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SMOC2 SPARC related modular calcium binding 2 [ Homo sapiens (human) ]

Gene ID: 64094, updated on 2-Nov-2024

Summary

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Official Symbol
SMOC2provided by HGNC
Official Full Name
SPARC related modular calcium binding 2provided by HGNC
Primary source
HGNC:HGNC:20323
See related
Ensembl:ENSG00000112562 MIM:607223; AllianceGenome:HGNC:20323
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
DTDP1; SMAP2; MST117; MSTP117; MSTP140; bA37D8.1; bA270C4A.1; dJ421D16.1
Summary
This gene encodes a member of the SPARC family (secreted protein acidic and rich in cysteine/osteonectin/BM-40), which are highly expressed during embryogenesis and wound healing. The gene product is a matricellular protein which promotes matrix assembly and can stimulate endothelial cell proliferation and migration, as well as angiogenic activity. Associated with pulmonary function, this secretory gene product contains a Kazal domain, two thymoglobulin type-1 domains, and two EF-hand calcium-binding domains. The encoded protein may serve as a target for controlling angiogenesis in tumor growth and myocardial ischemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
Expression
Broad expression in endometrium (RPKM 68.7), gall bladder (RPKM 54.9) and 18 other tissues See more
Orthologs
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Genomic context

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See SMOC2 in Genome Data Viewer
Location:
6q27
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (168441184..168667992)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (169784308..170014051)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (168841864..169068672)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378140 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:168811985-168813184 Neighboring gene uncharacterized LOC105378141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168855369-168855870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168857582-168858555 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:168870327-168871526 Neighboring gene uncharacterized LOC124901466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:168897617-168898335 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:168929287-168929424 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:168941003-168941930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169007268-169007804 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91285 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91305 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:169059822-169060322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169067581-169068082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169068083-169068582 Neighboring gene uncharacterized LOC124901467 Neighboring gene uncharacterized LOC124901468

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. Identification of a novel smooth muscle associated protein, smap2, upregulated during neointima formation in a rat carotid endarterectomy model. Nishimoto S, et al. Biochim Biophys Acta, 2002 Jun 7. PMID 12031507
  2. SMOC2 promotes an epithelial-mesenchymal transition and a pro-metastatic phenotype in epithelial cells of renal cell carcinoma origin. Feng D, et al. Cell Death Dis, 2022 Jul 22. PMID 35869056, Free PMC Article
  3. Secreted modular calcium-binding protein 2 haplotypes are associated with pulmonary function. Wilk JB, et al. Am J Respir Crit Care Med, 2007 Mar 15. PMID 17204727, Free PMC Article
  4. SMOC2 gene variant and the risk of vitiligo in Jordanian Arabs. Alkhateeb A, et al. Eur J Dermatol, 2010 Nov-Dec. PMID 20965805
  5. The Intestinal Stem Cell Marker SMOC2 Is an Independent Prognostic Marker Associated With Better Survival in Gastric Cancer. Hyun CL, et al. Anticancer Res, 2021 Jul. PMID 34230168

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. FTO Positively Regulates Odontoblastic Differentiation via SMOC2 in Human Stem Cells from the Apical Papilla under Inflammatory Microenvironment.
    Title: FTO Positively Regulates Odontoblastic Differentiation via SMOC2 in Human Stem Cells from the Apical Papilla under Inflammatory Microenvironment.
  2. MicroRNA-19a-3p Acts as an Oncogene in Gastric Cancer and Exerts the Effect by Targeting SMOC2.
    Title: MicroRNA-19a-3p Acts as an Oncogene in Gastric Cancer and Exerts the Effect by Targeting SMOC2.
  3. SMOC2 promotes an epithelial-mesenchymal transition and a pro-metastatic phenotype in epithelial cells of renal cell carcinoma origin.
    Title: SMOC2 promotes an epithelial-mesenchymal transition and a pro-metastatic phenotype in epithelial cells of renal cell carcinoma origin.
  4. Prognostic and clinicopathological significance of TMEFF2, SMOC-2, and SOX17 expression in endometrial carcinoma.
    Title: Prognostic and clinicopathological significance of TMEFF2, SMOC-2, and SOX17 expression in endometrial carcinoma.
  5. The Intestinal Stem Cell Marker SMOC2 Is an Independent Prognostic Marker Associated With Better Survival in Gastric Cancer.
    Title: The Intestinal Stem Cell Marker SMOC2 Is an Independent Prognostic Marker Associated With Better Survival in Gastric Cancer.
  6. SMOC2, an intestinal stem cell marker, is an independent prognostic marker associated with better survival in colorectal cancers.
    Title: SMOC2, an intestinal stem cell marker, is an independent prognostic marker associated with better survival in colorectal cancers.
  7. Downregulation of SMOC2 expression in papillary thyroid carcinoma and its prognostic significance.
    Title: Downregulation of SMOC2 expression in papillary thyroid carcinoma and its prognostic significance.
  8. SMOC2 expression was markedly up-regulated in human liver samples with non-alcoholic fatty liver disease.
    Title: Secreted modular calcium-binding protein 2 promotes high fat diet (HFD)-induced hepatic steatosis through enhancing lipid deposition, fibrosis and inflammation via targeting TGF-β1.
  9. we conclude that SMOC-2 might be a novel endometrial cancer stem cell signature gene and therapeutic target for endometrial cancer.
    Title: Targeting cancer stem cell signature gene SMOC-2 Overcomes chemoresistance and inhibits cell proliferation of endometrial carcinoma.
  10. SMOC2 can act as an inhibitor of mineralization; there is a possible role for SMOC2 to prevent calcification disorders.
    Title: SMOC2 inhibits calcification of osteoprogenitor and endothelial cells.
Submit: New GeneRIF Correction See all GeneRIFs (26)

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
Dentin dysplasia type I
MedGen: C0399379 OMIM: 125400 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genome-wide association study of generalized vitiligo in an isolated European founder population identifies SMOC2, in close proximity to IDDM8.
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

Pathways from PubChem

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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 ISA
Inferred from Sequence Alignment
more info
 PubMed 
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 extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of DNA biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA biosynthetic process IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in positive regulation of angiogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of angiogenesis IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in positive regulation of endothelial cell chemotaxis IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in positive regulation of endothelial cell migration IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of fibroblast growth factor receptor signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of mitotic cell cycle IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of vascular endothelial growth factor signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of vascular wound healing IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in basement membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cell periphery IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular space IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
SPARC-related modular calcium-binding protein 2
Names
SMAP-2
SMOC-2
secreted modular calcium-binding protein 2
smooth muscle associated protein 2
thyroglobulin type-1 repeat containing protein

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_032781.1 RefSeqGene

    Range
    5034..231842
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001166412.2 → NP_001159884.1  SPARC-related modular calcium-binding protein 2 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001159884.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AI032288, BC028420
    Consensus CDS
    CCDS55076.1
    UniProtKB/Swiss-Prot
    B3KPS7, Q4G169, Q5TAT7, Q5TAT8, Q86VV9, Q96SF3, Q9H1L3, Q9H1L4, Q9H3U0, Q9H3U7, Q9H4F7, Q9HCV2
    Related
    ENSP00000348630.3, ENST00000356284.7
    Conserved Domains (4) summary
    smart00280
    Location:39 → 84
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:215 → 281
    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
    pfam16597
    Location:154 → 212
    Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain
    cl08302
    Location:352 → 410
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

  2. NM_022138.3 → NP_071421.1  SPARC-related modular calcium-binding protein 2 isoform 1 precursor

    See identical proteins and their annotated locations for NP_071421.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB014737, AI032288, AL136099, BC028420
    Consensus CDS
    CCDS5307.1
    UniProtKB/Swiss-Prot
    Q9H3U7
    Related
    ENSP00000346537.5, ENST00000354536.9
    Conserved Domains (4) summary
    smart00280
    Location:39 → 84
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:226 → 292
    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
    pfam16597
    Location:154 → 223
    Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain
    cl08302
    Location:363 → 421
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    168441184..168667992
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011536066.2 → XP_011534368.1  SPARC-related modular calcium-binding protein 2 isoform X2

    See identical proteins and their annotated locations for XP_011534368.1

    Conserved Domains (4) summary
    smart00280
    Location:39 → 84
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:215 → 281
    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
    pfam16597
    Location:154 → 212
    Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain
    cl08302
    Location:352 → 410
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

  2. XM_011536065.2 → XP_011534367.1  SPARC-related modular calcium-binding protein 2 isoform X1

    Conserved Domains (4) summary
    smart00280
    Location:39 → 84
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:226 → 292
    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:363 → 424
    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 ...
    pfam16597
    Location:154 → 223
    Thyroglob_assoc; Thyroglobulin_1 repeat associated disordered domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    169784308..170014051
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356216.1 → XP_054212191.1  SPARC-related modular calcium-binding protein 2 isoform X2

  2. XM_054356215.1 → XP_054212190.1  SPARC-related modular calcium-binding protein 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H3U7.2 GenPept UniProtKB/Swiss-Prot:Q9H3U7

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