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

Gene ID: 81555, updated on 5-Mar-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
Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; regulation of ER to Golgi vesicle-mediated transport; and vesicle fusion with Golgi apparatus. Located in Golgi apparatus; endoplasmic reticulum; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in placenta (RPKM 14.2), thyroid (RPKM 12.3) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (144158162..144170659, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (144690356..144702848, complement)
105.20220307 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

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. 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
  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. Yip1A structures the mammalian endoplasmic reticulum. Dykstra KM, et al. Mol Biol Cell, 2010 May 1. PMID 20237155, Free PMC Article
  4. 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
  5. 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). Liu X, et al. J Zhejiang Univ Sci B, 2023 Mar 15. PMID 36916000, Free PMC Article

See all (53) 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)

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

  • 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_2023_10

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

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