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    SCHIP1 schwannomin interacting protein 1 [ Homo sapiens (human) ]

    Gene ID: 29970, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SCHIP1provided by HGNC
    Official Full Name
    schwannomin interacting protein 1provided by HGNC
    Primary source
    HGNC:HGNC:15678
    See related
    Ensembl:ENSG00000151967 MIM:619206; AllianceGenome:HGNC:15678
    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
    SCHIP-1
    Summary
    Enables identical protein binding activity. Predicted to be involved in positive regulation of hippo signaling. Predicted to act upstream of or within several processes, including face morphogenesis; fibroblast migration; and luteinization. Located in several cellular components, including cell junction; cytosol; and nuclear body. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in brain (RPKM 38.6), heart (RPKM 21.8) and 13 other tissues See more
    Orthologs
    all
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    Genomic context

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    See SCHIP1 in Genome Data Viewer
    Location:
    3q25.32-q25.33
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (159273244..159897359)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (162047599..162671965)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (158991033..159615148)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909452 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:158654234-158655433 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:158708772-158709358 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:158770193-158770383 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:158780440-158780973 Neighboring gene IQCJ-SCHIP1 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20753 Neighboring gene IQ motif containing J Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:158946859-158947462 Neighboring gene MPRA-validated peak4886 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr3:159058830-159059398 Neighboring gene microRNA 3919 Neighboring gene ribosomal protein S2 pseudogene 19 Neighboring gene NANOG hESC enhancer GRCh37_chr3:159349871-159350381 Neighboring gene IQCJ-SCHIP1 readthrough antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 6431 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14850 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:159481881-159482458 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14851 Neighboring gene C9orf78 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:159492749-159493294 Neighboring gene uncharacterized LOC101928351 Neighboring gene uncharacterized LOC124906299 Neighboring gene Sharpr-MPRA regulatory region 8585 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:159589810-159591009 Neighboring gene RNA, U2 small nuclear 31, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20755 Neighboring gene IL12A antisense RNA 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:159704282-159705481 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:159706332-159706832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:159706833-159707333 Neighboring gene long intergenic non-protein coding RNA 1100 Neighboring gene interleukin 12A

    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. Homozygous nonsense mutation in SCHIP1/IQCJ-SCHIP1 causes a neurodevelopmental brain malformation syndrome. Elsaid MF, et al. Clin Genet, 2018 Feb. PMID 28787085
    2. Assignment of the schwannomin-interacting protein 1 (SCHIP1) gene to human chromosome band 3q25 by in situ hybridization and with somatic cell hybrids. Goutebroze L, et al. Cytogenet Cell Genet, 2001. PMID 11701967
    3. Schip1 is a novel podocyte foot process protein that mediates actin cytoskeleton rearrangements and forms a complex with Nherf2 and ezrin. Perisic L, et al. PLoS One, 2015. PMID 25807495, Free PMC Article
    4. Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape. Cole JB, et al. PLoS Genet, 2016 Aug. PMID 27560698, Free PMC Article
    5. Cloning and characterization of SCHIP-1, a novel protein interacting specifically with spliced isoforms and naturally occurring mutant NF2 proteins. Goutebroze L, et al. Mol Cell Biol, 2000 Mar. PMID 10669747, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. This is the first report of a SCHIP1/IQCJ-SCHIP1 point mutation in humans associated with a neurological-developmental phenotype
      Title: Homozygous nonsense mutation in SCHIP1/IQCJ-SCHIP1 causes a neurodevelopmental brain malformation syndrome.
    2. SNPs within genes SCHIP1 and PDE8A were associated with measures of facial size in both the GWAS and replication cohorts and passed a stringent genomewide significance threshold adjusted for multiple testing of 34 correlated traits. For both SCHIP1 and PDE8A, we demonstrated clear expression in the developing mouse face by both whole-mount in situ hybridization and RNA-seq
      Title: Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape.
    3. Schip1 associates with the cortical actin cytoskeleton network and modulates its dynamics in response to PDGF signaling via interaction with the Nherf2/ezrin complex.
      Title: Schip1 is a novel podocyte foot process protein that mediates actin cytoskeleton rearrangements and forms a complex with Nherf2 and ezrin.
    4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. chromosome 3 mapping by in situ hybridization and somatic cell hybrids
      Title: Assignment of the schwannomin-interacting protein 1 (SCHIP1) gene to human chromosome band 3q25 by in situ hybridization and with somatic cell hybrids.
    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
    Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies.
    EBI GWAS Catalog
    Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae.
    EBI GWAS Catalog
    Newly identified genetic risk variants for celiac disease related to the immune response.
    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

    Readthrough IQCJ-SCHIP1

    Readthrough gene: IQCJ-SCHIP1, Included gene: IQCJ

    Homology

    Clone Names

    • FLJ39160

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of hippo signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cell junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    schwannomin-interacting protein 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_001197107.2 → NP_001184036.1  schwannomin-interacting protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001184036.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (2, also known as SCHIP-1-D241/253) that is shorter than isoform 1.
      Source sequence(s)
      AC107312, AF145715, BC036535, CA431197
      Consensus CDS
      CCDS56292.1
      UniProtKB/TrEMBL
      B2RBH3
      Related
      ENSP00000400942.2, ENST00000412423.8
      Conserved Domains (1) summary
      pfam10148
      Location:242 → 468
      SCHIP-1; Schwannomin-interacting protein 1

    2. NM_001197108.2 → NP_001184037.1  schwannomin-interacting protein 1 isoform 3

      See identical proteins and their annotated locations for NP_001184037.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (3, also known as SCHIP-1-D22/253) that is shorter than isoform 1.
      Source sequence(s)
      AC107312, AF145714, BC036535, CA431197
      Consensus CDS
      CCDS56293.1
      UniProtKB/Swiss-Prot
      P0DPB3
      Related
      ENSP00000436076.1, ENST00000527095.7
      Conserved Domains (1) summary
      pfam10148
      Location:23 → 249
      SCHIP-1; Schwannomin-interacting protein 1

    3. NM_001197109.2 → NP_001184038.1  schwannomin-interacting protein 1 isoform 4

      See identical proteins and their annotated locations for NP_001184038.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (4) has a distinct and shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK091871
      Consensus CDS
      CCDS56294.1
      UniProtKB/Swiss-Prot
      P0DPB3
      Related
      ENSP00000404860.2, ENST00000445224.6
      Conserved Domains (1) summary
      pfam10148
      Location:12 → 235
      SCHIP-1; Schwannomin-interacting protein 1

    4. NM_001394282.1 → NP_001381211.1  schwannomin-interacting protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC021654
      Consensus CDS
      CCDS93418.1
      UniProtKB/TrEMBL
      A0A8I5KTZ3, B2RBH3
      Conserved Domains (1) summary
      pfam10148
      Location:228 → 451
      SCHIP-1; Schwannomin-interacting protein 1

    5. NM_001394283.1 → NP_001381212.1  schwannomin-interacting protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC021654
      Consensus CDS
      CCDS93418.1
      UniProtKB/TrEMBL
      A0A8I5KTZ3, B2RBH3
      Conserved Domains (1) summary
      pfam10148
      Location:228 → 451
      SCHIP-1; Schwannomin-interacting protein 1

    6. NM_001394284.1 → NP_001381213.1  schwannomin-interacting protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC021654, AC092943
      Consensus CDS
      CCDS93418.1
      UniProtKB/TrEMBL
      A0A8I5KTZ3, B2RBH3
      Conserved Domains (1) summary
      pfam10148
      Location:228 → 451
      SCHIP-1; Schwannomin-interacting protein 1

    7. NM_001394285.1 → NP_001381214.1  schwannomin-interacting protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC021654, AC092943
      Consensus CDS
      CCDS93418.1
      UniProtKB/TrEMBL
      A0A8I5KTZ3, B2RBH3
      Related
      ENSP00000508586.1, ENST00000689690.1
      Conserved Domains (1) summary
      pfam10148
      Location:228 → 451
      SCHIP-1; Schwannomin-interacting protein 1

    8. NM_001394286.1 → NP_001381215.1  schwannomin-interacting protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC021654, AC092943
      Consensus CDS
      CCDS93418.1
      UniProtKB/TrEMBL
      A0A8I5KTZ3, B2RBH3
      Conserved Domains (1) summary
      pfam10148
      Location:228 → 451
      SCHIP-1; Schwannomin-interacting protein 1

    9. NM_001394287.1 → NP_001381216.1  schwannomin-interacting protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC021654
      UniProtKB/TrEMBL
      C9J366
      Related
      ENSP00000417305.3, ENST00000460298.3

    10. NM_001394288.1 → NP_001381217.1  schwannomin-interacting protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC021654
      UniProtKB/TrEMBL
      C9J366

    11. NM_001394289.1 → NP_001381218.1  schwannomin-interacting protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC021654
      UniProtKB/TrEMBL
      C9J366

    12. NM_001394290.1 → NP_001381219.1  schwannomin-interacting protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC021654, AC092943
      UniProtKB/TrEMBL
      C9J366

    13. NM_001394291.1 → NP_001381220.1  schwannomin-interacting protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC021654, AC092943
      UniProtKB/TrEMBL
      C9J366

    14. NM_001394292.1 → NP_001381221.1  schwannomin-interacting protein 1 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC021654

    15. NM_001394293.1 → NP_001381222.1  schwannomin-interacting protein 1 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC021654
      UniProtKB/TrEMBL
      B2RBH3

    16. NM_001394294.1 → NP_001381223.1  schwannomin-interacting protein 1 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC021654
      Consensus CDS
      CCDS93419.1
      UniProtKB/TrEMBL
      C9JWG6
      Related
      ENSP00000419230.1, ENST00000482804.1
      Conserved Domains (1) summary
      pfam10148
      Location:28 → 251
      SCHIP-1; Schwannomin-interacting protein 1

    17. NM_001394295.1 → NP_001381224.1  schwannomin-interacting protein 1 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AC021654

    18. NM_001394296.1 → NP_001381225.1  schwannomin-interacting protein 1 isoform 11

      Status: VALIDATED

      Source sequence(s)
      AC021654

    19. NM_001414415.1 → NP_001401344.1  schwannomin-interacting protein 1 isoform 12

      Status: VALIDATED

      Source sequence(s)
      AC021654

    20. NM_001414416.1 → NP_001401345.1  schwannomin-interacting protein 1 isoform 13

      Status: VALIDATED

      Source sequence(s)
      AC021654

    21. NM_001414417.1 → NP_001401346.1  schwannomin-interacting protein 1 isoform 14

      Status: VALIDATED

      Source sequence(s)
      AC021654

    22. NM_001414418.1 → NP_001401347.1  schwannomin-interacting protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC021654
      UniProtKB/TrEMBL
      A0A8I5KTZ3

    23. NM_001414419.1 → NP_001401348.1  schwannomin-interacting protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC021654
      UniProtKB/TrEMBL
      A0A8I5KTZ3

    24. NM_001414420.1 → NP_001401349.1  schwannomin-interacting protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC021654, AC092943

    25. NM_001414421.1 → NP_001401350.1  schwannomin-interacting protein 1 isoform 19

      Status: VALIDATED

      Source sequence(s)
      AC021654

    26. NM_001414422.1 → NP_001401351.1  schwannomin-interacting protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC021654

    27. NM_001414423.1 → NP_001401352.1  schwannomin-interacting protein 1 isoform 15

      Status: VALIDATED

      Source sequence(s)
      AC021654

    28. NM_001414424.1 → NP_001401353.1  schwannomin-interacting protein 1 isoform 16

      Status: VALIDATED

      Source sequence(s)
      AC021654

    29. NM_001414425.1 → NP_001401354.1  schwannomin-interacting protein 1 isoform 17

      Status: VALIDATED

      Source sequence(s)
      AC021654

    30. NM_001414426.1 → NP_001401355.1  schwannomin-interacting protein 1 isoform 18

      Status: VALIDATED

      Source sequence(s)
      AC021654

    31. NM_014575.4 → NP_055390.1  schwannomin-interacting protein 1 isoform 1

      See identical proteins and their annotated locations for NP_055390.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC107312, AF145713, BC036535, CA431197
      Consensus CDS
      CCDS3186.1
      UniProtKB/Swiss-Prot
      P0DPB3
      UniProtKB/TrEMBL
      B2RBH3
      Related
      ENSP00000491030.1, ENST00000638749.2
      Conserved Domains (1) summary
      pfam10148
      Location:255 → 481
      SCHIP-1; Schwannomin-interacting protein 1

    RNA

    1. NR_182428.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC021654

    2. NR_182429.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC021654

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      159273244..159897359
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      162047599..162671965
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0DPB3.1 GenPept UniProtKB/Swiss-Prot:P0DPB3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials