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SYDE1 synapse defective Rho GTPase homolog 1 [ Homo sapiens (human) ]

Gene ID: 85360, updated on 3-Apr-2024

Summary

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Official Symbol
SYDE1provided by HGNC
Official Full Name
synapse defective Rho GTPase homolog 1provided by HGNC
Primary source
HGNC:HGNC:25824
See related
Ensembl:ENSG00000105137 MIM:617377; AllianceGenome:HGNC:25824
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
7h3; SYD1
Summary
The protein encoded by this gene is a Rho GTPase-activating protein highly expressed in placenta. The encoded protein is involved in cytoskeletal remodeling and trophoblast cell migration. Decreased expression of this gene has been associated with intrauterine growth restriction (IUGR). [provided by RefSeq, Feb 2017]
Expression
Ubiquitous expression in fat (RPKM 9.3), placenta (RPKM 9.2) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
19p13.12
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (15107401..15114974)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (15232344..15239918)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (15218212..15225785)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene caspase 14 Neighboring gene olfactory receptor family 1 subfamily I member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:15219898-15220448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:15222723-15223250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:15223251-15223776 Neighboring gene ilvB acetolactate synthase like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:15235337-15236102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:15236103-15236866 Neighboring gene ILVBL antisense RNA 1 Neighboring gene olfactory receptor family 10 subfamily B member 1 pseudogene

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. Functional relevance of a six mesenchymal gene signature in epithelial-mesenchymal transition (EMT) reversal by the triple angiokinase inhibitor, nintedanib (BIBF1120). Huang RY, et al. Oncotarget, 2015 Sep 8. PMID 26061747, Free PMC Article
  2. Analysis of the placental tissue transcriptome of normal and preeclampsia complicated pregnancies. Trifonova EA, et al. Acta Naturae, 2014 Apr. PMID 25093114, Free PMC Article
  3. Association of dysfunctional synapse defective 1 (SYDE1) with restricted fetal growth - SYDE1 regulates placental cell migration and invasion. Lo HF, et al. J Pathol, 2017 Feb. PMID 27917469
  4. mSYD1A, a mammalian synapse-defective-1 protein, regulates synaptogenic signaling and vesicle docking. Wentzel C, et al. Neuron, 2013 Jun 19. PMID 23791195, Free PMC Article
  5. The shieldin complex mediates 53BP1-dependent DNA repair. Noordermeer SM, et al. Nature, 2018 Aug. PMID 30022168, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. a novel mechanism for GCM1 and SYDE1 in regulation of trophoblast cell migration and invasion during placental development
    Title: Association of dysfunctional synapse defective 1 (SYDE1) with restricted fetal growth - SYDE1 regulates placental cell migration and invasion.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ13511

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 GTPase activator activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables GTPase activator activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables GTPase regulator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables GTPase regulator activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within actin cytoskeleton organization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in activation of GTPase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within cell migration IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within cell migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of trophoblast cell migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of Ras protein signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of cytoskeleton organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in synaptic membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
rho GTPase-activating protein SYDE1
Names
protein syd-1 homolog 1
synapse defective 1, Rho GTPase, homolog 1
synapse defective protein 1 homolog 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_001300910.2 → NP_001287839.1  rho GTPase-activating protein SYDE1 isoform 2

    See identical proteins and their annotated locations for NP_001287839.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    AC004794
    Consensus CDS
    CCDS74299.1
    UniProtKB/TrEMBL
    B2RD93
    Related
    ENSP00000470733.1, ENST00000600440.5
    Conserved Domains (1) summary
    cl02570
    Location:329 → 534
    RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...

  2. NM_033025.6 → NP_149014.3  rho GTPase-activating protein SYDE1 isoform 1

    See identical proteins and their annotated locations for NP_149014.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC004794
    Consensus CDS
    CCDS12324.1
    UniProtKB/Swiss-Prot
    Q6ZW31, Q7L2I8, Q8N6J2, Q9H8K4
    UniProtKB/TrEMBL
    A0A2X0SFL9
    Related
    ENSP00000341489.1, ENST00000342784.7
    Conserved Domains (1) summary
    cl02570
    Location:396 → 601
    RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    15107401..15114974
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439579.1 → XP_047295535.1  rho GTPase-activating protein SYDE1 isoform X1

  2. XM_047439580.1 → XP_047295536.1  rho GTPase-activating protein SYDE1 isoform X2

  3. XM_024451750.2 → XP_024307518.1  rho GTPase-activating protein SYDE1 isoform X3

    Conserved Domains (1) summary
    cl02570
    Location:396 → 473
    RhoGAP; GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to ...

  4. XM_047439581.1 → XP_047295537.1  rho GTPase-activating protein SYDE1 isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    15232344..15239918
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322456.1 → XP_054178431.1  rho GTPase-activating protein SYDE1 isoform X1

  2. XM_054322457.1 → XP_054178432.1  rho GTPase-activating protein SYDE1 isoform X2

  3. XM_054322458.1 → XP_054178433.1  rho GTPase-activating protein SYDE1 isoform X3

  4. XM_054322459.1 → XP_054178434.1  rho GTPase-activating protein SYDE1 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZW31.1 GenPept UniProtKB/Swiss-Prot:Q6ZW31

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