This gene encodes a multi-domain secreted protein that may have a critical role in ocular and limb development. Mutations in this gene are associated with microphthalmia and limb anomalies. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011] See more...

Aliases for SMOC1 Gene

Aliases for SMOC1 Gene

  • SPARC Related Modular Calcium Binding 1 2 3 5
  • SPARC-Related Modular Calcium-Binding Protein 1 3 4
  • Secreted Modular Calcium-Binding Protein 1 3 4
  • SMOC-1 4
  • SMOC1 5
  • OAS 3

External Ids for SMOC1 Gene

Previous GeneCards Identifiers for SMOC1 Gene

  • GC14P067851
  • GC14P064142
  • GC14P068336
  • GC14P069415
  • GC14P070346
  • GC14P050514

Summaries for SMOC1 Gene

Entrez Gene Summary for SMOC1 Gene

  • This gene encodes a multi-domain secreted protein that may have a critical role in ocular and limb development. Mutations in this gene are associated with microphthalmia and limb anomalies. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]

GeneCards Summary for SMOC1 Gene

SMOC1 (SPARC Related Modular Calcium Binding 1) is a Protein Coding gene. Diseases associated with SMOC1 include Microphthalmia With Limb Anomalies and Microphthalmia. Gene Ontology (GO) annotations related to this gene include calcium ion binding and extracellular matrix binding. An important paralog of this gene is SMOC2.

UniProtKB/Swiss-Prot Summary for SMOC1 Gene

  • Plays essential roles in both eye and limb development. Probable regulator of osteoblast differentiation.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SMOC1 Gene

Genomics for SMOC1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SMOC1 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
GH14J069878 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 616.7 +27.0 26969 4.6 GATAD2A ZNF629 KDM1A ZNF692 ZNF7 PRDM1 ZIC2 RBFOX2 PKNOX1 POLR2A SMOC1 piR-39972-010 SLC8A3
GH14J069853 Enhancer 0.3 Ensembl 600.7 -0.1 -130 0.4 PRDM10 REST SMOC1 piR-50444-112 SLC10A1
GH14J069995 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 24.8 +144.3 144288 6.8 CREB1 PRDM10 ZNF629 ZNF692 TARDBP ZHX2 FOXA1 RFX1 ZIC2 ZSCAN4 SMOC1 MED6 ADAM20 SRSF5 DCAF5 ERH SLC10A1 TTC9 SNORD169 lnc-SLC10A1-2
GH14J069985 Enhancer 0.9 Ensembl ENCODE dbSUPER 28.3 +131.3 131270 0.8 CEBPG CEBPA CEBPB FOS JUND MAX EP300 USF2 ATF4 HLF SMOC1 TTC9 SNORD169 lnc-SLC10A1-2 SLC8A3
GH14J069876 Enhancer 1 Ensembl ENCODE 18.4 +22.9 22928 0.7 HNRNPL GATAD2A REST TFE3 NFKBIZ KDM1A FOXA1 RXRB IRF2 SP1 SMOC1 piR-39972-010 SLC8A3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SMOC1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SMOC1

Top Transcription factor binding sites by QIAGEN in the SMOC1 gene promoter:
  • AREB6
  • E47
  • HNF-4alpha1
  • HTF
  • Nkx2-5
  • p53
  • SRF
  • SRF (504 AA)
  • Tal-1beta
  • ZID

Genomic Locations for SMOC1 Gene

Genomic Locations for SMOC1 Gene
chr14:69,854,131-70,032,366
(GRCh38/hg38)
Size:
178,236 bases
Orientation:
Plus strand
chr14:70,320,848-70,499,083
(GRCh37/hg19)
Size:
178,236 bases
Orientation:
Plus strand

Genomic View for SMOC1 Gene

Genes around SMOC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMOC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMOC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMOC1 Gene

Proteins for SMOC1 Gene

  • Protein details for SMOC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H4F8-SMOC1_HUMAN
    Recommended name:
    SPARC-related modular calcium-binding protein 1
    Protein Accession:
    Q9H4F8
    Secondary Accessions:
    • A8K1S3
    • B2R7P5
    • Q96F78

    Protein attributes for SMOC1 Gene

    Size:
    434 amino acids
    Molecular mass:
    48163 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SMOC1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMOC1 Gene

Post-translational modifications for SMOC1 Gene

  • Glycosylated.
  • Glycosylation at Ser37, Thr163, Ser168, Ser172, Asn214, Thr300, Thr301, Ser351, and Asn374
  • Modification sites at PhosphoSitePlus

Other Protein References for SMOC1 Gene

No data available for DME Specific Peptides for SMOC1 Gene

Domains & Families for SMOC1 Gene

Gene Families for SMOC1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for SMOC1 Gene

GenScript: Design optimal peptide antigens:
  • Secreted modular calcium-binding protein 1 (SMOC1_HUMAN)
genes like me logo Genes that share domains with SMOC1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SMOC1 Gene

Function for SMOC1 Gene

Molecular function for SMOC1 Gene

UniProtKB/Swiss-Prot Function:
Plays essential roles in both eye and limb development. Probable regulator of osteoblast differentiation.

Phenotypes From GWAS Catalog for SMOC1 Gene

Gene Ontology (GO) - Molecular Function for SMOC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 23088713
GO:0046872 metal ion binding IEA --
GO:0050840 extracellular matrix binding IEA --
genes like me logo Genes that share ontologies with SMOC1: view
genes like me logo Genes that share phenotypes with SMOC1: view

Human Phenotype Ontology for SMOC1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SMOC1 Gene

MGI Knock Outs for SMOC1:
  • Smoc1 Smoc1<tm1a(EUCOMM)Wtsi>
  • Smoc1 Smoc1<tm1b(EUCOMM)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for SMOC1

CRISPR Products

miRNA for SMOC1 Gene

miRTarBase miRNAs that target SMOC1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMOC1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SMOC1 Gene

Localization for SMOC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMOC1 Gene

Secreted, extracellular space, extracellular matrix, basement membrane. Note=In or around the basement membrane.

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 SMOC1 gene
Compartment Confidence
extracellular 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SMOC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005604 basement membrane IEA --
genes like me logo Genes that share ontologies with SMOC1: view

Pathways & Interactions for SMOC1 Gene

PathCards logo

SuperPathways for SMOC1 Gene

No Data Available

SIGNOR curated interactions for SMOC1 Gene

Gene Ontology (GO) - Biological Process for SMOC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001654 eye development IMP 21194678
GO:0007275 multicellular organism development IEA --
GO:0030154 cell differentiation IEA --
GO:0045667 regulation of osteoblast differentiation IMP 20359165
GO:0060173 limb development IMP 21194678
genes like me logo Genes that share ontologies with SMOC1: view

No data available for Pathways by source for SMOC1 Gene

Drugs & Compounds for SMOC1 Gene

No Compound Related Data Available

Transcripts for SMOC1 Gene

mRNA/cDNA for SMOC1 Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMOC1

Alternative Splicing Database (ASD) splice patterns (SP) for SMOC1 Gene

No ASD Table

Relevant External Links for SMOC1 Gene

GeneLoc Exon Structure for
SMOC1

Expression for SMOC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SMOC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SMOC1 Gene

This gene is overexpressed in Liver (x4.9).

Protein differential expression in normal tissues from HIPED for SMOC1 Gene

This gene is overexpressed in Testis (31.9), Bone marrow mesenchymal stem cell (8.9), and Ovary (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SMOC1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SMOC1

SOURCE GeneReport for Unigene cluster for SMOC1 Gene:

Hs.497349

mRNA Expression by UniProt/SwissProt for SMOC1 Gene:

Q9H4F8-SMOC1_HUMAN
Tissue specificity: Widely expressed in many tissues with a strongest signal in ovary. No expression in spleen.

Evidence on tissue expression from TISSUES for SMOC1 Gene

  • Nervous system(4.8)
  • Lung(4.3)
  • Heart(2.2)
  • Liver(2.2)
  • Skin(2.1)
  • Muscle(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SMOC1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • skeleton
Regions:
Head and neck:
  • brain
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • skull
Thorax:
  • chest wall
  • clavicle
  • heart
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SMOC1: view

No data available for Protein tissue co-expression partners for SMOC1 Gene

Orthologs for SMOC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SMOC1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SMOC1 30 31
  • 99.54 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SMOC1 30 31
  • 93.39 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SMOC1 30 31
  • 93.01 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Smoc1 30
  • 90.45 (n)
Mouse
(Mus musculus)
Mammalia Smoc1 30 17 31
  • 90.15 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SMOC1 31
  • 86 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SMOC1 31
  • 34 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SMOC1 30 31
  • 81.97 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SMOC1 31
  • 81 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia smoc1 30
  • 76.25 (n)
Zebrafish
(Danio rerio)
Actinopterygii SMOC1 (2 of 2) 31
  • 72 (a)
OneToMany
smoc1 30
  • 70.37 (n)
SMOC1 (1 of 2) 31
  • 66 (a)
OneToMany
Dr.14033 30
Fruit Fly
(Drosophila melanogaster)
Insecta magu 31
  • 17 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea T04F3.2 31
  • 25 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 29 (a)
OneToMany
Species where no ortholog for SMOC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)

Evolution for SMOC1 Gene

ENSEMBL:
Gene Tree for SMOC1 (if available)
TreeFam:
Gene Tree for SMOC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SMOC1: view image

Paralogs for SMOC1 Gene

Paralogs for SMOC1 Gene

(1) SIMAP similar genes for SMOC1 Gene using alignment to 1 proteins:

  • SMOC1_HUMAN
genes like me logo Genes that share paralogs with SMOC1: view

Variants for SMOC1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SMOC1 Gene

SNP ID Clinical significance and condition Chr 14 pos Variation AA Info Type
30728 Pathogenic: Microphthalmia with limb anomalies 69,953,533(+) G/A SPLICE_DONOR_VARIANT
721765 Likely Benign: not provided 69,953,523(+) C/T SYNONYMOUS_VARIANT
722130 Likely Benign: not provided 70,010,782(+) G/A SYNONYMOUS_VARIANT
724952 Likely Benign: not provided 70,013,399(+) G/A SYNONYMOUS_VARIANT
730045 Likely Benign: not provided 69,952,291(+) G/C MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for SMOC1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SMOC1 Gene

Variant ID Type Subtype PubMed ID
dgv266e201 CNV deletion 23290073
esv2405310 CNV deletion 18987734
esv2658279 CNV deletion 23128226
esv2748822 CNV deletion 23290073
esv2748823 CNV deletion 23290073
esv2748824 CNV deletion 23290073
esv2748825 CNV deletion 23290073
esv2748826 CNV deletion 23290073
esv2748827 CNV deletion 23290073
esv2748828 CNV deletion 23290073
esv2748831 CNV deletion 23290073
esv3581278 CNV loss 25503493
esv3634846 CNV loss 21293372
esv3634847 CNV loss 21293372
esv3634849 CNV loss 21293372
nsv1070642 CNV deletion 25765185
nsv1134386 CNV deletion 24896259
nsv1143753 CNV deletion 24896259
nsv1337 CNV insertion 18451855
nsv456336 CNV gain 19166990
nsv523796 CNV loss 19592680
nsv565007 CNV gain 21841781
nsv817638 CNV gain 17921354
nsv832824 CNV gain 17160897
nsv976351 CNV duplication 23825009

Variation tolerance for SMOC1 Gene

Residual Variation Intolerance Score: 29.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.75; 46.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMOC1 Gene

Human Gene Mutation Database (HGMD)
SMOC1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMOC1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMOC1 Gene

Disorders for SMOC1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for SMOC1 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
microphthalmia with limb anomalies
  • mla
microphthalmia
  • microphthalmos
diaphragmatic eventration
chromosome 2q35 duplication syndrome
  • syndactyly, type i; sdty1
coloboma of macula
  • agenesis of macula
- elite association - COSMIC cancer census association via MalaCards
Search SMOC1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SMOC1_HUMAN
  • Ophthalmoacromelic syndrome (OAS) [MIM:206920]: A rare disorder presenting with ocular anomalies, ranging from mild microphthalmia to true anophthalmia, and limb anomalies. Limb malformations include fused 4th and 5th metacarpals and short 5th finger in hands, and oligodactyly in foot (four toes). Most patients have bilateral anophthalmia/ microphthalmia, but unilateral abnormality is also noted. Other malformations are rare, but venous or vertebral anomaly was recognized each in single cases. {ECO:0000269 PubMed:21194678, ECO:0000269 PubMed:21194680, ECO:0000269 PubMed:21750680, ECO:0000269 PubMed:23646827}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SMOC1

genes like me logo Genes that share disorders with SMOC1: view

No data available for Genatlas for SMOC1 Gene

Publications for SMOC1 Gene

  1. Characterization of SMOC-1, a novel modular calcium-binding protein in basement membranes. (PMID: 12130637) Vannahme C … Hartmann U (The Journal of biological chemistry 2002) 2 3 4
  2. Loss of the BMP antagonist, SMOC-1, causes Ophthalmo-acromelic (Waardenburg Anophthalmia) syndrome in humans and mice. (PMID: 21750680) Rainger J … Fitzpatrick DR (PLoS genetics 2011) 3 4
  3. Mutations in the SPARC-related modular calcium-binding protein 1 gene, SMOC1, cause waardenburg anophthalmia syndrome. (PMID: 21194680) Abouzeid H … Schorderet DF (American journal of human genetics 2011) 3 4
  4. SMOC1 is essential for ocular and limb development in humans and mice. (PMID: 21194678) Okada I … Saitsu H (American journal of human genetics 2011) 3 4
  5. Secretome analysis of human BMSCs and identification of SMOC1 as an important ECM protein in osteoblast differentiation. (PMID: 20359165) Choi YA … Park EK (Journal of proteome research 2010) 3 4

Products for SMOC1 Gene

  • Signalway Proteins for SMOC1

Sources for SMOC1 Gene