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    SH3GL3 SH3 domain containing GRB2 like 3, endophilin A3 [ Homo sapiens (human) ]

    Gene ID: 6457, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SH3GL3provided by HGNC
    Official Full Name
    SH3 domain containing GRB2 like 3, endophilin A3provided by HGNC
    Primary source
    HGNC:HGNC:10832
    See related
    Ensembl:ENSG00000140600 MIM:603362; AllianceGenome:HGNC:10832
    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
    CNSA3; EEN-B2; SH3D2C; SH3P13; HsT19371
    Summary
    Enables identical protein binding activity. Predicted to be involved in synaptic vesicle uncoating. Predicted to be located in acrosomal vesicle and early endosome membrane. Predicted to be part of early endosome. Predicted to be active in several cellular components, including glutamatergic synapse; postsynaptic density, intracellular component; and postsynaptic endosome. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis (RPKM 8.3), brain (RPKM 5.2) and 1 other tissue See more
    Orthologs
    mouse all
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    Genomic context

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    See SH3GL3 in Genome Data Viewer
    Location:
    15q25.2
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (83447341..83633820)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (81315250..81486674)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (84116093..84287495)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370933 Neighboring gene uncharacterized LOC105370934 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:84047926-84049125 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:84052681-84053310 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:84067046-84068245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9973 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:84124682-84125286 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:84198348-84198848 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41536 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41540 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41539 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41541 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41543 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41546 Neighboring gene ADAMTS like 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:84361608-84362108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:84362109-84362609 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41575 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41592 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41598 Neighboring gene RNA, U6 small nuclear 401, pseudogene Neighboring gene tubulin alpha pseudogene 4

    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. SH3GL3 acts as a novel tumor suppressor in glioblastoma tumorigenesis by inhibiting STAT3 signaling. Nie Z, et al. Biochem Biophys Res Commun, 2021 Mar 12. PMID 33524871
    2. SH3GL3 functions as a potent tumor suppressor in lung cancer in a SH3 domain dependent manner. Lin Z, et al. Biochem Biophys Res Commun, 2021 Jan 1. PMID 33168185
    3. The role of SH3GL3 in myeloma cell migration/invasion, stemness and chemo-resistance. Chen R, et al. Oncotarget, 2016 Nov 8. PMID 27683032, Free PMC Article
    4. LncRNA MIR210HG promotes the proliferation, migration, and invasion of lung cancer cells by inhibiting the transcription of SH3GL3. Zou F, et al. Kaohsiung J Med Sci, 2023 Dec. PMID 37916731
    5. SH3GL3 associates with the Huntingtin exon 1 protein and promotes the formation of polygln-containing protein aggregates. Sittler A, et al. Mol Cell, 1998 Oct. PMID 9809064

    See all (61) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LncRNA MIR210HG promotes the proliferation, migration, and invasion of lung cancer cells by inhibiting the transcription of SH3GL3.
      Title: LncRNA MIR210HG promotes the proliferation, migration, and invasion of lung cancer cells by inhibiting the transcription of SH3GL3.
    2. SH3GL3 acts as a novel tumor suppressor in glioblastoma tumorigenesis by inhibiting STAT3 signaling.
      Title: SH3GL3 acts as a novel tumor suppressor in glioblastoma tumorigenesis by inhibiting STAT3 signaling.
    3. SH3GL3 functions as a potent tumor suppressor in lung cancer in a SH3 domain dependent manner.
      Title: SH3GL3 functions as a potent tumor suppressor in lung cancer in a SH3 domain dependent manner.
    4. Endophilin-A3 functionally associates with CD166-containing early endocytic carriers and physically interacts with the cargo. Study provides strong evidence that the construction of endocytic sites from which CD166 is taken up in an endophilin-A3-dependent manner is driven by extracellular galectin-8, revealing the existence of a previously uncharacterized clathrin-independent endocytic modality in cancer cells.
      Title: Endophilin-A3 and Galectin-8 control the clathrin-independent endocytosis of CD166.
    5. Our findings indicate that SH3GL3 plays an important role in myeloma cell migration/invasion, stemness and chemo-resistance. The SH3GL3-mediated myeloma cell migration/invasion is mediated by FAK/PI3K signaling pathway.
      Title: The role of SH3GL3 in myeloma cell migration/invasion, stemness and chemo-resistance.
    6. Aberrant DNA methylation of SH3GL3 gene is associated with colorectal cancer.
      Title: Genome-wide analysis of aberrant DNA methylation for identification of potential biomarkers in colorectal cancer patients.
    7. SH3GL3 as a novel glioma invasion-associated candidate gene that likely contribute to the invasive phenotype of malignant gliomas.
      Title: Identification and functional validation of CDH11, PCSK6 and SH3GL3 as novel glioma invasion-associated candidate genes.
    8. These data implicate ataxin-2 to play a role in endocytic receptor cycling.[Endophilin A3]
      Title: Ataxin-2 associates with the endocytosis complex and affects EGF receptor trafficking.
    9. importance of hapln1b and sh3gl3 in embryonic vascular development
      Title: Discovery and characterization of novel vascular and hematopoietic genes downstream of etsrp in zebrafish.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of height and body mass index in Australian twin families.
    EBI GWAS Catalog
    Identification of ten loci associated with height highlights new biological pathways in human growth.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    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 identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables lipid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in central nervous system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of clathrin-dependent endocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in synaptic vesicle uncoating IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in acrosomal vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in glutamatergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in postsynaptic density, intracellular component IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynaptic endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in presynapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    endophilin-A3
    Names
    SH3 domain containing GRB2 like endophilin A3
    SH3 domain protein 2C
    SH3 domain-containing GRB2-like protein 3
    SH3-domain GRB2-like 3
    endophilin-3

    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_001301108.2 → NP_001288037.1  endophilin-A3 isoform b

      See identical proteins and their annotated locations for NP_001288037.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (EEN-B2-L2) uses an alternate splice site, and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant EEN-B2-L1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a. Variants 2, 9, and 14 all encode the same isoform (b).
      Source sequence(s)
      AK307442, AK309086, BC035598
      Conserved Domains (2) summary
      cd11803
      Location:219 → 273
      SH3_Endophilin_A; Src homology 3 domain of Endophilin-A
      cl12013
      Location:1 → 178
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    2. NM_001301109.2 → NP_001288038.1  endophilin-A3 isoform c

      See identical proteins and their annotated locations for NP_001288038.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (EEN-B2-L3) includes three additional exons, and it thus differs in its 5' UTR and initiates translation at an alternate start codon, compared to variant EEN-B2-L1. The encoded isoform (c) has a distinct N-terminus and is longer than isoform a.
      Source sequence(s)
      AF036271, AK309086, BC035598
      Consensus CDS
      CCDS73772.1
      UniProtKB/Swiss-Prot
      Q99963
      Related
      ENSP00000320092.5, ENST00000324537.5
      Conserved Domains (2) summary
      cd07615
      Location:33 → 255
      BAR_Endophilin_A3; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A3
      cd11803
      Location:296 → 350
      SH3_Endophilin_A; Src homology 3 domain of Endophilin-A

    3. NM_001324182.2 → NP_001311111.1  endophilin-A3 isoform d

      Status: VALIDATED

      Source sequence(s)
      AC025483, AC087738, AC090083

    4. NM_001324183.2 → NP_001311112.1  endophilin-A3 isoform c

      Status: VALIDATED

      Source sequence(s)
      AC025483, AC087738, AC090083
      Consensus CDS
      CCDS73772.1
      UniProtKB/Swiss-Prot
      Q99963
      Conserved Domains (2) summary
      cd07615
      Location:33 → 255
      BAR_Endophilin_A3; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A3
      cd11803
      Location:296 → 350
      SH3_Endophilin_A; Src homology 3 domain of Endophilin-A

    5. NM_001324184.2 → NP_001311113.1  endophilin-A3 isoform e

      Status: VALIDATED

      Source sequence(s)
      AC025483, AC087738, AC090083
      Conserved Domains (2) summary
      cd07615
      Location:1 → 212
      BAR_Endophilin_A3; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A3
      cd11803
      Location:253 → 307
      SH3_Endophilin_A; Src homology 3 domain of Endophilin-A

    6. NM_001324185.2 → NP_001311114.1  endophilin-A3 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9), as well as variants 2 and 14, encodes isoform b (also called isoform f).
      Source sequence(s)
      AC025483, AC087738, AC090083
      Conserved Domains (2) summary
      cd11803
      Location:219 → 273
      SH3_Endophilin_A; Src homology 3 domain of Endophilin-A
      cl12013
      Location:1 → 178
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    7. NM_001324186.2 → NP_001311115.1  endophilin-A3 isoform e

      Status: VALIDATED

      Source sequence(s)
      AC025483, AC087738, AC090083
      Conserved Domains (2) summary
      cd07615
      Location:1 → 212
      BAR_Endophilin_A3; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A3
      cd11803
      Location:253 → 307
      SH3_Endophilin_A; Src homology 3 domain of Endophilin-A

    8. NM_001324187.1 → NP_001311116.1  endophilin-A3 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (14), as well as variants 2 and 9, encodes isoform b (also called isoform f).
      Source sequence(s)
      AC025483, AC087738, AC090083
      Conserved Domains (2) summary
      cd11803
      Location:219 → 273
      SH3_Endophilin_A; Src homology 3 domain of Endophilin-A
      cl12013
      Location:1 → 178
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    9. NM_003027.5 → NP_003018.3  endophilin-A3 isoform a

      See identical proteins and their annotated locations for NP_003018.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (EEN-B2-L1) encodes isoform a.
      Source sequence(s)
      AF036269, AK309086, BC035598
      Consensus CDS
      CCDS10325.2
      UniProtKB/Swiss-Prot
      O43553, O43554, Q99963
      UniProtKB/TrEMBL
      Q8IVP1
      Related
      ENSP00000391372.2, ENST00000427482.7
      Conserved Domains (2) summary
      cd07615
      Location:25 → 247
      BAR_Endophilin_A3; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A3
      cd11803
      Location:288 → 342
      SH3_Endophilin_A; Src homology 3 domain of Endophilin-A

    RNA

    1. NR_125370.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an additional exon in the 3' region, compared to variant EEN-B2-L1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant EEN-B2-L1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK309086, BC035598, BC042864

    2. NR_136711.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC025483, AC087738, AC090083

    3. NR_136712.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC025483, AC087738, AC090083

    4. NR_136713.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC025483, AC087738, AC090083

    5. NR_136714.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC025483, AC087738, AC090083
      Related
      ENST00000563901.5

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      83447341..83633820
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521889.2 → XP_011520191.1  endophilin-A3 isoform X1

      See identical proteins and their annotated locations for XP_011520191.1

      UniProtKB/Swiss-Prot
      Q99963
      Conserved Domains (2) summary
      cd07615
      Location:33 → 255
      BAR_Endophilin_A3; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A3
      cd11803
      Location:296 → 350
      SH3_Endophilin_A; Src homology 3 domain of Endophilin-A

    2. XM_047432940.1 → XP_047288896.1  endophilin-A3 isoform X3

    3. XM_011521892.3 → XP_011520194.1  endophilin-A3 isoform X4

      Conserved Domains (1) summary
      cl12013
      Location:33 → 217
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    4. XM_017022486.3 → XP_016877975.1  endophilin-A3 isoform X2

      Conserved Domains (2) summary
      cd11803
      Location:219 → 273
      SH3_Endophilin_A; Src homology 3 domain of Endophilin-A
      cl12013
      Location:1 → 178
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    RNA

    1. XR_007064483.1 RNA Sequence

    2. XR_007064484.1 RNA Sequence

    3. XR_931879.3 RNA Sequence

    4. XR_007064485.1 RNA Sequence

    5. XR_001751372.2 RNA Sequence

    6. XR_007064486.1 RNA Sequence

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791797.1 Reference GRCh38.p14 PATCHES

      Range
      53135..224537
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054333169.1 → XP_054189144.1  endophilin-A3 isoform X1

    2. XM_054333171.1 → XP_054189146.1  endophilin-A3 isoform X3

    3. XM_054333172.1 → XP_054189147.1  endophilin-A3 isoform X4

    4. XM_054333170.1 → XP_054189145.1  endophilin-A3 isoform X2

    RNA

    1. XR_008485826.1 RNA Sequence

    2. XR_008485828.1 RNA Sequence

    3. XR_008485827.1 RNA Sequence

    4. XR_008485829.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      81315250..81486674
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378616.1 → XP_054234591.1  endophilin-A3 isoform X1

    2. XM_054378618.1 → XP_054234593.1  endophilin-A3 isoform X3

    3. XM_054378619.1 → XP_054234594.1  endophilin-A3 isoform X4

    4. XM_054378617.1 → XP_054234592.1  endophilin-A3 isoform X2

    RNA

    1. XR_008489004.1 RNA Sequence

    2. XR_008489006.1 RNA Sequence

    3. XR_008489005.1 RNA Sequence

    4. XR_008489007.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99963.1 GenPept UniProtKB/Swiss-Prot:Q99963

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