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

Gene ID: 29970, updated on 3-Apr-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 animal organ development; face morphogenesis; and fibroblast migration. Located in several cellular components, including cell junction; cytosol; and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]
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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Location:
3q25.32-q25.33
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (159273244..159897359)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (162047599..162671965)
105.20220307 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
  • 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. 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
  4. 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
  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 (30) 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
    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
    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
    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

  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
    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_2023_10

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

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Chemical Information
Molecular Biology Databases
Research Materials
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