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

Gene ID: 6457, updated on 5-Mar-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; early endosome membrane; and presynapse. Predicted to be part of early endosome. Predicted to be active in glutamatergic synapse; postsynaptic density, intracellular component; and postsynaptic endosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis (RPKM 8.3), brain (RPKM 5.2) and 1 other tissue See more
Orthologs
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Genomic context

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Location:
15q25.2
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (83447341..83633820)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (81315250..81486674)
105.20220307 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
  • 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. Neural Wiskott-Aldrich syndrome protein is recruited to rafts and associates with endophilin A in response to epidermal growth factor. Otsuki M, et al. J Biol Chem, 2003 Feb 21. PMID 12477732
  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 (60) 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 Variation Viewer (GRCh37.p13)

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_2023_10

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

Gene LinkOut

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