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    SMOC1 SPARC related modular calcium binding 1 [ Homo sapiens (human) ]

    Gene ID: 64093, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SMOC1provided by HGNC
    Official Full Name
    SPARC related modular calcium binding 1provided by HGNC
    Primary source
    HGNC:HGNC:20318
    See related
    Ensembl:ENSG00000198732 MIM:608488; AllianceGenome:HGNC:20318
    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
    OAS
    Summary
    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]
    Expression
    Biased expression in brain (RPKM 47.3), testis (RPKM 23.8) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMOC1 in Genome Data Viewer
    Location:
    14q24.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (69879416..70032366)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (64087047..64239860)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (70346133..70499083)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA11 Neighboring gene uncharacterized LOC100506358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:70309156-70309730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:70309731-70310303 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5883 Neighboring gene ribosomal protein L7a pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:70419797-70420298 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:70445787-70446286 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:70454077-70454578 Neighboring gene small nucleolar RNA, C/D box 169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8650 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:70477330-70478529 Neighboring gene Sharpr-MPRA regulatory region 14883 Neighboring gene Sharpr-MPRA regulatory region 1041 Neighboring gene MPRA-validated peak2186 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:70527273-70528472 Neighboring gene Sharpr-MPRA regulatory region 1623 Neighboring gene solute carrier family 8 member A3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5885 Neighboring gene ADAM metallopeptidase domain 20 pseudogene Neighboring gene uncharacterized LOC107984686 Neighboring gene MPRA-validated peak2187 silencer

    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. Downregulation of SMOC1 is associated with progression of colorectal traditional serrated adenomas. Aoki H, et al. BMC Gastroenterol, 2024 Mar 1. PMID 38429655, Free PMC Article
    2. Genetic association suggests that SMOC1 mediates between prenatal sex hormones and digit ratio. Lawrance-Owen AJ, et al. Hum Genet, 2013 Apr. PMID 23263445
    3. A novel homozygous variant in the SMOC1 gene underlying Waardenburg anophthalmia syndrome. Ullah A, et al. Ophthalmic Genet, 2017 Jul-Aug. PMID 28085523
    4. A novel mutation in SMOC1 and variable phenotypic expression in two patients with Waardenburg anophthalmia syndrome. Jamshidi J, et al. Eur J Med Genet, 2017 Nov. PMID 28807869
    5. SPARC-related modular calcium binding 1 regulates aortic valve calcification by disrupting BMPR-II/p-p38 signalling. Wang Y, et al. Cardiovasc Res, 2022 Feb 21. PMID 33757126, Free PMC Article

    See all (46) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Downregulation of SMOC1 is associated with progression of colorectal traditional serrated adenomas.
      Title: Downregulation of SMOC1 is associated with progression of colorectal traditional serrated adenomas.
    2. SPARC-related modular calcium binding 1 regulates aortic valve calcification by disrupting BMPR-II/p-p38 signalling.
      Title: SPARC-related modular calcium binding 1 regulates aortic valve calcification by disrupting BMPR-II/p-p38 signalling.
    3. SMOC1 and IL-4 and IL-13 Cytokines Interfere with Ca(2+) Mobilization in Primary Human Keratinocytes.
      Title: SMOC1 and IL-4 and IL-13 Cytokines Interfere with Ca(2+) Mobilization in Primary Human Keratinocytes.
    4. Secreted modular calcium-binding protein 1 binds and activates thrombin to account for platelet hyperreactivity in diabetes.
      Title: Secreted modular calcium-binding protein 1 binds and activates thrombin to account for platelet hyperreactivity in diabetes.
    5. Exome sequencing identified two variants in the SMOC1 gene, each inherited from one of the parents: c.709G>T - p.(Glu237*) on exon 8 and c.1223G>A - p.(Cys408Tyr) on exon 11, both predicted to be pathogenic by different bioinformatics software. Brain histopathology showed an abnormal cortical neuronal migration, which could be related to the SMOC1 protein function, given its role in cellular signaling
      Title: A fetal case of microphthalmia and limb anomalies with abnormal neuronal migration associated with SMOC1 biallelic variants.
    6. Missense mutation in exon 3 of SMOC1 segregated with the Waardenburg anophthalmia syndrome in the Iranian family.
      Title: A novel mutation in SMOC1 and variable phenotypic expression in two patients with Waardenburg anophthalmia syndrome.
    7. This is the first report of Waardenburg anophthalmia syndrome (WAS) caused by a SMOC1 variant in a Pakistani population. The mutation identified in the present investigation extends the body of evidence implicating the gene SMOC-1 in causing WAS.
      Title: A novel homozygous variant in the SMOC1 gene underlying Waardenburg anophthalmia syndrome.
    8. SMOC binds to Pro-EGF, but does not induce Erk phosphorylation via the EGFR.
      Title: SMOC Binds to Pro-EGF, but Does Not Induce Erk Phosphorylation via the EGFR.
    9. IL-17A but not IL-22 suppresses the replication of hepatitis B virus by inducing the expression of MxA and OAS.
      Title: IL-17A but not IL-22 suppresses the replication of hepatitis B virus mediated by over-expression of MxA and OAS mRNA in the HepG2.2.15 cell line.
    10. SMOC1 provides a link between prenatal hormone exposure and digit ratio.
      Title: Genetic association suggests that SMOC1 mediates between prenatal sex hormones and digit ratio.
    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
    Microphthalmia with limb anomalies
    MedGen: C0599973 OMIM: 206920 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Genetic association suggests that SMOC1 mediates between prenatal sex hormones and digit ratio.
    EBI GWAS Catalog
    Genome-wide association study of ancestry-specific TB risk in the South African Coloured population.
    EBI GWAS Catalog
    Multistage genome-wide association meta-analyses identified two new loci for bone mineral density.
    EBI GWAS Catalog
    Seventy-five genetic loci influencing the human red blood cell.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Microarray analysis indicates HIV-1 Tat-induced upregulation of SPARC related modular calcium binding 1 (SMOC1) in primary human brain microvascular endothelial cells PubMed
    Vif vif HIV-1 Vif upregulates the expression of SPARC related modular calcium binding 1 (SMOC1) in Vif-expression T cells PubMed

    Go to the HIV-1, Human Interaction Database

    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 calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables extracellular matrix binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables heparin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in eye development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in limb development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of osteoblast differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in basement membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    SPARC-related modular calcium-binding protein 1
    Names
    secreted modular calcium-binding protein 1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_028217.1 RefSeqGene

      Range
      5020..157970
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001034852.3 → NP_001030024.1  SPARC-related modular calcium-binding protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001030024.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AJ249900, AK098441, BC011548, BQ183777, DA805236
      Consensus CDS
      CCDS32110.1
      UniProtKB/Swiss-Prot
      Q9H4F8
      Related
      ENSP00000355110.4, ENST00000361956.8
      Conserved Domains (4) summary
      cd00104
      Location:47 → 87
      KAZAL_FS; Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the ...
      pfam00086
      Location:95 → 158
      Thyroglobulin_1; Thyroglobulin type-1 repeat
      pfam16597
      Location:159 → 217
      Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain
      cd16240
      Location:315 → 429
      EFh_SPARC_SMOC1; EF-hand, extracellular calcium-binding (EC) motif, found in secreted modular calcium-binding protein 1 (SMOC-1)

    2. NM_001425244.1 → NP_001412173.1  SPARC-related modular calcium-binding protein 1 isoform 3 precursor

      Status: REVIEWED

      Source sequence(s)
      AL135747, AL157789

    3. NM_001425245.1 → NP_001412174.1  SPARC-related modular calcium-binding protein 1 isoform 4 precursor

      Status: REVIEWED

      Source sequence(s)
      AL135747, AL157789

    4. NM_022137.6 → NP_071420.1  SPARC-related modular calcium-binding protein 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_071420.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site at the 3' terminal exon compared to variant 1. This results in an isoform (2) that is 1 aa shorter than isoform 1.
      Source sequence(s)
      AJ249900, AK098441, AK289988, BC008608, BC011548, BQ183777, DA805236
      Consensus CDS
      CCDS9798.1
      UniProtKB/Swiss-Prot
      A8K1S3, B2R7P5, Q96F78, Q9H4F8
      Related
      ENSP00000370680.4, ENST00000381280.4
      Conserved Domains (4) summary
      cd00104
      Location:47 → 87
      KAZAL_FS; Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the ...
      pfam00086
      Location:95 → 158
      Thyroglobulin_1; Thyroglobulin type-1 repeat
      pfam16597
      Location:159 → 217
      Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain
      cd16240
      Location:315 → 429
      EFh_SPARC_SMOC1; EF-hand, extracellular calcium-binding (EC) motif, found in secreted modular calcium-binding protein 1 (SMOC-1)

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      69879416..70032366
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      64087047..64239860
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H4F8.1 GenPept UniProtKB/Swiss-Prot:Q9H4F8

    Gene LinkOut

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

    Chemical Information
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