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    SMAP2 small ArfGAP2 [ Homo sapiens (human) ]

    Gene ID: 64744, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SMAP2provided by HGNC
    Official Full Name
    small ArfGAP2provided by HGNC
    Primary source
    HGNC:HGNC:25082
    See related
    Ensembl:ENSG00000084070 MIM:616916; AllianceGenome:HGNC:25082
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SMAP1L
    Summary
    Predicted to enable GTPase activator activity. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in lymph node (RPKM 80.3), spleen (RPKM 58.9) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMAP2 in Genome Data Viewer
    Location:
    1p34.2
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (40344834..40423326)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (40214315..40292887)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (40839399..40888998)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 723 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 724 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:40781816-40782452 and GRCh37_chr1:40782453-40783089 Neighboring gene collagen type IX alpha 2 chain Neighboring gene ribosomal protein L21 pseudogene 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 844 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 727 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:40839657-40840156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 845 Neighboring gene Sharpr-MPRA regulatory region 11139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 728 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:40916242-40917441 Neighboring gene ZFP69 zinc finger protein B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 729 Neighboring gene ZFP69 zinc finger protein Neighboring gene EXO5 divergent transcript

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Putative association of SMAPIL polymorphisms with risk of aspirin intolerance in asthmatics. Kim JY, et al. J Asthma, 2010 Nov. PMID 20831471
    2. The carboxy-terminal region of SMAP2 directs subcellular localization as well as Arf protein specificity. Sakakura I, et al. Biochem Biophys Res Commun, 2011 Jan 14. PMID 21147065
    3. The Arf GTPase-activating protein SMAP1 promotes transferrin receptor endocytosis and interacts with SMAP2. Kobayashi N, et al. Biochem Biophys Res Commun, 2014 Oct 24. PMID 25281535
    4. Transport of the cholera toxin B-subunit from recycling endosomes to the Golgi requires clathrin and AP-1. Matsudaira T, et al. J Cell Sci, 2015 Aug 15. PMID 26136365
    5. SMAP2, a novel ARF GTPase-activating protein, interacts with clathrin and clathrin assembly protein and functions on the AP-1-positive early endosome/trans-Golgi network. Natsume W, et al. Mol Biol Cell, 2006 Jun. PMID 16571680, Free PMC Article

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SMAP2 immunoprecipitated clathrin and AP-1 through a putative clathrin-binding domain and a CALM-binding domain, and SMAP2 mutants that did not interact with clathrin or AP-1 could not localize to recycling endosomes
      Title: Transport of the cholera toxin B-subunit from recycling endosomes to the Golgi requires clathrin and AP-1.
    2. Results also demonstrated a physical association between SMAP1 and SMAP2, which might serve as a basis for a functional interaction, and identified the intramolecular domains responsible for this association
      Title: The Arf GTPase-activating protein SMAP1 promotes transferrin receptor endocytosis and interacts with SMAP2.
    3. In the current study, there were identified sequences in the carboxy-terminal region of SMAP2 that are critical for its specific subcellular localization and its specificity for Arf proteins.
      Title: The carboxy-terminal region of SMAP2 directs subcellular localization as well as Arf protein specificity.
    4. analyses revealed that three common polymorphisms, rs2982510, rs2294752, and rs446738, were putatively associated with the increased susceptibility to AIA
      Title: Putative association of SMAPIL polymorphisms with risk of aspirin intolerance in asthmatics.
    5. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Putative association of SMAPIL polymorphisms with risk of aspirin intolerance in asthmatics.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    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)

    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 GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    stromal membrane-associated protein 2
    Names
    stromal membrane-associated GTPase-activating protein 2

    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.

    mRNA and Protein(s)

    1. NM_001198978.2 → NP_001185907.1  stromal membrane-associated protein 2 isoform 3

      See identical proteins and their annotated locations for NP_001185907.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has an alternate 5' exon compared to variant 1. The resulting isoform (3) has a shorter and distinct N-terminus, as compared to isoform 1.
      Source sequence(s)
      AL133206, DC411665
      Consensus CDS
      CCDS55592.1
      UniProtKB/Swiss-Prot
      Q8WU79
      Related
      ENSP00000361793.1, ENST00000372708.5
      Conserved Domains (2) summary
      pfam01412
      Location:4 → 96
      ArfGap; Putative GTPase activating protein for Arf
      pfam09606
      Location:247 → 391
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

    2. NM_001198979.2 → NP_001185908.1  stromal membrane-associated protein 2 isoform 2

      See identical proteins and their annotated locations for NP_001185908.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate 5' exon compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus, as compared to isoform 1.
      Source sequence(s)
      AK308280, BC014512, BC021133
      Consensus CDS
      CCDS72763.1
      UniProtKB/TrEMBL
      A0A087WV97
      Related
      ENSP00000479285.1, ENST00000614549.4
      Conserved Domains (1) summary
      cl28907
      Location:31 → 117
      ArfGap; GTPase-activating protein (GAP) for the ADP ribosylation factors (ARFs)

    3. NM_001198980.1 → NP_001185909.1  stromal membrane-associated protein 2 isoform 4

      See identical proteins and their annotated locations for NP_001185909.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has an alternate 5' exon, resulting in a downstream AUG start codon, compared to variant 1. The resulting isoform (4) is shorter at the N-terminus, as compared to isoform 1.
      Source sequence(s)
      AK316218, BC014512, BC021133, BU617889
      Consensus CDS
      CCDS55593.1
      UniProtKB/Swiss-Prot
      Q8WU79
      Related
      ENSP00000442835.1, ENST00000539317.2
      Conserved Domains (2) summary
      pfam09606
      Location:197 → 341
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      cl28907
      Location:1 → 42
      ArfGap; GTPase-activating protein (GAP) for the ADP ribosylation factors (ARFs)

    4. NM_022733.3 → NP_073570.1  stromal membrane-associated protein 2 isoform 1

      See identical proteins and their annotated locations for NP_073570.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL133206, BC021133, DA082592
      Consensus CDS
      CCDS451.1
      UniProtKB/Swiss-Prot
      B2R7T1, B7Z5B5, B7Z8V2, D3DPV2, Q5QPL2, Q8WU79, Q96C93, Q9NST2, Q9UJL8
      Related
      ENSP00000361803.3, ENST00000372718.8
      Conserved Domains (1) summary
      cd08859
      Location:16 → 122
      ArfGap_SMAP2; Stromal membrane-associated protein 2; a subfamily of the ArfGAP family

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      40344834..40423326
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428009.1 → XP_047283965.1  stromal membrane-associated protein 2 isoform X1

    2. XM_047428011.1 → XP_047283967.1  stromal membrane-associated protein 2 isoform X2

    3. XM_047428017.1 → XP_047283973.1  stromal membrane-associated protein 2 isoform X3

    4. XM_047428014.1 → XP_047283970.1  stromal membrane-associated protein 2 isoform X2

    5. XM_011541960.3 → XP_011540262.1  stromal membrane-associated protein 2 isoform X2

      Conserved Domains (1) summary
      pfam01412
      Location:8 → 101
      ArfGap; Putative GTPase activating protein for Arf

    6. XM_047428015.1 → XP_047283971.1  stromal membrane-associated protein 2 isoform X3

    7. XM_047428013.1 → XP_047283969.1  stromal membrane-associated protein 2 isoform X2

    8. XM_047428012.1 → XP_047283968.1  stromal membrane-associated protein 2 isoform X2

    9. XM_047428016.1 → XP_047283972.1  stromal membrane-associated protein 2 isoform X3

    10. XM_047428010.1 → XP_047283966.1  stromal membrane-associated protein 2 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      40214315..40292887
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338264.1 → XP_054194239.1  stromal membrane-associated protein 2 isoform X1

    2. XM_054338265.1 → XP_054194240.1  stromal membrane-associated protein 2 isoform X2

    3. XM_054338271.1 → XP_054194246.1  stromal membrane-associated protein 2 isoform X3

    4. XM_054338268.1 → XP_054194243.1  stromal membrane-associated protein 2 isoform X2

    5. XM_054338267.1 → XP_054194242.1  stromal membrane-associated protein 2 isoform X2

    6. XM_054338269.1 → XP_054194244.1  stromal membrane-associated protein 2 isoform X3

    7. XM_054338266.1 → XP_054194241.1  stromal membrane-associated protein 2 isoform X2

    8. XM_054338270.1 → XP_054194245.1  stromal membrane-associated protein 2 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WU79.1 GenPept UniProtKB/Swiss-Prot:Q8WU79

    Gene LinkOut

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