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SMAP1 small ArfGAP 1 [ Homo sapiens (human) ]

Gene ID: 60682, updated on 3-Apr-2024

Summary

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Official Symbol
SMAP1provided by HGNC
Official Full Name
small ArfGAP 1provided by HGNC
Primary source
HGNC:HGNC:19651
See related
Ensembl:ENSG00000112305 MIM:611372; AllianceGenome:HGNC:19651
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
SMAP-1
Summary
The protein encoded by this gene is similar to the mouse stromal membrane-associated protein-1. This similarity suggests that this human gene product is also a type II membrane glycoprotein involved in the erythropoietic stimulatory activity of stromal cells. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in brain (RPKM 17.8), esophagus (RPKM 10.4) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
6q13
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (70667883..70862015)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (71848459..72042553)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (71377586..71571718)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:71318535-71319052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:71319053-71319569 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:71326667-71326868 Neighboring gene spermine synthase pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24733 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17321 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:71386575-71387144 Neighboring gene solute carrier family 25 member 6 pseudogene 6 Neighboring gene transmembrane protein 192 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24734 Neighboring gene NADH:ubiquinone oxidoreductase subunit AB1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:71481211-71481711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17323 Neighboring gene beta-1,3-glucuronyltransferase 2 Neighboring gene uncharacterized LOC105377850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:71666023-71666538 Neighboring gene uncharacterized LOC124901229

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. Cloning, characterization and chromosome mapping of the human SMAP1 gene. Marcos I, et al. Gene, 2002 Jun 12. PMID 12119110
  2. 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
  3. Involvement of small ArfGAP1 (SMAP1), a novel Arf6-specific GTPase-activating protein, in microsatellite instability oncogenesis. Sangar F, et al. Oncogene, 2014 May 22. PMID 23752192
  4. Mutation screening of three candidate genes, ELOVL5, SMAP1 and GLULD1 in autosomal recessive retinitis pigmentosa. Barragan I, et al. Int J Mol Med, 2005 Dec. PMID 16273301
  5. Involvement of stromal membrane-associated protein (SMAP-1) in erythropoietic microenvironment. Sato Y, et al. J Biochem, 1998 Jul. PMID 9644265

See all (41) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Pals1 functions in redundancy with SMAP1 to inhibit Arf6 in order to prevent Rac1-dependent colorectal cancer cell migration and invasion.
    Title: Pals1 functions in redundancy with SMAP1 to inhibit Arf6 in order to prevent Rac1-dependent colorectal cancer cell migration and invasion.
  2. The study identified a region on chromosome 6 comprising the genes SMAP1, B3GAT2, and RIMS1 as novel susceptibility locus for pediatric venous thromboembolism.
    Title: Rare genetic variants in SMAP1, B3GAT2, and RIMS1 contribute to pediatric venous thromboembolism.
  3. 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.
  4. SMAP1 loss-of-function mutations in microsatellite instability colorectal cancer may contribute to the emerging oncogenic pathway involving abnormal Arf6 regulation.
    Title: Involvement of small ArfGAP1 (SMAP1), a novel Arf6-specific GTPase-activating protein, in microsatellite instability oncogenesis.
  5. SMAP1 may be an ADP-ribosylation factor 6 (Arf6)GAP that specifically regulates one of the multiple functions of Arf6, namely, clathrin-dependent endocytosis
    Title: A novel GTPase-activating protein for ARF6 directly interacts with clathrin and regulates clathrin-dependent endocytosis.
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

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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Replication interactions

Interaction Pubs
Knockdown of small ArfGAP 1 (SMAP1) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat 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

Clone Names

  • FLJ13159, FLJ42245

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables clathrin binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in positive regulation of erythrocyte differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of clathrin-dependent endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
stromal membrane-associated protein 1
Names
stromal membrane-associated GTPase-activating 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.

mRNA and Protein(s)

  1. NM_001044305.3 → NP_001037770.1  stromal membrane-associated protein 1 isoform A

    See identical proteins and their annotated locations for NP_001037770.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (A).
    Source sequence(s)
    AF442495, BC036123, DB480952
    Consensus CDS
    CCDS43478.1
    UniProtKB/Swiss-Prot
    Q53H70, Q5SYQ2, Q6PK24, Q8IYB5, Q8NDH4, Q96L38, Q96L39, Q9H8X4
    UniProtKB/TrEMBL
    A8K333
    Related
    ENSP00000359484.3, ENST00000370455.8
    Conserved Domains (1) summary
    pfam01412
    Location:20 → 120
    ArfGap; Putative GTPase activating protein for Arf

  2. NM_001281439.2 → NP_001268368.1  stromal membrane-associated protein 1 isoform C

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple coding region differences, compared to variant 1, one of which results in a frameshift. The resulting protein (isoform C) has a distinct C-terminus and is shorter than isoform A.
    Source sequence(s)
    AF442495, AK023221, AL121961, BC008672, BC036123, DB480952
    Consensus CDS
    CCDS64459.1
    UniProtKB/TrEMBL
    B2RDK5
    Related
    ENSP00000359481.3, ENST00000370452.7
    Conserved Domains (1) summary
    pfam01412
    Location:20 → 120
    ArfGap; Putative GTPase activating protein for Arf

  3. NM_001281440.1 → NP_001268369.1  stromal membrane-associated protein 1 isoform D

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (D) has a distinct N-terminus and is shorter than isoform A.
    Source sequence(s)
    AF442495, AK307807, BC036123, DA527013
    Consensus CDS
    CCDS75478.1
    UniProtKB/TrEMBL
    A0A087X1X9, A8K333
    Related
    ENSP00000484538.1, ENST00000619054.4
    Conserved Domains (1) summary
    pfam01412
    Location:30 → 110
    ArfGap; Putative GTPase activating protein for Arf

  4. NM_021940.5 → NP_068759.2  stromal membrane-associated protein 1 isoform B

    See identical proteins and their annotated locations for NP_068759.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform B), compared to isoform A.
    Source sequence(s)
    AF442495, BC036123
    Consensus CDS
    CCDS4973.1
    UniProtKB/TrEMBL
    B2RDK5
    Related
    ENSP00000313382.5, ENST00000316999.9
    Conserved Domains (2) summary
    pfam01412
    Location:20 → 120
    ArfGap; Putative GTPase activating protein for Arf
    pfam09606
    Location:283 → 431
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    70667883..70862015
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011536047.4 → XP_011534349.1  stromal membrane-associated protein 1 isoform X6

    UniProtKB/TrEMBL
    B2RDK5
    Conserved Domains (1) summary
    pfam01412
    Location:20 → 120
    ArfGap; Putative GTPase activating protein for Arf

  2. XM_005248760.6 → XP_005248817.1  stromal membrane-associated protein 1 isoform X4

    Conserved Domains (1) summary
    pfam01412
    Location:20 → 120
    ArfGap; Putative GTPase activating protein for Arf

  3. XM_047419230.1 → XP_047275186.1  stromal membrane-associated protein 1 isoform X5

  4. XM_047419227.1 → XP_047275183.1  stromal membrane-associated protein 1 isoform X1

  5. XM_047419228.1 → XP_047275184.1  stromal membrane-associated protein 1 isoform X2

  6. XM_047419229.1 → XP_047275185.1  stromal membrane-associated protein 1 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    71848459..72042553
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356169.1 → XP_054212144.1  stromal membrane-associated protein 1 isoform X6

  2. XM_054356167.1 → XP_054212142.1  stromal membrane-associated protein 1 isoform X4

  3. XM_054356168.1 → XP_054212143.1  stromal membrane-associated protein 1 isoform X5

  4. XM_054356164.1 → XP_054212139.1  stromal membrane-associated protein 1 isoform X1

  5. XM_054356165.1 → XP_054212140.1  stromal membrane-associated protein 1 isoform X2

  6. XM_054356166.1 → XP_054212141.1  stromal membrane-associated protein 1 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IYB5.2 GenPept UniProtKB/Swiss-Prot:Q8IYB5

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