Details for: YIF1B

Gene ID: 90522

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: YIF1B

Ensembl ID: ENSG00000167645

Description: Yip1 interacting factor homolog B, membrane trafficking protein

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • granulocyte monocyte progenitor cell CL0000557
    CSI 17.62
    rCSI 15.26%
    PRS 77.07
  • hematopoietic stem cell CL0000037
    CSI 11.91
    rCSI 7.91%
    PRS 75.22
  • plasmablast CL0000980
    CSI 10.31
    rCSI 8.11%
    PRS 78.81
  • Langerhans cell CL0000453
    CSI 9.09
    rCSI 13.88%
    PRS 85.74
  • erythrocyte CL0000232
    CSI 7.89
    rCSI 17.91%
    PRS 74.25
  • promyelocyte CL0000836
    CSI 7.45
    rCSI 10.75%
    PRS 80.05
  • placental villous trophoblast CL2000060
    CSI 7.31
    rCSI 11.29%
    PRS 71.34
  • promonocyte CL0000559
    CSI 6.55
    rCSI 11.22%
    PRS 80.08
  • common myeloid progenitor CL0000049
    CSI 6.46
    rCSI 5.22%
    PRS 74.41
  • megakaryocyte CL0000556
    CSI 6.26
    rCSI 27.18%
    PRS 80.84
  • intermediate monocyte CL0002393
    CSI 6.23
    rCSI 9.39%
    PRS 77.56
  • interneuron CL0000099
    CSI 5.79
    rCSI 11.63%
    PRS 61.55
  • CD4-positive, CD25-positive, alpha-beta regulatory T cell CL0000792
    CSI 5.66
    rCSI 5.56%
    PRS 86.94
  • megakaryocyte-erythroid progenitor cell CL0000050
    CSI 5.06
    rCSI 4.57%
    PRS 69.73
  • retinal cone cell CL0000573
    CSI 4.86
    rCSI 7.82%
    PRS 61.72
  • myeloid dendritic cell CL0000782
    CSI 4.71
    rCSI 6.83%
    PRS 86.41
  • plasmacytoid dendritic cell, human CL0001058
    CSI 4.4
    rCSI 3.07%
    PRS 75.44
  • conventional dendritic cell CL0000990
    CSI 3.57
    rCSI 2.98%
    PRS 77.08
  • CD16-positive, CD56-dim natural killer cell, human CL0000939
    CSI 3.57
    rCSI 2.38%
    PRS 87.49
  • CD14-positive monocyte CL0001054
    CSI 3.52
    rCSI 4.39%
    PRS 82.44
  • eosinophil CL0000771
    CSI 3.52
    rCSI 23.12%
    PRS 92.13
  • dendritic cell, human CL0001056
    CSI 3.35
    rCSI 5.15%
    PRS 81.59
  • cerebellar granule cell CL0001031
    CSI 3.33
    rCSI 4.9%
    PRS 65.14
  • lung macrophage CL1001603
    CSI 3.28
    rCSI 7.33%
    PRS 80.23
  • deuterosomal cell CL4033044
    CSI 3
    rCSI 10.16%
    PRS 72.83
  • pro-B cell CL0000826
    CSI 2.97
    rCSI 2.46%
    PRS 74.75
  • pulmonary artery endothelial cell CL1001568
    CSI 2.91
    rCSI 3.95%
    PRS 82.09
  • CD4-positive helper T cell CL0000492
    CSI 2.9
    rCSI 2.2%
    PRS 85.42
  • rod bipolar cell CL0000751
    CSI 2.74
    rCSI 4.93%
    PRS 65.42
  • intestine goblet cell CL0019031
    CSI 2.7
    rCSI 2.4%
    PRS 70.24
  • T follicular helper cell CL0002038
    CSI 2.67
    rCSI 2%
    PRS 86.22
  • naive T cell CL0000898
    CSI 2.66
    rCSI 1.85%
    PRS 86.81
  • alternatively activated macrophage CL0000890
    CSI 2.59
    rCSI 3.26%
    PRS 83.06
  • mesenchymal cell CL0008019
    CSI 2.49
    rCSI 6.34%
    PRS 65.93
  • inflammatory macrophage CL0000863
    CSI 2.48
    rCSI 4.24%
    PRS 90.56
  • IgA plasma cell CL0000987
    CSI 2.46
    rCSI 2.52%
    PRS 82.98
  • pulmonary ionocyte CL0017000
    CSI 2.46
    rCSI 2.99%
    PRS 79.25
  • erythroid progenitor cell CL0000038
    CSI 2.45
    rCSI 14.03%
    PRS 79.67
  • neural crest cell CL0011012
    CSI 2.39
    rCSI 1.89%
    PRS 59.7
  • epithelial cell of lung CL0000082
    CSI 2.37
    rCSI 1.96%
    PRS 72.61
  • effector memory CD8-positive, alpha-beta T cell, terminally differentiated CL0001062
    CSI 2.35
    rCSI 11.8%
    PRS 84.71
  • sst GABAergic cortical interneuron CL4023017
    CSI 2.33
    rCSI 3.01%
    PRS 54.79
  • mesodermal cell CL0000222
    CSI 2.33
    rCSI 2.8%
    PRS 70.37
  • epithelial cell of lower respiratory tract CL0002632
    CSI 2.29
    rCSI 1.77%
    PRS 75.66
  • L6b glutamatergic cortical neuron CL4023038
    CSI 2.27
    rCSI 7.09%
    PRS 55.24
  • CD14-low, CD16-positive monocyte CL0002396
    CSI 2.27
    rCSI 1.75%
    PRS 74.37
  • myeloid leukocyte CL0000766
    CSI 2.22
    rCSI 2.05%
    PRS 73.96
  • intestinal tuft cell CL0019032
    CSI 2.19
    rCSI 3.35%
    PRS 76.56
  • early lymphoid progenitor CL0000936
    CSI 2.19
    rCSI 1.92%
    PRS 77.83
  • CD8-positive, alpha-beta cytotoxic T cell CL0000794
    CSI 2.16
    rCSI 2.58%
    PRS 88.95
  • alveolar type 1 fibroblast cell CL4028004
    CSI 2.13
    rCSI 2.33%
    PRS 75.1
  • multi-ciliated epithelial cell CL0005012
    CSI 2.1
    rCSI 2.1%
    PRS 65.98
  • Hofbauer cell CL3000001
    CSI 2.07
    rCSI 3.92%
    PRS 81.89
  • stem cell CL0000034
    CSI 2.04
    rCSI 1.96%
    PRS 64.33
  • extravillous trophoblast CL0008036
    CSI 2.01
    rCSI 2.48%
    PRS 69.48
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 1.96
    rCSI 2.44%
    PRS 51.46
  • elicited macrophage CL0000861
    CSI 1.95
    rCSI 1.79%
    PRS 81.18
  • dendritic cell CL0000451
    CSI 1.9
    rCSI 2.34%
    PRS 80.47
  • duct epithelial cell CL0000068
    CSI 1.84
    rCSI 2.69%
    PRS 77.27
  • ciliated epithelial cell CL0000067
    CSI 1.82
    rCSI 1.6%
    PRS 60.6
  • CD14-positive, CD16-positive monocyte CL0002397
    CSI 1.77
    rCSI 2.31%
    PRS 84.42
  • group 3 innate lymphoid cell CL0001071
    CSI 1.75
    rCSI 1.32%
    PRS 78.26
  • VIP GABAergic cortical interneuron CL4023016
    CSI 1.72
    rCSI 2.06%
    PRS 53.28
  • platelet CL0000233
    CSI 1.72
    rCSI 7.15%
    PRS 72.15
  • common dendritic progenitor CL0001029
    CSI 1.72
    rCSI 2.15%
    PRS 82.17
  • CD1c-positive myeloid dendritic cell CL0002399
    CSI 1.66
    rCSI 2.01%
    PRS 80.95
  • glioblast CL0000030
    CSI 1.66
    rCSI 2.64%
    PRS 64.02
  • neuroblast (sensu Vertebrata) CL0000031
    CSI 1.66
    rCSI 2.12%
    PRS 68.83
  • mononuclear phagocyte CL0000113
    CSI 1.65
    rCSI 3.63%
    PRS 76.54
  • radial glial cell CL0000681
    CSI 1.61
    rCSI 2.24%
    PRS 70.92
  • ciliated cell CL0000064
    CSI 1.61
    rCSI 2.61%
    PRS 67.99
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 1.61
    rCSI 2.7%
    PRS 53.43
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 1.55
    rCSI 2.74%
    PRS 52.54
  • lung ciliated cell CL1000271
    CSI 1.5
    rCSI 1.73%
    PRS 63.53
  • granulocyte CL0000094
    CSI 1.43
    rCSI 2.19%
    PRS 80.91
  • club cell CL0000158
    CSI 1.43
    rCSI 2.09%
    PRS 67.26
  • retina horizontal cell CL0000745
    CSI 1.3
    rCSI 1.99%
    PRS 68.81
  • peripheral nervous system neuron CL2000032
    CSI 1.16
    rCSI 1.58%
    PRS 63.56
  • IgG plasma cell CL0000985
    CSI 0.99
    rCSI 1.18%
    PRS 85.6
  • mammary gland epithelial cell CL0002327
    CSI 0.98
    rCSI 3.46%
    PRS 82.46
  • vascular associated smooth muscle cell CL0000359
    CSI 0.93
    rCSI 3.03%
    PRS 71.21
  • basophil mast progenitor cell CL0002028
    CSI 0.93
    rCSI 4.98%
    PRS 93.5
  • forebrain radial glial cell CL0013000
    CSI 0.78
    rCSI 2.49%
    PRS 75.8
  • podocyte CL0000653
    CSI 0.77
    rCSI 3.44%
    PRS 72.57
  • primitive red blood cell CL0002355
    CSI 0.72
    rCSI 3.87%
    PRS 81.11
  • type EC enteroendocrine cell CL0000577
    CSI 0.66
    rCSI 2.34%
    PRS 78.35
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 0.55
    rCSI 1.99%
    PRS 51.56
  • Cajal-Retzius cell CL0000695
    CSI 0.46
    rCSI 3.61%
    PRS 80.04
  • pre-conventional dendritic cell CL0002010
    CSI 0.34
    rCSI 4.48%
    PRS 92.33
  • megakaryocyte progenitor cell CL0000553
    CSI 0.22
    rCSI 4.09%
    PRS 92.73

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

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Comma-separated if multiple.

Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [YIF1B](/details-gene/90522) (Yip1 interacting factor homolog B) is a protein-coding gene located on chromosome 19q13.2 that plays a fundamental role in intracellular membrane trafficking. Functional annotations strongly link it to the transport of proteins and vesicles between the endoplasmic reticulum and the Golgi apparatus. **Overall**, expression data indicates that [YIF1B](/details-gene/90522) is a highly significant gene in hematopoietic progenitor cells, including [granulocyte monocyte progenitor cell](/details-cell/CL0000557) and [hematopoietic stem cell](/details-cell/CL0000037), as well as in highly secretory cells like the [plasmablast](/details-cell/CL0000980). Clinically, mutations in [YIF1B](/details-gene/90522) are associated with severe post-natal neurodevelopmental syndromes, highlighting its critical importance in cellular maintenance and function, particularly within the nervous system [Link](https://doi.org/10.1007/s00401-020-02128-8). ## Cellular Roles and Expression Landscape The expression profile of [YIF1B](/details-gene/90522) underscores its importance in cells characterized by high rates of protein synthesis, processing, and secretion, as well as in cellular differentiation. **Overall**, the gene shows the highest significance in the hematopoietic system, particularly in progenitor and precursor populations. It is a top marker in [granulocyte monocyte progenitor cell](/details-cell/CL0000557), [hematopoietic stem cell](/details-cell/CL0000037), [promyelocyte](/details-cell/CL0000836), and [common myeloid progenitor](/details-cell/CL0000049). This pattern suggests a crucial role for [YIF1B](/details-gene/90522) in maintaining the robust protein trafficking machinery required for the differentiation and maturation of myeloid-lineage cells. Beyond progenitors, [YIF1B](/details-gene/90522) is also highly significant in terminally differentiated cells with demanding secretory functions. Its high CSI in [plasmablast](/details-cell/CL0000980), a precursor to antibody-secreting plasma cells, is consistent with its role in the ER-Golgi pathway. Similarly, its significance in [Langerhans cell](/details-cell/CL0000453) may relate to the processing and presentation of antigens. The gene's notable expression in non-immune cell types such as [placental villous trophoblast](/details-cell/CL2000060), [interneuron](/details-cell/CL0000099), and [retinal cone cell](/details-cell/CL0000573) indicates that its fundamental role in membrane trafficking is essential across diverse, functionally specialized cells. ## Pathways and Molecular Function [YIF1B](/details-gene/90522)'s functional annotations place it squarely within the core machinery of the secretory pathway. Its protein product is an integral component of the [endoplasmic reticulum membrane](/details-cell/GO:0005789), the [endoplasmic reticulum-golgi intermediate compartment](/details-cell/GO:0005793), and the [Golgi membrane](/details-cell/GO:0000139). The primary biological process associated with [YIF1B](/details-gene/90522) is [endoplasmic reticulum to golgi vesicle-mediated transport](/details-cell/GO:0006888), a critical step for moving newly synthesized proteins from their site of origin to the Golgi apparatus for further modification and sorting. It is specifically localized to [copii-coated er to golgi transport vesicle](/details-cell/GO:0030134), which are responsible for this anterograde transport. This function has been experimentally validated, demonstrating that [YIF1B](/details-gene/90522) is involved in the anterograde traffic pathway and is essential for maintaining normal Golgi architecture [Link](https://doi.org/10.1111/tra.12306). Its molecular function includes [protein binding](/details-cell/GO:0005515), which likely facilitates its interactions with other components of the trafficking machinery to ensure the fidelity of protein transport. ## Research Directions The established role of [YIF1B](/details-gene/90522) in fundamental membrane trafficking, combined with its association with severe neurological disease, opens several avenues for future investigation. While the available data highlights its basal importance, research should focus on how disruptions in this ubiquitous process lead to tissue-specific pathology. **Proposed Hypotheses:** 1. Given its high significance in hematopoietic progenitors, [YIF1B](/details-gene/90522) is likely essential for myelopoiesis. We hypothesize that conditional knockout of [YIF1B](/details-gene/90522) in hematopoietic stem cells will lead to a severe block in the differentiation of granulocytes and monocytes due to the inability to properly traffic and secrete key cytokines and cell surface receptors required for lineage commitment. 2. The neurological deficits caused by [YIF1B](/details-gene/90522) mutations suggest a specialized neuronal requirement for its function. We hypothesize that loss-of-function mutations in [YIF1B](/details-gene/90522) disproportionately affect neurons by disrupting the transport of specific cargo, such as synaptic vesicle precursors or ion channels, to distal axons and dendrites, thereby compromising synaptic transmission and neuronal viability. This is supported by findings linking mutations to Golgi and primary cilium alterations in neurodevelopmental syndromes [Link](https://doi.org/10.1093/brain/awaa235). **Experimental Approach:** To test the second hypothesis, patient-derived induced pluripotent stem cells (iPSCs) carrying truncating mutations in [YIF1B](/details-gene/90522) could be differentiated into cortical neurons. Using isogenic, CRISPR-corrected iPSC lines as a control, researchers could employ high-resolution live-cell imaging to track the trafficking of fluorescently-tagged synaptic proteins (e.g., synaptophysin) from the Golgi to synaptic terminals. Furthermore, proteomic analysis of Golgi-derived vesicles from mutant and control neurons could identify specific cargo whose transport is impaired, providing a direct molecular link between the trafficking defect and the observed neuropathology. **Therapeutic Potential:** As the pathology associated with [YIF1B](/details-gene/90522) stems from loss-of-function mutations, therapeutic strategies would need to focus on functional restoration rather than inhibition. This makes [YIF1B](/details-gene/90522) a challenging drug target for small molecules. The most direct, albeit technically demanding, approach would be gene therapy aimed at re-introducing a functional copy of the [YIF1B](/details-gene/90522) gene into affected cells, particularly in the central nervous system. The systemic importance of this gene in a fundamental cellular process suggests that any therapeutic intervention would require high specificity to avoid off-target effects.

Genular Protein ID: 1985017164

Symbol: YIF1B_HUMAN

Name: YIP1-interacting factor homolog B

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 12975309

Title: The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment.

PubMed ID: 12975309

DOI: 10.1101/gr.1293003

PubMed ID: 15498874

Title: Large-scale cDNA transfection screening for genes related to cancer development and progression.

PubMed ID: 15498874

DOI: 10.1073/pnas.0404089101

PubMed ID: 17974005

Title: The full-ORF clone resource of the German cDNA consortium.

PubMed ID: 17974005

DOI: 10.1186/1471-2164-8-399

PubMed ID: 15057824

Title: The DNA sequence and biology of human chromosome 19.

PubMed ID: 15057824

DOI: 10.1038/nature02399

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 18669648

Title: A quantitative atlas of mitotic phosphorylation.

PubMed ID: 18669648

DOI: 10.1073/pnas.0805139105

PubMed ID: 19690332

Title: Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.

PubMed ID: 19690332

DOI: 10.1126/scisignal.2000007

PubMed ID: 20068231

Title: Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.

PubMed ID: 20068231

DOI: 10.1126/scisignal.2000475

PubMed ID: 21269460

Title: Initial characterization of the human central proteome.

PubMed ID: 21269460

DOI: 10.1186/1752-0509-5-17

PubMed ID: 26077767

Title: Yif1B Is Involved in the Anterograde Traffic Pathway and the Golgi Architecture.

PubMed ID: 26077767

DOI: 10.1111/tra.12306

PubMed ID: 30877195

Title: Lysosomal targeting of the ABC transporter TAPL is determined by membrane-localized charged residues.

PubMed ID: 30877195

DOI: 10.1074/jbc.ra118.007071

PubMed ID: 32006098

Title: Truncating mutations in YIF1B cause a progressive encephalopathy with various degrees of mixed movement disorder, microcephaly, and epilepsy.

PubMed ID: 32006098

DOI: 10.1007/s00401-020-02128-8

PubMed ID: 33103737

Title: YIF1B mutations cause a post-natal neurodevelopmental syndrome associated with Golgi and primary cilium alterations.

PubMed ID: 33103737

DOI: 10.1093/brain/awaa235

Sequence Information:

  • Length: 314
  • Mass: 34435
  • Checksum: 93A2521A3332D3AD
  • Sequence:
  • MHPAGLAAAA AGTPRLRKWP SKRRIPVSQP GMADPHQLFD DTSSAQSRGY GAQRAPGGLS 
    YPAASPTPHA AFLADPVSNM AMAYGSSLAA QGKELVDKNI DRFIPITKLK YYFAVDTMYV 
    GRKLGLLFFP YLHQDWEVQY QQDTPVAPRF DVNAPDLYIP AMAFITYVLV AGLALGTQDR 
    FSPDLLGLQA SSALAWLTLE VLAILLSLYL VTVNTDLTTI DLVAFLGYKY VGMIGGVLMG 
    LLFGKIGYYL VLGWCCVAIF VFMIRTLRLK ILADAAAEGV PVRGARNQLR MYLTMAVAAA 
    QPMLMYWLTF HLVR

Genular Protein ID: 1004595385

Symbol: Q9H5F7_HUMAN

Name: N/A

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 11181995

Title: The sequence of the human genome.

PubMed ID: 11181995

DOI: 10.1126/science.1058040

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

Sequence Information:

  • Length: 142
  • Mass: 14931
  • Checksum: A89A2B0E3F35BE00
  • Sequence:
  • MLSCCLEPAA WDCGAEGRDG REEMVLGWKR DRGTTPRTLP ASPSAGTPLW GAGHVLGDAG 
    ESPLPSHPCP NRWSCCWSRK SCGVLAGWRC GSEAAPLTQP PEVGGLRQDP GVRGNPSLPA 
    PPQPVMRRLT FGPGPAPASD RP