tissue specificity: Expressed in most embryo-fetal and adult tissues. Abundant in primary chondrocytes, osteoblasts, cerebellum, kidney, lung, stomach, heart, pancreas and fetal brain. Very low or no expression in the spleen, thymus, esophagus, bladder and thyroid gland.

Evidence on tissue expression from TISSUES for DYM Gene

  • Nervous system(4.9)

Phenotype-based relationships between genes and organs from Gene ORGANizer for DYM Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cheek
  • chin
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with DYM: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for DYM Gene

Orthologs for DYM Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DYM Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DYM 33 34
  • 99.75 (n)
cow
(Bos Taurus)
Mammalia DYM 33 34
  • 92.38 (n)
dog
(Canis familiaris)
Mammalia DYM 33 34
  • 91.43 (n)
oppossum
(Monodelphis domestica)
Mammalia DYM 34
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Dym 33 16 34
  • 86.2 (n)
rat
(Rattus norvegicus)
Mammalia Dym 33
  • 84.26 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia DYM 34
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves DYM 33 34
  • 78.79 (n)
lizard
(Anolis carolinensis)
Reptilia DYM 34
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia dym 33
  • 72.36 (n)
Str.16119 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.33862 33
zebrafish
(Danio rerio)
Actinopterygii dym 33 34
  • 65.97 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6709 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009765 33
  • 52.38 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG8230 33 34
  • 50.41 (n)
worm
(Caenorhabditis elegans)
Secernentea C47D12.2 33 34
  • 49 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G04200 33
  • 44.69 (n)
rice
(Oryza sativa)
Liliopsida Os01g0773100 33
  • 46.58 (n)
Species where no ortholog for DYM was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • 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)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for DYM Gene

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

Paralogs for DYM Gene

No data available for Paralogs for DYM Gene

Variants for DYM Gene

Sequence variations from dbSNP and Humsavar for DYM Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type
rs120074163 Pathogenic, Dyggve-Melchior-Clausen syndrome (DMC) [MIM:223800] 49,257,065(-) TAGCA(A/T)ATATG reference, missense
rs120074164 Pathogenic, Smith-McCort dysplasia 1 (SMC1) [MIM:607326] 49,379,693(-) CCAAA(A/G)AACTA reference, missense
rs120074165 Pathogenic, Smith-McCort dysplasia 1 (SMC1) [MIM:607326] 49,118,866(-) ACTCC(C/T)GCCTG intron-variant, reference, missense
rs120074161 Pathogenic 49,430,347(-) GAGTA(C/G/T)TTGAA reference, synonymous-codon, stop-gained, utr-variant-5-prime
rs120074162 Pathogenic 49,378,592(-) ACTTA(A/T)GAAGA reference, stop-gained

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

Variant ID Type Subtype PubMed ID
dgv1598n106 CNV tandem duplication 24896259
dgv1599n106 CNV deletion 24896259
dgv985e212 CNV loss 25503493
esv1022137 CNV insertion 17803354
esv1452367 CNV insertion 17803354
esv1556786 CNV insertion 17803354
esv1577618 CNV insertion 17803354
esv2543335 CNV insertion 19546169
esv2661405 CNV deletion 23128226
esv2669820 CNV deletion 23128226
esv2677151 CNV deletion 23128226
esv2717077 CNV deletion 23290073
esv2717078 CNV deletion 23290073
esv2717079 CNV deletion 23290073
esv2717080 CNV deletion 23290073
esv2717081 CNV deletion 23290073
esv2717082 CNV deletion 23290073
esv2717083 CNV deletion 23290073
esv3360803 CNV duplication 20981092
esv3555364 CNV deletion 23714750
esv3583044 CNV loss 25503493
esv3583045 CNV loss 25503493
esv3583051 CNV loss 25503493
esv3642486 CNV loss 21293372
esv3642490 CNV loss 21293372
esv3642493 CNV loss 21293372
nsv1055175 CNV gain 25217958
nsv1072802 CNV deletion 25765185
nsv1123176 CNV deletion 24896259
nsv1125324 CNV deletion 24896259
nsv1142917 CNV tandem duplication 24896259
nsv2292 CNV deletion 18451855
nsv2293 CNV insertion 18451855
nsv458067 CNV loss 19166990
nsv458068 CNV loss 19166990
nsv513496 CNV insertion 21212237
nsv520341 CNV loss 19592680
nsv522529 CNV loss 19592680
nsv522553 CNV loss 19592680
nsv576860 CNV loss 21841781
nsv576861 CNV loss 21841781
nsv828227 CNV loss 20364138
nsv833646 CNV gain 17160897
nsv833649 CNV loss 17160897
nsv953538 CNV duplication 24416366
nsv954137 CNV deletion 24416366
nsv978628 CNV duplication 23825009

Variation tolerance for DYM Gene

Residual Variation Intolerance Score: 13.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.61; 45.19% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for DYM Gene

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

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

Disorders for DYM Gene

MalaCards: The human disease database

(7) MalaCards diseases for DYM Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
smith-mccort dysplasia
  • smith mccort dysplasia
dyggve-melchior-clausen disease
  • dyggve-melchior-clausen syndrome
osteochondrodysplasia
  • mucopolysaccharidosis iv
dwarfism
rectal prolapse
  • procidentia, rectum
- elite association - COSMIC cancer census association via MalaCards
Search DYM in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

DYM_HUMAN
  • Dyggve-Melchior-Clausen syndrome (DMC) [MIM:223800]: A rare autosomal recessive disorder belonging to the group of spondyloepimetaphyseal dysplasias. DMC is characterized by progressive short stature with short trunk dwarfism, microcephaly, protruding sternum, and psychomotor retardation. Radiological features include a platyspondyly with double vertebral humps, an epiphyso-metaphyseal dysplasia and lacy pelvis iliac crests. {ECO:0000269 PubMed:12491225, ECO:0000269 PubMed:12554689, ECO:0000269 PubMed:18996921}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Smith-McCort dysplasia 1 (SMC1) [MIM:607326]: A rare autosomal recessive osteochondrodysplasia with skeletal features identical to those of Dyggve-Melchior-Clausen syndrome, but with normal intelligence and no microcephaly. It is characterized by short limbs and trunk with barrel-shaped chest. The radiographic phenotype includes platyspondyly, generalized abnormalities of the epiphyses and metaphyses, and a distinctive lacy appearance of the iliac crest. {ECO:0000269 PubMed:12491225, ECO:0000269 PubMed:18996921, ECO:0000269 PubMed:19005420}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for DYM

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

No data available for Genatlas for DYM Gene

Publications for DYM Gene

  1. The gene responsible for Dyggve-Melchior-Clausen syndrome encodes a novel peripheral membrane protein dynamically associated with the Golgi apparatus. (PMID: 18996921) Dimitrov A … El Ghouzzi V (Human molecular genetics 2009) 3 4 22 60
  2. Mutations in a novel gene Dymeclin (FLJ20071) are responsible for Dyggve-Melchior-Clausen syndrome. (PMID: 12554689) El Ghouzzi V … Cormier-Daire V (Human molecular genetics 2003) 3 4 22 60
  3. Mental retardation and abnormal skeletal development (Dyggve-Melchior-Clausen dysplasia) due to mutations in a novel, evolutionarily conserved gene. (PMID: 12491225) Cohn DH … Rimoin DL (American journal of human genetics 2003) 3 4 22 60
  4. Genome-wide association study of body height in African Americans: the Women's Health Initiative SNP Health Association Resource (SHARe). (PMID: 22021425) Carty CL … Kooperberg C (Human molecular genetics 2012) 3 45 60
  5. Dymeclin, the gene underlying Dyggve-Melchior-Clausen syndrome, encodes a protein integral to extracellular matrix and golgi organization and is associated with protein secretion pathways critical in bone development. (PMID: 21280149) Denais C … Machado RD (Human mutation 2011) 3 4 60

Products for DYM Gene

Sources for DYM Gene

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