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SPRED1 sprouty related EVH1 domain containing 1 [ Homo sapiens (human) ]

Gene ID: 161742, updated on 7-Apr-2024

Summary

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Official Symbol
SPRED1provided by HGNC
Official Full Name
sprouty related EVH1 domain containing 1provided by HGNC
Primary source
HGNC:HGNC:20249
See related
Ensembl:ENSG00000166068 MIM:609291; AllianceGenome:HGNC:20249
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
LGSS; NFLS; hSpred1; spred-1; PPP1R147
Summary
The protein encoded by this gene is a member of the Sprouty family of proteins and is phosphorylated by tyrosine kinase in response to several growth factors. The encoded protein can act as a homodimer or as a heterodimer with SPRED2 to regulate activation of the MAP kinase cascade. Defects in this gene are a cause of neurofibromatosis type 1-like syndrome (NFLS). [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in thyroid (RPKM 21.9), brain (RPKM 13.6) and 23 other tissues See more
Orthologs
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Genomic context

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See SPRED1 in Genome Data Viewer
Location:
15q14
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (38252836..38357249)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (36058115..36162546)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (38545037..38649450)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene transmembrane and coiled-coil domains 5A Neighboring gene long intergenic non-protein coding RNA 2345 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:38364669-38365534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6298 Neighboring gene long intergenic non-protein coding RNA 1852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9198 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9199 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9200 Neighboring gene Sharpr-MPRA regulatory region 4108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6300 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6303 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6304 Neighboring gene MPRA-validated peak2297 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr15:38679220-38679403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9203 Neighboring gene CTD small phosphatase 2 pseudogene Neighboring gene uncharacterized LOC105370774 Neighboring gene family with sequence similarity 98 member B Neighboring gene RAS guanyl releasing protein 1

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. SPRED1 deletion confers resistance to MAPK inhibition in melanoma. Ablain J, et al. J Exp Med, 2021 Mar 1. PMID 33306107, Free PMC Article
  2. Constitutional mismatch repair deficiency is the diagnosis in 0.41% of pathogenic NF1/SPRED1 variant negative children suspected of sporadic neurofibromatosis type 1. Perez-Valencia JA, et al. Genet Med, 2020 Dec. PMID 32773772, Free PMC Article
  3. A Pilot Study of Aberrant CpG Island Hypermethylation of SPRED1 in Acute Myeloloid Leukemia. Sun J, et al. Int J Med Sci, 2019. PMID 30745814, Free PMC Article
  4. The first Slovak Legius syndrome patient carrying the SPRED1 gene mutation. Sekelska M, et al. Gen Physiol Biophys, 2017 Apr. PMID 28150585
  5. Family with Legius syndrome (neurofibromatosis type 1-like syndrome). Sakai N, et al. J Dermatol, 2015 Jul. PMID 25981987

See all (75) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Long noncoding RNA LOC646029 functions as a ceRNA to suppress ovarian cancer progression through the miR-627-3p/SPRED1 axis.
    Title: Long noncoding RNA LOC646029 functions as a ceRNA to suppress ovarian cancer progression through the miR-627-3p/SPRED1 axis.
  2. SPOCK2 and SPRED1 function downstream of EZH2 to impede the malignant progression of lung adenocarcinoma in vitro and in vivo.
    Title: SPOCK2 and SPRED1 function downstream of EZH2 to impede the malignant progression of lung adenocarcinoma in vitro and in vivo.
  3. SPRED1 deletion confers resistance to MAPK inhibition in melanoma.
    Title: SPRED1 deletion confers resistance to MAPK inhibition in melanoma.
  4. A Study on the Expression of SPRED1 and PBRM1 (Baf180) and their Clinical Significances in Patients with Gastric Cancer.
    Title: A Study on the Expression of SPRED1 and PBRM1 (Baf180) and their Clinical Significances in Patients with Gastric Cancer.
  5. Moyamoya syndrome in a child with Legius syndrome: Introducing a cerebral vasculopathy to the SPRED1 phenotype?
    Title: Moyamoya syndrome in a child with Legius syndrome: Introducing a cerebral vasculopathy to the SPRED1 phenotype?
  6. Constitutional mismatch repair deficiency is the diagnosis in 0.41% of pathogenic NF1/SPRED1 variant negative children suspected of sporadic neurofibromatosis type 1.
    Title: Constitutional mismatch repair deficiency is the diagnosis in 0.41% of pathogenic NF1/SPRED1 variant negative children suspected of sporadic neurofibromatosis type 1.
  7. Simultaneous Detection of NF1, SPRED1, LZTR1, and NF2 Gene Mutations by Targeted NGS in an Italian Cohort of Suspected NF1 Patients.
    Title: Simultaneous Detection of NF1, SPRED1, LZTR1, and NF2 Gene Mutations by Targeted NGS in an Italian Cohort of Suspected NF1 Patients.
  8. These data provide structural insight into the interaction of Spred1 and neurofibromin.
    Title: Pathogenic Mutations Associated with Legius Syndrome Modify the Spred1 Surface and Are Involved in Direct Binding to the Ras Inactivator Neurofibromin.
  9. SPRED1 is down-regulated by E2 and negatively correlated to ER status in BC cells. SPRED1 was a new direct target of miR-196a which participated in miR-196a-promoted BC development and was suppressed by ligand-activated ER-alpha signal pathway.
    Title: Estrogen-induced miR-196a elevation promotes tumor growth and metastasis via targeting SPRED1 in breast cancer.
  10. Aberrant methylation statuses of the SPRED1 promoter regions are associated with the downregulation of gene transcription in acute myeloid leukemia.
    Title: A Pilot Study of Aberrant CpG Island Hypermethylation of SPRED1 in Acute Myeloloid Leukemia.
Submit: New GeneRIF Correction See all GeneRIFs (44)

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

Associated conditions

Description Tests
Legius syndrome
MedGen: C1969623 OMIM: 611431 GeneReviews: Legius Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2013-03-14)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2013-03-14)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide association study of HLA-DQB1*06:02 negative essential hypersomnia.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
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

  • FLJ33903

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables phosphatase binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein kinase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein serine/threonine kinase inhibitor activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables stem cell factor receptor binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in negative regulation of ERK1 and ERK2 cascade ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of MAPK cascade IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of MAPK cascade IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of angiogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of cell migration involved in sprouting angiogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of epithelial to mesenchymal transition ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of lens fiber cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of peptidyl-threonine phosphorylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of protein kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transforming growth factor beta receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of DNA damage response, signal transduction by p53 class mediator ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in regulation of MAPK cascade TAS
Traceable Author Statement
more info
 PubMed 
involved_in regulation of protein deacetylation ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in vasculogenesis involved in coronary vascular morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in caveola IEA
Inferred from Electronic Annotation
more info
  
colocalizes_with cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
sprouty-related, EVH1 domain-containing protein 1
Names
protein phosphatase 1, regulatory subunit 147
suppressor of Ras/MAPK activation

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_008980.1 RefSeqGene

    Range
    4986..109399
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_152594.3 → NP_689807.1  sprouty-related, EVH1 domain-containing protein 1

    See identical proteins and their annotated locations for NP_689807.1

    Status: REVIEWED

    Source sequence(s)
    AC069381, AY299089, DA405650
    Consensus CDS
    CCDS32193.1
    UniProtKB/Swiss-Prot
    B2RPJ8, Q05D53, Q7Z699, Q8N256
    Related
    ENSP00000299084.4, ENST00000299084.9
    Conserved Domains (2) summary
    cd10574
    Location:13 → 125
    EVH1_SPRED-like; Sprouty-related EVH1 domain-containing-like proteins EVH1 domain
    pfam05210
    Location:333 → 428
    Sprouty; Sprouty protein (Spry)

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
    38252836..38357249
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047432199.1 → XP_047288155.1  sprouty-related, EVH1 domain-containing protein 1 isoform X2

  2. XM_047432200.1 → XP_047288156.1  sprouty-related, EVH1 domain-containing protein 1 isoform X2

  3. XM_005254202.4 → XP_005254259.1  sprouty-related, EVH1 domain-containing protein 1 isoform X1

    Conserved Domains (2) summary
    cd10574
    Location:25 → 137
    EVH1_SPRED-like; Sprouty-related EVH1 domain-containing-like proteins EVH1 domain
    pfam05210
    Location:345 → 440
    Sprouty; Sprouty protein (Spry)

  4. XM_047432201.1 → XP_047288157.1  sprouty-related, EVH1 domain-containing protein 1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    36058115..36162546
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054377382.1 → XP_054233357.1  sprouty-related, EVH1 domain-containing protein 1 isoform X2

  2. XM_054377383.1 → XP_054233358.1  sprouty-related, EVH1 domain-containing protein 1 isoform X2

  3. XM_054377381.1 → XP_054233356.1  sprouty-related, EVH1 domain-containing protein 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z699.2 GenPept UniProtKB/Swiss-Prot:Q7Z699

Gene LinkOut

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