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SNX19 sorting nexin 19 [ Homo sapiens (human) ]

Gene ID: 399979, updated on 3-Apr-2024

Summary

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Official Symbol
SNX19provided by HGNC
Official Full Name
sorting nexin 19provided by HGNC
Primary source
HGNC:HGNC:21532
See related
Ensembl:ENSG00000120451 AllianceGenome:HGNC:21532
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CHET8
Summary
Islet antigen-2 (IA-2) is an autoantigen in type 1 diabetes and plays a role in insulin secretion. IA-2 is found in dense-core secretory vesicles and interacts with the product of this gene, a sorting nexin. In mouse pancreatic beta-cells, the encoded protein influenced insulin secretion by stabilizing the number of dense-core secretory vesicles. [provided by RefSeq, Dec 2016]
Expression
Ubiquitous expression in testis (RPKM 9.7), thyroid (RPKM 8.9) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See SNX19 in Genome Data Viewer
Location:
11q24.3-q25
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (130866250..130916479, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (130901996..130952245, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (130736145..130786374, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene protein phosphatase 1 regulatory subunit 10 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:130674453-130674952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:130695964-130696543 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:130696544-130697122 Neighboring gene long intergenic non-protein coding RNA 2551 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:130731366-130731866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:130731867-130732367 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:130735401-130735900 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:130741218-130742417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5756 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4082 Neighboring gene uncharacterized LOC105369577 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:130868662-130869861 Neighboring gene RNA, 7SL, cytoplasmic 167, pseudogene

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. SNX19 restricts endolysosome motility through contacts with the endoplasmic reticulum. Saric A, et al. Nat Commun, 2021 Jul 27. PMID 34315878, Free PMC Article
  2. Schizophrenia risk variants influence multiple classes of transcripts of sorting nexin 19 (SNX19). Ma L, et al. Mol Psychiatry, 2020 Apr. PMID 30635639
  3. Single molecule in situ hybridization reveals distinct localizations of schizophrenia risk-related transcripts SNX19 and AS3MT in human brain. Takahashi Y, et al. Mol Psychiatry, 2021 Jul. PMID 33649454
  4. Use of chromatin immunoprecipitation to clone novel E2F target promoters. Weinmann AS, et al. Mol Cell Biol, 2001 Oct. PMID 11564866, Free PMC Article
  5. Screening of chondrogenic factors with a real-time fluorescence-monitoring cell line ATDC5-C2ER: identification of sorting nexin 19 as a novel factor. Kan A, et al. Arthritis Rheum, 2009 Nov. PMID 19877062

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Single molecule in situ hybridization reveals distinct localizations of schizophrenia risk-related transcripts SNX19 and AS3MT in human brain.
    Title: Single molecule in situ hybridization reveals distinct localizations of schizophrenia risk-related transcripts SNX19 and AS3MT in human brain.
  2. SNX19 restricts endolysosome motility through contacts with the endoplasmic reticulum.
    Title: SNX19 restricts endolysosome motility through contacts with the endoplasmic reticulum.
  3. Schizophrenia risk variants influence multiple classes of transcripts of sorting nexin 19 (SNX19).
    Title: Schizophrenia risk variants influence multiple classes of transcripts of sorting nexin 19 (SNX19).
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Polymorphisms associated with both noncardioembolic stroke and coronary heart disease: vienna stroke registry.
  5. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: Five common gene variants identify elevated genetic risk for coronary heart disease.
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

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
EBI GWAS Catalog

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

  • FLJ21600, FLJ42432, KIAA0254, DKFZp667I205, DKFZp667E0114

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables phosphatidylinositol binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chondrocyte differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in dense core granule maturation IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in establishment of localization in cell IEA
Inferred from Electronic Annotation
more info
  
involved_in exocytosis IEA
Inferred from Electronic Annotation
more info
  
involved_in insulin secretion IGI
Inferred from Genetic Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in early endosome membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
sorting nexin-19

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.

Genomic

  1. NG_053190.2 RefSeqGene

    Range
    5000..55229
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001301089.2 → NP_001288018.1  sorting nexin-19 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice junction at the 3' end of the first exon and starts translation at a downstream AUG compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AP000824, AP001093, AP003486
    Consensus CDS
    CCDS73416.1
    UniProtKB/TrEMBL
    B7ZAU9, E9PLV3
    Related
    ENSP00000435122.1, ENST00000528555.5
    Conserved Domains (2) summary
    pfam08628
    Location:225 → 325
    Nexin_C; Sorting nexin C terminal
    cl02563
    Location:1 → 39
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  2. NM_001347918.2 → NP_001334847.2  sorting nexin-19 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AP000824, AP001093, AP003486
    UniProtKB/TrEMBL
    A8K8U2
    Conserved Domains (4) summary
    smart00313
    Location:95 → 272
    PXA; Domain associated with PX domains
    PRK10263
    Location:270 → 332
    PRK10263; DNA translocase FtsK; Provisional
    pfam08628
    Location:804 → 905
    Nexin_C; Sorting nexin C terminal
    cl02563
    Location:532 → 642
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  3. NM_001347919.2 → NP_001334848.2  sorting nexin-19 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AP000824, AP001093, AP003486
    UniProtKB/TrEMBL
    A8K8U2
    Conserved Domains (3) summary
    cd06893
    Location:532 → 659
    PX_SNX19; The phosphoinositide binding Phox Homology domain of Sorting Nexin 19
    smart00313
    Location:95 → 272
    PXA; Domain associated with PX domains
    PRK10263
    Location:270 → 332
    PRK10263; DNA translocase FtsK; Provisional

  4. NM_001347920.2 → NP_001334849.2  sorting nexin-19 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AP000824, AP001093, AP003486
    UniProtKB/TrEMBL
    A8K8U2
    Conserved Domains (3) summary
    cd06893
    Location:532 → 659
    PX_SNX19; The phosphoinositide binding Phox Homology domain of Sorting Nexin 19
    smart00313
    Location:95 → 272
    PXA; Domain associated with PX domains
    PRK10263
    Location:270 → 332
    PRK10263; DNA translocase FtsK; Provisional

  5. NM_001347921.2 → NP_001334850.2  sorting nexin-19 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AP000824, AP001093
    Consensus CDS
    CCDS86261.1
    UniProtKB/TrEMBL
    A8K8U2
    Related
    ENSP00000435390.1, ENST00000533214.1
    Conserved Domains (3) summary
    cd06893
    Location:532 → 659
    PX_SNX19; The phosphoinositide binding Phox Homology domain of Sorting Nexin 19
    smart00313
    Location:95 → 272
    PXA; Domain associated with PX domains
    PRK10263
    Location:270 → 332
    PRK10263; DNA translocase FtsK; Provisional

  6. NM_001347922.2 → NP_001334851.2  sorting nexin-19 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AP000824, AP001093, AP003486
    UniProtKB/TrEMBL
    B4E3P7
    Conserved Domains (2) summary
    pfam08628
    Location:287 → 388
    Nexin_C; Sorting nexin C terminal
    cl02563
    Location:2 → 102
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  7. NM_001347923.2 → NP_001334852.2  sorting nexin-19 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AP000824, AP001093, AP003486
    UniProtKB/TrEMBL
    B7ZAU9
    Conserved Domains (2) summary
    pfam08628
    Location:269 → 370
    Nexin_C; Sorting nexin C terminal
    cl02563
    Location:27 → 84
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

  8. NM_001347924.2 → NP_001334853.1  sorting nexin-19 isoform 9

    Status: REVIEWED

    Source sequence(s)
    AP000824, AP001093, AP003486
    UniProtKB/TrEMBL
    B7ZAU9

  9. NM_001347925.2 → NP_001334854.1  sorting nexin-19 isoform 10

    Status: REVIEWED

    Source sequence(s)
    AP000824, AP001093, AP003486
    UniProtKB/TrEMBL
    B7ZAU9

  10. NM_001347926.2 → NP_001334855.1  sorting nexin-19 isoform 11

    Status: REVIEWED

    Source sequence(s)
    AP000824, AP001093, AP003486
    UniProtKB/Swiss-Prot
    Q92543

  11. NM_001347927.2 → NP_001334856.1  sorting nexin-19 isoform 12

    Status: REVIEWED

    Source sequence(s)
    AP000824, AP001093, AP003486
    Consensus CDS
    CCDS86260.1
    UniProtKB/TrEMBL
    B4DGR7, E9PJV7
    Related
    ENSP00000433699.1, ENST00000534726.5

  12. NM_014758.3 → NP_055573.3  sorting nexin-19 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AP000824, AP001093, AP003486
    Consensus CDS
    CCDS31721.1
    UniProtKB/Swiss-Prot
    E9PKB9, Q8IV55, Q92543
    UniProtKB/TrEMBL
    A8K8U2
    Related
    ENSP00000265909.4, ENST00000265909.9
    Conserved Domains (4) summary
    cd06893
    Location:532 → 659
    PX_SNX19; The phosphoinositide binding Phox Homology domain of Sorting Nexin 19
    smart00313
    Location:95 → 272
    PXA; Domain associated with PX domains
    PRK10263
    Location:270 → 332
    PRK10263; DNA translocase FtsK; Provisional
    pfam08628
    Location:844 → 945
    Nexin_C; Sorting nexin C terminal

RNA

  1. NR_144939.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP000824, AP001093, AP003486

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    130866250..130916479 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047426940.1 → XP_047282896.1  sorting nexin-19 isoform X1

  2. XM_047426943.1 → XP_047282899.1  sorting nexin-19 isoform X3

  3. XM_047426941.1 → XP_047282897.1  sorting nexin-19 isoform X2

  4. XM_047426942.1 → XP_047282898.1  sorting nexin-19 isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    130901996..130952245 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054368765.1 → XP_054224740.1  sorting nexin-19 isoform X5

  2. XM_054368766.1 → XP_054224741.1  sorting nexin-19 isoform X1

  3. XM_054368769.1 → XP_054224744.1  sorting nexin-19 isoform X3

  4. XM_054368767.1 → XP_054224742.1  sorting nexin-19 isoform X2

  5. XM_054368768.1 → XP_054224743.1  sorting nexin-19 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92543.2 GenPept UniProtKB/Swiss-Prot:Q92543

Gene LinkOut

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