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    LYSET lysosomal enzyme trafficking factor [ Homo sapiens (human) ]

    Gene ID: 26175, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LYSETprovided by HGNC
    Official Full Name
    lysosomal enzyme trafficking factorprovided by HGNC
    Primary source
    HGNC:HGNC:20218
    See related
    Ensembl:ENSG00000153485 MIM:619332; AllianceGenome:HGNC:20218
    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
    DMAN; GCAF; TMEM251; C14orf109
    Summary
    Involved in lysosomal transport; lysosome organization; and regulation of vesicle-mediated transport. Located in Golgi cisterna. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in prostate (RPKM 12.5), kidney (RPKM 10.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LYSET in Genome Data Viewer
    Location:
    14q32.12
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (93184974..93188463)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (87416913..87420404)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (93651319..93654808)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93604409-93604908 Neighboring gene cytochrome b5 type A pseudogene 3 Neighboring gene modulator of apoptosis 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:93672647-93673506 Neighboring gene GON7 subunit of KEOPS complex Neighboring gene ubiquitin protein ligase E3 component n-recognin 7 Neighboring gene ribosomal protein L18a pseudogene 1

    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. LYSET/TMEM251- a novel key component of the mannose 6-phosphate pathway. Qiao W, et al. Autophagy, 2023 Jul. PMID 36633450, Free PMC Article
    2. Lysosomal enzyme trafficking factor LYSET enables nutritional usage of extracellular proteins. Pechincha C, et al. Science, 2022 Oct 7. PMID 36074822
    3. Biallelic TMEM251 variants in patients with severe skeletal dysplasia and extreme short stature. Ain NU, et al. Hum Mutat, 2021 Jan. PMID 33252156
    4. The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection. Richards CM, et al. Science, 2022 Oct 7. PMID 36074821, Free PMC Article
    5. GCAF(TMEM251) regulates lysosome biogenesis by activating the mannose-6-phosphate pathway. Zhang W, et al. Nat Commun, 2022 Sep 12. PMID 36096887, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LYSET/TMEM251- a novel key component of the mannose 6-phosphate pathway.
      Title: LYSET/TMEM251- a novel key component of the mannose 6-phosphate pathway.
    2. Lysosomal enzyme trafficking factor LYSET enables nutritional usage of extracellular proteins.
      Title: Lysosomal enzyme trafficking factor LYSET enables nutritional usage of extracellular proteins.
    3. The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection.
      Title: The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection.
    4. Biallelic TMEM251 variants in patients with severe skeletal dysplasia and extreme short stature.
      Title: Biallelic TMEM251 variants in patients with severe skeletal dysplasia and extreme short stature.
    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
    Dysostosis multiplex, Ain-Naz type
    MedGen: C5444223 OMIM: 619345 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

    • DKFZp564F1123

    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 lysosomal transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lysosome organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi cisterna IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lysosomal enzyme trafficking factor
    Names
    GNPTAB cleavage and activity factor
    UPF0694 transmembrane protein C14orf109
    transmembrane protein 251

    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_001098621.4 → NP_001092091.2  lysosomal enzyme trafficking factor isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AI056285, AL110118, CX785861
      Consensus CDS
      CCDS45158.2
      UniProtKB/Swiss-Prot
      J3KQ65, Q8N6I4, Q9Y4S5
      Related
      ENSP00000388431.3, ENST00000415050.3
      Conserved Domains (1) summary
      pfam15190
      Location:34 → 161
      TMEM251; Transmembrane protein 251

    2. NM_015676.3 → NP_056491.1  lysosomal enzyme trafficking factor isoform 2

      See identical proteins and their annotated locations for NP_056491.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate first exon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AI056285, AL110118, AW404266, BC030119
      Consensus CDS
      CCDS41980.1
      UniProtKB/Swiss-Prot
      Q8N6I4
      Related
      ENSP00000283534.4, ENST00000283534.4
      Conserved Domains (1) summary
      pfam15190
      Location:2 → 129
      DUF4583; Domain of unknown function (DUF4583)

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      93184974..93188463
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187601.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      299536..303025
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      87416913..87420404
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N6I4.4 GenPept UniProtKB/Swiss-Prot:Q8N6I4

    Gene LinkOut

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

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