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    YIF1B Yip1 interacting factor homolog B, membrane trafficking protein [ Homo sapiens (human) ]

    Gene ID: 90522, updated on 2-Nov-2024

    Summary

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    Official Symbol
    YIF1Bprovided by HGNC
    Official Full Name
    Yip1 interacting factor homolog B, membrane trafficking proteinprovided by HGNC
    Primary source
    HGNC:HGNC:30511
    See related
    Ensembl:ENSG00000167645 MIM:619109; AllianceGenome:HGNC:30511
    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
    FinGER8; KABAMAS
    Summary
    Involved in endoplasmic reticulum to Golgi vesicle-mediated transport. Located in Golgi apparatus; endoplasmic reticulum; and endoplasmic reticulum-Golgi intermediate compartment. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in colon (RPKM 13.5), small intestine (RPKM 9.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See YIF1B in Genome Data Viewer
    Location:
    19q13.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (38303558..38321887, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (41105724..41119757, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (38794198..38806587, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr19:38746806-38746993 Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 14A Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38751829-38752766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38752767-38753703 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38753844-38754761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10565 Neighboring gene serine peptidase inhibitor, Kunitz type 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38785153-38785654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38788840-38789473 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38791160-38791852 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:38792217-38792464 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38794013-38794750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38794751-38795488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38795489-38796226 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:38798184-38798353 Neighboring gene chromosome 19 open reading frame 33 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38810313-38810936 Neighboring gene potassium two pore domain channel subfamily K member 6 Neighboring gene Sharpr-MPRA regulatory region 11361 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10568 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10569 Neighboring gene cation channel sperm associated auxiliary subunit gamma Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38833985-38834934 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38842313-38842814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38842815-38843314 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38852625-38853566 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38865120-38865750 Neighboring gene proteasome 26S subunit, non-ATPase 8

    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. YIF1B-Related Neurodevelopmental Disorder. Adam MP, et al. , 1993. PMID 39265055
    2. Truncating mutations in YIF1B cause a progressive encephalopathy with various degrees of mixed movement disorder, microcephaly, and epilepsy. AlMuhaizea M, et al. Acta Neuropathol, 2020 Apr. PMID 32006098
    3. Prognostic and immune regulating roles of YIF1B in Pan-Cancer: a potential target for both survival and therapy response evaluation. Liu J, et al. Biosci Rep, 2020 Jul 31. PMID 32648580, Free PMC Article
    4. Unconventional secretion of unglycosylated ORF8 is critical for the cytokine storm during SARS-CoV-2 infection. Lin X, et al. PLoS Pathog, 2023 Jan. PMID 36689483, Free PMC Article
    5. Lysosomal targeting of the ABC transporter TAPL is determined by membrane-localized charged residues. Graab P, et al. J Biol Chem, 2019 May 3. PMID 30877195, Free PMC Article

    See all (45) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Truncating mutations in YIF1B cause a progressive encephalopathy with various degrees of mixed movement disorder, microcephaly, and epilepsy.
      Title: Truncating mutations in YIF1B cause a progressive encephalopathy with various degrees of mixed movement disorder, microcephaly, and epilepsy.
    2. Prognostic and immune regulating roles of YIF1B in Pan-Cancer: a potential target for both survival and therapy response evaluation.
      Title: Prognostic and immune regulating roles of YIF1B in Pan-Cancer: a potential target for both survival and therapy response evaluation.
    3. YIF1B mutations cause a post-natal neurodevelopmental syndrome associated with Golgi and primary cilium alterations.
      Title: YIF1B mutations cause a post-natal neurodevelopmental syndrome associated with Golgi and primary cilium alterations.
    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

    Associated conditions

    Description Tests
    Kaya-Barakat-Masson syndrome
    MedGen: C5436856 OMIM: 619125 GeneReviews: YIF1B-Related Neurodevelopmental Disorder
    		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

    • FLJ23477, FLJ50074, MGC39135

    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 endoplasmic reticulum to Golgi vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein targeting to membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in COPII-coated ER to Golgi transport vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in endoplasmic reticulum-Golgi intermediate compartment IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum-Golgi intermediate compartment IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum-Golgi intermediate compartment membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein YIF1B
    Names
    YIP1-interacting factor homolog B

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001039671.3 → NP_001034760.1  protein YIF1B isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and 5' coding region, compared to variant 5. The resulting isoform (3) has a shorter and distinct N-terminus, compared to isoform 5.
      Source sequence(s)
      AC011479, AK027130, BE877226, BM703847, BX379501, CA487891
      Consensus CDS
      CCDS46066.1
      UniProtKB/TrEMBL
      K7EPQ7
      Related
      ENSP00000329559.7, ENST00000329420.12
      Conserved Domains (1) summary
      pfam03878
      Location:65 → 292
      YIF1; YIF1

    2. NM_001039672.3 → NP_001034761.1  protein YIF1B isoform 5

      See identical proteins and their annotated locations for NP_001034761.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) encodes the longest isoform (5).
      Source sequence(s)
      AC011479, AK027130, AW630507, BC091477
      Consensus CDS
      CCDS33010.1
      UniProtKB/Swiss-Prot
      H7BXS8, Q5BJH7, Q5JPC2, Q8WY70, Q96C02, Q96IC4
      Related
      ENSP00000343435.5, ENST00000339413.11
      Conserved Domains (1) summary
      pfam03878
      Location:80 → 307
      YIF1; YIF1

    3. NM_001039673.3 → NP_001034762.1  protein YIF1B isoform 4

      See identical proteins and their annotated locations for NP_001034762.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, compared to variant 5. The resulting isoform (4) lacks a 3-aa segment near the N-terminus, compared to isoform 5.
      Source sequence(s)
      AC011479, AK027130, AW630507, BC007644
      UniProtKB/Swiss-Prot
      Q5BJH7
      UniProtKB/TrEMBL
      Q9H5F7
      Conserved Domains (1) summary
      pfam03878
      Location:77 → 304
      YIF1; YIF1

    4. NM_001145461.2 → NP_001138933.1  protein YIF1B isoform 6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and 5' coding region, compared to variant 5. The resulting isoform (6) has a shorter and distinct N-terminus, compared to isoform 5.
      Source sequence(s)
      AC011479, AK027130, BM703847, CA487891, CA488303
      UniProtKB/TrEMBL
      K7EPQ7
      Conserved Domains (1) summary
      pfam03878
      Location:58 → 292
      YIF1

    5. NM_001145462.2 → NP_001138934.1  protein YIF1B isoform 2

      See identical proteins and their annotated locations for NP_001138934.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 5. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 5.
      Source sequence(s)
      AC011479, AK027130, BC091477, CF127536
      Consensus CDS
      CCDS12512.1
      UniProtKB/TrEMBL
      K7EPQ7
      Related
      ENSP00000465230.1, ENST00000591784.5
      Conserved Domains (1) summary
      pfam03878
      Location:49 → 276
      YIF1; YIF1

    6. NM_001145463.2 → NP_001138935.1  protein YIF1B isoform 7

      See identical proteins and their annotated locations for NP_001138935.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) uses an alternate in-frame splice site in the 5' coding region and includes an additional exon that results in a frameshift in the 3' coding region, compared to variant 5. The resulting isoform (7) lacks a 3-aa segment near the N-terminus and has a shorter and distinct C-terminus, compared to isoform 5.
      Source sequence(s)
      AC011479, AK027130, AL833382, AW630507
      Consensus CDS
      CCDS46067.1
      UniProtKB/Swiss-Prot
      Q5BJH7
      UniProtKB/TrEMBL
      Q9H5F7
      Related
      ENSP00000337411.7, ENST00000337679.12
      Conserved Domains (1) summary
      pfam03878
      Location:77 → 280
      YIF1; YIF1

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      38303558..38321887 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439648.1 → XP_047295604.1  protein YIF1B isoform X1

      Related
      ENSP00000466428.1, ENST00000592694.5

    2. XM_047439647.1 → XP_047295603.1  protein YIF1B isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      41105724..41119757 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322554.1 → XP_054178529.1  protein YIF1B isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001013617.1: Suppressed sequence

      Description
      NM_001013617.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.

    2. NM_001031731.1: Suppressed sequence

      Description
      NM_001031731.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    3. NM_033557.3: Suppressed sequence

      Description
      NM_033557.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which may retain intronic sequence at its 5' end.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5BJH7.1 GenPept UniProtKB/Swiss-Prot:Q5BJH7

    Gene LinkOut

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

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