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SGSM3 small G protein signaling modulator 3 [ Homo sapiens (human) ]

Gene ID: 27352, updated on 3-Apr-2024

Summary

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Official Symbol
SGSM3provided by HGNC
Official Full Name
small G protein signaling modulator 3provided by HGNC
Primary source
HGNC:HGNC:25228
See related
Ensembl:ENSG00000100359 MIM:610440; AllianceGenome:HGNC:25228
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
MAP; CIP85; RUSC3; RUTBC3; RABGAP5; RabGAP-5; rabGAPLP
Summary
Enables GTPase activator activity and small GTPase binding activity. Involved in several processes, including Rap protein signal transduction; positive regulation of GTPase activity; and regulation of Rab protein signal transduction. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in stomach (RPKM 33.5), prostate (RPKM 23.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
22q13.1
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (40370594..40410289)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (40842001..40880672)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (40766598..40806293)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene trinucleotide repeat containing adaptor 6B Neighboring gene ribosomal protein L7 pseudogene 52 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19082 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:40591286-40591820 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:40591821-40592353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19083 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40624195-40624696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40633809-40634710 Neighboring gene uncharacterized LOC124905121 Neighboring gene MPRA-validated peak4496 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr22:40740204-40740376 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40742019-40742532 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40742533-40743046 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40743047-40743559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19085 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19086 Neighboring gene adenylosuccinate lyase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40812395-40812894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19092 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19091 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:40851734-40851957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19093 Neighboring gene myocardin related transcription factor A Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:40867879-40868537 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40894439-40894938 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40906589-40907133 Neighboring gene MRTFA antisense RNA 1 Neighboring gene uncharacterized LOC105373037

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. Evaluation of 4-bp insertion/deletion polymorphism within the 3'UTR of SGSM3 in bladder cancer using mismatch PCR-RFLP method: A preliminary report. Hashemi M, et al. J Cell Biochem, 2018 Aug. PMID 29693742
  2. Association between an insertion/deletion polymorphism within 3'UTR of SGSM3 and risk of hepatocellular carcinoma. Wang C, et al. Tumour Biol, 2014 Jan. PMID 23918301
  3. Genetic variants of ESR1 and SGSM3 are associated with the susceptibility of breast cancer in the Chinese population. Tan T, et al. Breast Cancer, 2017 May. PMID 27432265
  4. The connexin43-interacting protein, CIP85, mediates the internalization of connexin43 from the plasma membrane. Cochrane K, et al. Cell Commun Adhes, 2013 Aug. PMID 23586710
  5. A GTPase-activating protein controls Rab5 function in endocytic trafficking. Haas AK, et al. Nat Cell Biol, 2005 Sep. PMID 16086013

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Intellectual disability syndrome associated with a homozygous founder variant in SGSM3 in Ashkenazi Jews.
    Title: Intellectual disability syndrome associated with a homozygous founder variant in SGSM3 in Ashkenazi Jews.
  2. findings support an association between 4-bp ins/del polymorphism in the 3'UTR of SGSM3 and the risk of bladder cancer in an Iranian population.
    Title: Evaluation of 4-bp insertion/deletion polymorphism within the 3'UTR of SGSM3 in bladder cancer using mismatch PCR-RFLP method: A preliminary report.
  3. SGSM3 gene polymorphism is associated with the risk of breast cancer in Chinese population.
    Title: Genetic variants of ESR1 and SGSM3 are associated with the susceptibility of breast cancer in the Chinese population.
  4. The CIP85 was observed to interact with clathrin, which suggested a role for CIP85 in the clathrin-mediated internalization of Cx43.
    Title: The connexin43-interacting protein, CIP85, mediates the internalization of connexin43 from the plasma membrane.
  5. rs56228771 may contribute to hepatocarcinogenesis, possibly by affecting SGSM3 expression through a miRNA-mediated regulation.
    Title: Association between an insertion/deletion polymorphism within 3'UTR of SGSM3 and risk of hepatocellular carcinoma.
  6. Identification of novel protein SGSM3 which modulates small G protein (RAP and RAB)-mediated signaling pathway.
    Title: Identification of three novel proteins (SGSM1, 2, 3) which modulate small G protein (RAP and RAB)-mediated signaling pathway.
  7. MAP decreased the AP-1-dependent promoter activity additively with merlin in NIH3T3 cells.Results suggest that MAP may play a cooperative role in the merlin-mediated growth suppression of cells.
    Title: MAP, a protein interacting with a tumor suppressor, merlin, through the run domain.
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
A genome-wide association study of northwestern Europeans involves the C-type natriuretic peptide signaling pathway in the etiology of human height variation.
EBI GWAS Catalog
Genome-wide association study identifies multiple loci associated with both mammographic density and breast cancer risk.
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

Clone Names

  • DKFZp761D051

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables GTPase activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables small GTPase binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables small GTPase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Rap protein signal transduction IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in activation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in plasma membrane to endosome transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of protein catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of Rab protein signal transduction IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in regulation of cell cycle IEA
Inferred from Electronic Annotation
more info
  
NOT involved_in regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in gap junction IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
small G protein signaling modulator 3
Names
RUN and SH3 containing 3
RUN and TBC1 domain containing 3
RUN and TBC1 domain-containing protein 3
merlin binding protein
merlin-associated protein
rab-GTPase-activating protein-like protein
small G protein signaling modulator 3 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.

mRNA and Protein(s)

  1. NM_001301849.2 → NP_001288778.1  small G protein signaling modulator 3 isoform 2

    See identical proteins and their annotated locations for NP_001288778.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has multiple differences in the coding region, one of which results in the use of an alternate start codon compared to variant 1. It encodes isoform 2 which has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK301042, AW512418, BC008078, BP283990, HY229847
    UniProtKB/TrEMBL
    B4DMS2, B4DVE3, E9PEL5
    Conserved Domains (3) summary
    cd11813
    Location:421 → 473
    SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
    smart00164
    Location:51 → 262
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    pfam02759
    Location:480 → 628
    RUN; RUN domain

  2. NM_001350039.2 → NP_001336968.1  small G protein signaling modulator 3 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL022238, AW512418, BC008078, BP283990, HY229847
    Conserved Domains (3) summary
    cd11813
    Location:484 → 536
    SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
    smart00164
    Location:114 → 325
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    pfam02759
    Location:563 → 731
    RUN; RUN domain

  3. NM_001350040.2 → NP_001336969.1  small G protein signaling modulator 3 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL022238, AW512418, BC008078, BP283990, HY231525
    Conserved Domains (3) summary
    cd11813
    Location:484 → 536
    SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
    smart00164
    Location:114 → 325
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    pfam02759
    Location:563 → 731
    RUN; RUN domain

  4. NM_001350041.2 → NP_001336970.1  small G protein signaling modulator 3 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AW512418, BC008078, BP283990, BU684524
    UniProtKB/TrEMBL
    B4DMS2, E9PEL5

  5. NM_001350042.2 → NP_001336971.1  small G protein signaling modulator 3 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AK301042, AL022238, AW512418, BC008078, BP283990, HY229847
    UniProtKB/TrEMBL
    B4DMS2, E9PEL5
    Conserved Domains (3) summary
    cd11813
    Location:421 → 473
    SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
    smart00164
    Location:51 → 262
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    pfam02759
    Location:500 → 668
    RUN; RUN domain

  6. NM_001350043.2 → NP_001336972.1  small G protein signaling modulator 3 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AL022238, AW512418, BC008078, BX424691, HY229847
    UniProtKB/TrEMBL
    B4DMS2, E9PEL5
    Conserved Domains (3) summary
    cd11813
    Location:417 → 469
    SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
    smart00164
    Location:47 → 258
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    pfam02759
    Location:496 → 664
    RUN; RUN domain

  7. NM_001350044.2 → NP_001336973.1  small G protein signaling modulator 3 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AK301042, AW512418, BC008078, BP283990, BX388288, DC389110, HY229847
    UniProtKB/TrEMBL
    B4DMS2, E9PEL5
    Conserved Domains (3) summary
    cd11813
    Location:421 → 473
    SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
    smart00164
    Location:51 → 262
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    pfam02759
    Location:500 → 651
    RUN; RUN domain

  8. NM_001350045.2 → NP_001336974.1  small G protein signaling modulator 3 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AK301042, AW512418, BC008078, BP283990, BX388288, HY229847
    UniProtKB/TrEMBL
    B4DMS2, E9PEL5
    Conserved Domains (3) summary
    cd11813
    Location:421 → 473
    SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
    smart00164
    Location:51 → 262
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    pfam02759
    Location:500 → 651
    RUN; RUN domain

  9. NM_001350046.2 → NP_001336975.1  small G protein signaling modulator 3 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AW512418, BC008078, BX424691, HY149764, HY229847
    UniProtKB/TrEMBL
    B4DMS2, E9PEL5
    Conserved Domains (3) summary
    cd11813
    Location:417 → 469
    SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
    smart00164
    Location:47 → 258
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    pfam02759
    Location:496 → 647
    RUN; RUN domain

  10. NM_001350047.2 → NP_001336976.1  small G protein signaling modulator 3 isoform 10

    Status: VALIDATED

    Source sequence(s)
    AW512418, BC008078, BX430401, HY231525
    UniProtKB/TrEMBL
    B4DMS2, E9PEL5

  11. NM_001350048.2 → NP_001336977.1  small G protein signaling modulator 3 isoform 11

    Status: VALIDATED

    Source sequence(s)
    AW512418, BC008078, BX428466, BX430401, HY149764, HY229847
    UniProtKB/TrEMBL
    B4DMS2, E9PEL5
    Conserved Domains (3) summary
    cd11813
    Location:318 → 370
    SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
    pfam00566
    Location:7 → 159
    RabGAP-TBC; Rab-GTPase-TBC domain
    pfam02759
    Location:397 → 548
    RUN; RUN domain

  12. NM_015705.6 → NP_056520.2  small G protein signaling modulator 3 isoform 1

    See identical proteins and their annotated locations for NP_056520.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AW512418, BC008078, BP283990, HY229847
    Consensus CDS
    CCDS14002.1
    UniProtKB/Swiss-Prot
    B0QY79, Q7Z709, Q96HU1, Q9NT69
    UniProtKB/TrEMBL
    B9A6J5
    Related
    ENSP00000248929.8, ENST00000248929.14
    Conserved Domains (3) summary
    cd11813
    Location:484 → 536
    SH3_SGSM3; Src Homology 3 domain of Small G protein Signaling Modulator 3
    smart00164
    Location:114 → 325
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    pfam02759
    Location:563 → 714
    RUN; RUN domain

RNA

  1. NR_146412.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL022238, AW512418, BC008078, BP283990, HY229847

  2. NR_146413.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL022238, AW512418, BC008078, BX424691, HY149764, HY229847

  3. NR_146414.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL022238, AW512418, BC008078, BX428466, DC386475, HY229847

  4. NR_146415.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL022238, AW512418, BC008078, BX428466, BX430401, HY149764, HY229847

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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    40370594..40410289
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047441336.1 → XP_047297292.1  small G protein signaling modulator 3 isoform X1

  2. XM_047441337.1 → XP_047297293.1  small G protein signaling modulator 3 isoform X2

  3. XM_047441338.1 → XP_047297294.1  small G protein signaling modulator 3 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    40842001..40880672
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054325558.1 → XP_054181533.1  small G protein signaling modulator 3 isoform X1

  2. XM_054325559.1 → XP_054181534.1  small G protein signaling modulator 3 isoform X2

  3. XM_054325560.1 → XP_054181535.1  small G protein signaling modulator 3 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96HU1.1 GenPept UniProtKB/Swiss-Prot:Q96HU1

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