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    YIPF5 Yip1 domain family member 5 [ Homo sapiens (human) ]

    Gene ID: 81555, updated on 10-Dec-2024

    Summary

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    Official Symbol
    YIPF5provided by HGNC
    Official Full Name
    Yip1 domain family member 5provided by HGNC
    Primary source
    HGNC:HGNC:24877
    See related
    Ensembl:ENSG00000145817 MIM:611483; AllianceGenome:HGNC:24877
    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
    MEDS2; SB140; SMAP5; YIP1A; SMAP-5; FinGER5; YIPFalpha1A
    Summary
    Involved in insulin processing and regulation of ER to Golgi vesicle-mediated transport. Located in Golgi apparatus; endoplasmic reticulum; and nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in placenta (RPKM 14.2), thyroid (RPKM 12.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See YIPF5 in Genome Data Viewer
    Location:
    5q31.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (144158162..144170659, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (144690356..144702848, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (143537726..143550223, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16486 Neighboring gene histocompatibility minor HB-1 Neighboring gene MPRA-validated peak5509 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:143456065-143456759 Neighboring gene NANOG hESC enhancer GRCh37_chr5:143504731-143505232 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:143543592-143544791 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23355 Neighboring gene RNA, 7SL, cytoplasmic 87, pseudogene Neighboring gene potassium channel tetramerization domain containing 16 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:143677189-143677923 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:143697432-143697944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23357 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:143762205-143763404 Neighboring gene NANOG hESC enhancer GRCh37_chr5:143867216-143867717 Neighboring gene CDC28 protein kinase regulatory subunit 1B pseudogene 5 Neighboring gene 60S ribosomal protein L9-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Yip1A structures the mammalian endoplasmic reticulum. Dykstra KM, et al. Mol Biol Cell, 2010 May 1. PMID 20237155, Free PMC Article
    2. Identification of discrete sites in Yip1A necessary for regulation of endoplasmic reticulum structure. Dykstra KM, et al. PLoS One, 2013. PMID 23342155, Free PMC Article
    3. Cloning, cellular localization, genomic organization, and tissue-specific expression of the TGFbeta1-inducible SMAP-5 gene. Stolle K, et al. Gene, 2005 May 23. PMID 15922870
    4. YIPF5 mutations cause neonatal diabetes and microcephaly through endoplasmic reticulum stress. De Franco E, et al. J Clin Invest, 2020 Dec 1. PMID 33164986, Free PMC Article
    5. Yip1A regulates the COPI-independent retrograde transport from the Golgi complex to the ER. Kano F, et al. J Cell Sci, 2009 Jul 1. PMID 19509059

    See all (62) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Balanced chromosomal rearrangements implicate YIPF5 and SPATC1L in non-obstructive oligoasthenozoospermia and oligozoospermia and of a derivative chromosome 22 in recurrent miscarriage.
      Title: Balanced chromosomal rearrangements implicate YIPF5 and SPATC1L in non-obstructive oligoasthenozoospermia and oligozoospermia and of a derivative chromosome 22 in recurrent miscarriage.
    2. Vitamin D receptor (VDR) mediates the quiescence of activated hepatic stellate cells (aHSCs) by regulating M2 macrophage exosomal smooth muscle cell-associated protein 5 (SMAP-5).
      Title: Vitamin D receptor (VDR) mediates the quiescence of activated hepatic stellate cells (aHSCs) by regulating M2 macrophage exosomal smooth muscle cell-associated protein 5 (SMAP-5).
    3. YIPF5 mutations cause neonatal diabetes and microcephaly through endoplasmic reticulum stress.
      Title: YIPF5 mutations cause neonatal diabetes and microcephaly through endoplasmic reticulum stress.
    4. YIPF5 positively regulates STING-mediated innate immune responses.
      Title: YIPF5 Is Essential for Innate Immunity to DNA Virus and Facilitates COPII-Dependent STING Trafficking.
    5. The significance of YIPF5 protein for the maintenance of the morphology of the Golgi was tested by RNA interference, revealing a number of specific morphological changes to this organelle on their depletion.
      Title: Functional characterisation of the YIPF protein family in mammalian cells.
    6. we propose a model for intracellular Brucella replication that exploits the host unfolded protein response and endoplasmic reticulum -derived vacuole formation machineries, both of which depend on Yip1A-mediated IRE1 activation.
      Title: Yip1A, a novel host factor for the activation of the IRE1 pathway of the unfolded protein response during Brucella infection.
    7. Findings suggest that the ability of Yip1A to bind its established binding partners may be uncoupled from its ability to control ER whorl formation.
      Title: Identification of discrete sites in Yip1A necessary for regulation of endoplasmic reticulum structure.
    8. Results reveal a conserved Yip1A-mediated mechanism for ER membrane organization that may serve to regulate cargo exit from the organelle.
      Title: Yip1A structures the mammalian endoplasmic reticulum.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Fine mapping of the CELIAC2 locus on chromosome 5q31-q33 in the Finnish and Hungarian populations.
    10. These results suggested that Yip1A has a role in COPI-independent retrograde transport from the Golgi to the ER and regulates the membrane recruitment of Rab6.
      Title: Yip1A regulates the COPI-independent retrograde transport from the Golgi complex to the ER.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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
    Microcephaly, epilepsy, and diabetes syndrome 2
    MedGen: C5543294 OMIM: 619278 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp313L2216

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in insulin processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of ER to Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of ER to Golgi vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vesicle fusion with Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in COPII-coated ER to Golgi transport vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum exit site IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein YIPF5
    Names
    YIP1 family member 5
    YPT-interacting protein 1 A
    five-pass transmembrane protein localizing in the Golgi apparatus and the endoplasmic reticulum 5
    golgi membrane protein SB140
    smooth muscle cell associated protein 5

    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_001024947.4 → NP_001020118.1  protein YIPF5 isoform a

      See identical proteins and their annotated locations for NP_001020118.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 encode the same protein (isoform a).
      Source sequence(s)
      AY640926, AY640928, BP310538
      Consensus CDS
      CCDS4279.1
      UniProtKB/Swiss-Prot
      D3DQF5, Q4VSN6, Q53EX4, Q8NHE5, Q969M3, Q9H338, Q9H3U4
      UniProtKB/TrEMBL
      B3KW34
      Related
      ENSP00000397704.2, ENST00000448443.6
      Conserved Domains (1) summary
      cl21557
      Location:89 → 257
      Yip1; Yip1 domain

    2. NM_001271732.2 → NP_001258661.1  protein YIPF5 isoform b

      See identical proteins and their annotated locations for NP_001258661.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in the 5' coding region and uses a downstream start codon, compared to variant 1. It encodes isoform b which has a shorter N-terminus compared to isoform a.
      Source sequence(s)
      AY640926, AY640929, BP310538
      Consensus CDS
      CCDS64277.1
      UniProtKB/TrEMBL
      E5RHH4
      Related
      ENSP00000425422.1, ENST00000513112.5
      Conserved Domains (1) summary
      cl21557
      Location:35 → 203
      Yip1; Yip1 domain

    3. NM_030799.9 → NP_110426.4  protein YIPF5 isoform a

      See identical proteins and their annotated locations for NP_110426.4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein (isoform a).
      Source sequence(s)
      AY640926, BP310538
      Consensus CDS
      CCDS4279.1
      UniProtKB/Swiss-Prot
      D3DQF5, Q4VSN6, Q53EX4, Q8NHE5, Q969M3, Q9H338, Q9H3U4
      UniProtKB/TrEMBL
      B3KW34
      Related
      ENSP00000274496.5, ENST00000274496.10
      Conserved Domains (1) summary
      cl21557
      Location:89 → 257
      Yip1; Yip1 domain

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      144158162..144170659 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      144690356..144702848 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q969M3.1 GenPept UniProtKB/Swiss-Prot:Q969M3

    Gene LinkOut

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

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