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

Gene ID: 90522, updated on 11-Apr-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
Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; protein targeting to membrane; and sperm axoneme assembly. Located in Golgi apparatus; endoplasmic reticulum; and endoplasmic reticulum-Golgi intermediate compartment. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in colon (RPKM 13.5), small intestine (RPKM 9.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
19q13.2
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (38303558..38321887, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (41105724..41119757, complement)
105.20220307 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
  • 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. 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
  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. 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
  4. YIF1B mutations cause a post-natal neurodevelopmental syndrome associated with Golgi and primary cilium alterations. Diaz J, et al. Brain, 2020 Oct 1. PMID 33103737
  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 (39) 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: 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

  • 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 Golgi membrane IEA
Inferred from Electronic Annotation
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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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_2023_10

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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