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SH2D3C SH2 domain containing 3C [ Homo sapiens (human) ]

Gene ID: 10044, updated on 2-Nov-2024

Summary

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Official Symbol
SH2D3Cprovided by HGNC
Official Full Name
SH2 domain containing 3Cprovided by HGNC
Primary source
HGNC:HGNC:16884
See related
Ensembl:ENSG00000095370 MIM:604722; AllianceGenome:HGNC:16884
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
CHAT; NSP3; SHEP1; PRO34088
Summary
This gene encodes an adaptor protein and member of a cytoplasmic protein family involved in cell migration. The encoded protein contains a putative Src homology 2 (SH2) domain and guanine nucleotide exchange factor-like domain which allows this signaling protein to form a complex with scaffolding protein Crk-associated substrate. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
Expression
Broad expression in spleen (RPKM 12.4), lung (RPKM 10.5) and 22 other tissues See more
Orthologs
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Genomic context

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See SH2D3C in Genome Data Viewer
Location:
9q34.11
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (127738317..127778666, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (139945763..139986120, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130500596..130540945, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene peptidyl-tRNA hydrolase 1 homolog Neighboring gene cilia and flagella associated protein 157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130476687-130477343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29045 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29047 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130478240-130478416 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130480462-130480664 Neighboring gene tetratricopeptide repeat domain 16 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130488893-130489394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130496147-130497053 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20308 Neighboring gene torsin family 2 member A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130504225-130504852 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130523547-130524424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130524425-130525300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130526508-130527090 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20309 Neighboring gene uncharacterized LOC107987132 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130539526-130539796 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29049 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29050 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130545551-130545741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29052 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20310 Neighboring gene Sharpr-MPRA regulatory region 7866 Neighboring gene Sharpr-MPRA regulatory region 2041 Neighboring gene microRNA 3960 Neighboring gene microRNA 2861 Neighboring gene cyclin dependent kinase 9

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. A novel signaling intermediate, SHEP1, directly couples Eph receptors to R-Ras and Rap1A. Dodelet VC, et al. J Biol Chem, 1999 Nov 5. PMID 10542222
  2. Splice variants and expression patterns of SHEP1, BCAR3 and NSP1, a gene family involved in integrin and receptor tyrosine kinase signaling. Vervoort VS, et al. Gene, 2007 Apr 15. PMID 17270363, Free PMC Article
  3. NSP-Cas protein structures reveal a promiscuous interaction module in cell signaling. Mace PD, et al. Nat Struct Mol Biol, 2011 Nov 13. PMID 22081014, Free PMC Article
  4. SHEP1 function in cell migration is impaired by a single amino acid mutation that disrupts association with the scaffolding protein cas but not with Ras GTPases. Dail M, et al. J Biol Chem, 2004 Oct 1. PMID 15272013
  5. AND-34/BCAR3 differs from other NSP homologs in induction of anti-estrogen resistance, cyclin D1 promoter activation and altered breast cancer cell morphology. Near RI, et al. J Cell Physiol, 2007 Sep. PMID 17427198, Free PMC Article

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The structure of the NSP3-p130Cas complex reveals that this closed conformation is instrumental for interaction of NSP proteins with a focal adhesion-targeting domain present in Cas proteins.
    Title: NSP-Cas protein structures reveal a promiscuous interaction module in cell signaling.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate.
  3. NSP3 overexpression did not induce anti-estrogen resistance in breast tumor cell lines.
    Title: AND-34/BCAR3 differs from other NSP homologs in induction of anti-estrogen resistance, cyclin D1 promoter activation and altered breast cancer cell morphology.
  4. This protein positively regulates T cell receptor-mediated interleukin-2 production by Jurkat cells.
    Title: A novel hematopoietic adaptor protein, Chat-H, positively regulates T cell receptor-mediated interleukin-2 production by Jurkat cells.
  5. SH2D3C (SHEP1) is less highly expressed than BCAR3 and NSP1 in breast cancer cells, and the expression patterns suggest differential roles for the three genes during breast cancer progression.
    Title: Splice variants and expression patterns of SHEP1, BCAR3 and NSP1, a gene family involved in integrin and receptor tyrosine kinase signaling.
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
Genetic variants associated with disordered eating.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ39664

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables guanyl-nucleotide exchange factor activity IEA
Inferred from Electronic Annotation
more info
  
enables phosphotyrosine residue 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 JNK cascade TAS
Traceable Author Statement
more info
 PubMed 
involved_in small GTPase-mediated signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in axon IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in ruffle membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
SH2 domain-containing protein 3C
Names
SH2 domain-containing Eph receptor-binding protein 1
cas/HEF1-associated signal transducer
chat-H
novel SH2-containing protein 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.

Genomic

  1. NG_030563.1 RefSeqGene

    Range
    5104..45453
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001142531.1 → NP_001136003.1  SH2 domain-containing protein 3C isoform c

    See identical proteins and their annotated locations for NP_001136003.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) includes an alternate exon in the 5' end resulting in use of a downstream start codon, compared to variant 1. It encodes isoform c which has a shorter N-terminus than isoform a. Variants 3 and 4 both encode isoform c.
    Source sequence(s)
    AI799905, AK294386, CU455802, DA054525
    Consensus CDS
    CCDS48028.1
    UniProtKB/TrEMBL
    B4DG32
    Conserved Domains (1) summary
    cl02485
    Location:231 → 400
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...

  2. NM_001142532.1 → NP_001136004.1  SH2 domain-containing protein 3C isoform c

    See identical proteins and their annotated locations for NP_001136004.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) includes an alternate exon in the 5' end resulting in use of a downstream start codon, compared to variant 1. It encodes isoform c which has a shorter N-terminus than isoform a. Variants 3 and 4 both encode isoform c.
    Source sequence(s)
    AI799905, AK311510, BX647905
    Consensus CDS
    CCDS48028.1
    UniProtKB/TrEMBL
    B4DG32
    Related
    ENSP00000394632.1, ENST00000429553.5
    Conserved Domains (1) summary
    cl02485
    Location:231 → 400
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...

  3. NM_001142533.1 → NP_001136005.1  SH2 domain-containing protein 3C isoform d

    See identical proteins and their annotated locations for NP_001136005.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) includes an alternate exon in the 5' coding region, compared to variant 1. It encodes isoform d, which is shorter and has a distinct N-terminus compared to isoform a.
    Source sequence(s)
    AI799905, AK056068, CU455802
    Consensus CDS
    CCDS48026.1
    UniProtKB/TrEMBL
    A8K7M6
    Related
    ENSP00000388536.1, ENST00000420366.5
    Conserved Domains (2) summary
    cd10337
    Location:55 → 189
    SH2_BCAR3; Src homology 2 (SH2) domain in the Breast Cancer Anti-estrogen Resistance protein 3
    cl02485
    Location:427 → 596
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...

  4. NM_001142534.1 → NP_001136006.1  SH2 domain-containing protein 3C isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) includes an alternate exon in the 5' coding region, compared to variant 1. It encodes isoform e, which is shorter and has a distinct N-terminus compared to isoform a.
    Source sequence(s)
    AI799905, AK291393, CU455802, DC302682
    Consensus CDS
    CCDS48027.1
    UniProtKB/TrEMBL
    A8K7M6
    Related
    ENSP00000485866.1, ENST00000629203.2
    Conserved Domains (2) summary
    cd10337
    Location:53 → 187
    SH2_BCAR3; Src homology 2 (SH2) domain in the Breast Cancer Anti-estrogen Resistance protein 3
    cl02485
    Location:425 → 594
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...

  5. NM_001252334.2 → NP_001239263.1  SH2 domain-containing protein 3C isoform f

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR and 5' coding region and initiates translation from an alternate start codon, compared to variant 1. The encoded isoform (f) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AI472242, AL162586, BX647905
    Consensus CDS
    CCDS59145.1
    UniProtKB/TrEMBL
    A8K7M6
    Related
    ENSP00000362373.3, ENST00000373276.7
    Conserved Domains (2) summary
    cd10337
    Location:145 → 279
    SH2_BCAR3; Src homology 2 (SH2) domain in the Breast Cancer Anti-estrogen Resistance protein 3
    cl02485
    Location:517 → 686
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...

  6. NM_005489.4 → NP_005480.2  SH2 domain-containing protein 3C isoform b

    See identical proteins and their annotated locations for NP_005480.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes alternate exons in the 5' coding region, compared to variant 1. It encodes isoform b, which is shorter and has a distinct N-terminus compared to isoform a.
    Source sequence(s)
    AL162426, BC027962, BI912337
    Consensus CDS
    CCDS6878.1
    UniProtKB/TrEMBL
    A8K7M6
    Related
    ENSP00000362374.4, ENST00000373277.8
    Conserved Domains (2) summary
    cd10337
    Location:56 → 190
    SH2_BCAR3; Src homology 2 (SH2) domain in the Breast Cancer Anti-estrogen Resistance protein 3
    cl02485
    Location:428 → 597
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...

  7. NM_170600.3 → NP_733745.1  SH2 domain-containing protein 3C isoform a

    See identical proteins and their annotated locations for NP_733745.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AI799905, BC032365, CU454732, DB161948
    Consensus CDS
    CCDS6877.1
    UniProtKB/Swiss-Prot
    A8K5S8, E9PG48, Q5HYE5, Q5JU31, Q6UY42, Q8N5H7, Q8N6X3, Q9Y2X5
    UniProtKB/TrEMBL
    A8K9K3
    Related
    ENSP00000317817.8, ENST00000314830.13
    Conserved Domains (2) summary
    cd10337
    Location:213 → 347
    SH2_BCAR3; Src homology 2 (SH2) domain in the Breast Cancer Anti-estrogen Resistance protein 3
    cl02485
    Location:585 → 754
    RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. ...

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    127738317..127778666 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    139945763..139986120 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N5H7.1 GenPept UniProtKB/Swiss-Prot:Q8N5H7

Gene LinkOut

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Chemical Information
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