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

Gene ID: 64093, updated on 17-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (69879416..70032366)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (64087047..64239860)
105.20220307 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
  • 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. 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
  2. A fetal case of microphthalmia and limb anomalies with abnormal neuronal migration associated with SMOC1 biallelic variants. Mancini C, et al. Eur J Med Genet, 2019 Nov. PMID 30445150
  3. 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
  4. A novel homozygous variant in the SMOC1 gene underlying Waardenburg anophthalmia syndrome. Ullah A, et al. Ophthalmic Genet, 2017 Jul-Aug. PMID 28085523
  5. Genetic association suggests that SMOC1 mediates between prenatal sex hormones and digit ratio. Lawrance-Owen AJ, et al. Hum Genet, 2013 Apr. PMID 23263445

See all (43) 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
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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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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_2023_10

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)

mRNA and Protein(s)

  1. XM_005267995.2 → XP_005268052.1  SPARC-related modular calcium-binding protein 1 isoform X1

    Conserved Domains (5) 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 ...
    cd00191
    Location:237 → 303
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd00252
    Location:375 → 436
    SPARC_EC; SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate ...
    pfam00086
    Location:95 → 158
    Thyroglobulin_1; Thyroglobulin type-1 repeat
    pfam16597
    Location:159 → 228
    Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain

  2. XM_005267996.2 → XP_005268053.1  SPARC-related modular calcium-binding protein 1 isoform X2

    Conserved Domains (5) 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 ...
    cd00191
    Location:237 → 303
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd00252
    Location:375 → 436
    SPARC_EC; SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate ...
    pfam00086
    Location:95 → 158
    Thyroglobulin_1; Thyroglobulin type-1 repeat
    pfam16597
    Location:159 → 228
    Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    64087047..64239860
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376573.1 → XP_054232548.1  SPARC-related modular calcium-binding protein 1 isoform X1

  2. XM_054376574.1 → XP_054232549.1  SPARC-related modular calcium-binding protein 1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H4F8.1 GenPept UniProtKB/Swiss-Prot:Q9H4F8

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