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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 1 and Dyggve-Melchior-Clausen Disease. Gene Ontology (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

GeneHancer (GH) Regulatory Elements for DYM Gene

Promoters and enhancers for DYM Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18I049459 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 556.5 +0.9 925 1.9 PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF302 ZNF207 DYM RPL17 MBD1 ENSG00000263895
GH18I049485 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 11.3 -28.5 -28519 8.4 MLX FEZF1 DMAP1 YY1 E2F8 ZNF143 SP3 NFYC ZFP41 SSRP1 C18orf32 GC18M049490 GC18M049512 GC18M049513 GC18M049514 GC18M049515 GC18M049516 GC18M049517 PIR54855 PIR54878
GH18I049810 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 10 -351.4 -351438 4.5 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B ZNF213 ACAA2 GC18P049824 SCARNA17 SNHG22 ENSG00000252139 RPL17 CXXC1 MBD1 DYM GC18M049798
GH18I049161 Enhancer 0.8 ENCODE 14.9 +299.2 299215 1.7 PKNOX1 BMI1 BATF RAD21 IRF4 ATF7 ETV6 BCLAF1 IKZF2 RUNX3 DYM GC18P049202 ENSG00000265128
GH18I049398 Enhancer 0.7 Ensembl ENCODE 16.9 +62.1 62146 1.6 SRF POLR2A IKZF1 ZFP36 BCLAF1 ZBTB17 DYM ENSG00000263895 PIR34022
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around DYM on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DYM gene promoter:

Genomic Locations for DYM Gene

Genomic Locations for DYM Gene
chr18:49,041,474-49,461,347
(GRCh38/hg38)
Size:
419,874 bases
Orientation:
Minus strand
chr18:46,570,039-46,987,717
(GRCh37/hg19)

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 Lys608

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

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 IDA,IEA 21280149
GO:0005794 Golgi apparatus IDA,IEA 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

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 Variation AA Info Type
rs111744206 likely-benign, Smith-McCort dysplasia, Dyggve-Melchior-Clausen syndrome 49,391,584(-) C/T intron_variant
rs113500346 likely-benign, Smith-McCort dysplasia, Dyggve-Melchior-Clausen syndrome 49,044,033(-) C/T 3_prime_UTR_variant, coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs120074161 pathogenic, Dyggve-Melchior-Clausen syndrome 49,430,347(-) G/A/C 5_prime_UTR_variant, coding_sequence_variant, stop_gained, synonymous_variant
rs120074162 pathogenic, Dyggve-Melchior-Clausen syndrome 49,378,592(-) A/G/T coding_sequence_variant, stop_gained, synonymous_variant
rs120074163 pathogenic, Dyggve-Melchior-Clausen syndrome, Dyggve-Melchior-Clausen syndrome (DMC) [MIM:223800] 49,257,065(-) T/A coding_sequence_variant, missense_variant

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)

Additional Variant Information 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

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

- 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.

Additional Disease Information for DYM

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 58
  2. 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 58
  3. 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 58
  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 44 58
  5. Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry. (PMID: 21998595) N'Diaye A … Haiman CA (PLoS genetics 2011) 3 44 58

Products for DYM Gene

Sources for DYM Gene

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