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    SNX29 sorting nexin 29 [ Homo sapiens (human) ]

    Gene ID: 92017, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SNX29provided by HGNC
    Official Full Name
    sorting nexin 29provided by HGNC
    Primary source
    HGNC:HGNC:30542
    See related
    Ensembl:ENSG00000048471 AllianceGenome:HGNC:30542
    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
    RUNDC2A; A-388D4.1
    Summary
    Predicted to enable phosphatidylinositol binding activity. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 5.6), lymph node (RPKM 3.2) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SNX29 in Genome Data Viewer
    Location:
    16p13.13-p13.12
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (11976734..12574287)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (12012847..12611331)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (12070591..12668144)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12066613-12067113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:12069255-12069906 Neighboring gene nuclear pore complex interacting protein family member B2 Neighboring gene TNF receptor superfamily member 17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10463 Neighboring gene ubiquitin like 5 pseudogene 4 Neighboring gene Sharpr-MPRA regulatory region 15429 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:12169236-12169786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7217 Neighboring gene Sharpr-MPRA regulatory region 9869 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12215085-12215584 Neighboring gene uncharacterized LOC642696 Neighboring gene ribosomal protein S23 pseudogene 6 Neighboring gene Sharpr-MPRA regulatory region 3169 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:12241842-12242399 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12257095-12257595 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:12355210-12355716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10466 Neighboring gene small nucleolar RNA ACA64 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:12404869-12405376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:12405377-12405883 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:12407183-12407683 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:12408231-12408918 Neighboring gene Sharpr-MPRA regulatory region 2664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12410661-12411592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12426104-12426604 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:12435179-12436378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10467 Neighboring gene uncharacterized LOC101927227 Neighboring gene uncharacterized LOC105371087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12479845-12480345 Neighboring gene Sharpr-MPRA regulatory region 12750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10470 Neighboring gene Sharpr-MPRA regulatory region 5052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12529425-12530112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12530113-12530799 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:12532613-12533114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10471 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12561965-12562466 Neighboring gene uncharacterized LOC124903644 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:12612096-12612755 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12616566-12617066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12620609-12621109 Neighboring gene uncharacterized LOC105371085 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10476 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12685995-12686514 Neighboring gene CRISPRi-validated cis-regulatory element chr16.1337 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:12707003-12708202 Neighboring gene Sharpr-MPRA regulatory region 11276 Neighboring gene uncharacterized LOC105371088 Neighboring gene Sharpr-MPRA regulatory region 10358 Neighboring gene calcineurin like phosphoesterase domain containing 1 Neighboring gene microRNA 4718

    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. SNX29, a new susceptibility gene shared with major mental disorders in Han Chinese population. Chen JH, et al. World J Biol Psychiatry, 2021 Sep. PMID 33143498
    2. Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci. Børglum AD, et al. Mol Psychiatry, 2014 Mar. PMID 23358160, Free PMC Article
    3. The Phox (PX) domain proteins and membrane traffic. Seet LF, et al. Biochim Biophys Acta, 2006 Aug. PMID 16782399
    4. Genome-wide association study on dimethylarginines reveals novel AGXT2 variants associated with heart rate variability but not with overall mortality. Seppälä I, et al. Eur Heart J, 2014 Feb. PMID 24159190
    5. Genome-wide contribution of genotype by environment interaction to variation of diabetes-related traits. Zheng JS, et al. PLoS One, 2013. PMID 24204828, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SNX29, a new susceptibility gene shared with major mental disorders in Han Chinese population.
      Title: SNX29, a new susceptibility gene shared with major mental disorders in Han Chinese population.
    2. The strongest associated SNP in the combined analysis, including Danish and German-Dutch samples, was rs12922317 in RUNDC2A.
      Title: Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity.
    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
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Genome-wide association study on dimethylarginines reveals novel AGXT2 variants associated with heart rate variability but not with overall mortality.
    EBI GWAS Catalog
    Genome-wide contribution of genotype by environment interaction to variation of diabetes-related traits.
    EBI GWAS Catalog
    Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Genome-wide shRNA screening identifies SNX29, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ00143, FLJ12363, FLJ40609

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol binding IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    sorting nexin-29
    Names
    RUN domain containing 2A
    RUN domain-containing protein 2A

    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_001376490.1 → NP_001363419.1  sorting nexin-29 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC007216, AC007601
      Conserved Domains (1) summary
      pfam02759
      Location:44 → 177
      RUN; RUN domain

    2. NM_032167.5 → NP_115543.3  sorting nexin-29 isoform 1

      See identical proteins and their annotated locations for NP_115543.3

      Status: VALIDATED

      Source sequence(s)
      AC007601, AC010333, AI369689, AK074072, AL135642, AL137333, BM692924, HY078299
      Consensus CDS
      CCDS10553.2
      UniProtKB/Swiss-Prot
      B5MDW2, Q8N2X2, Q8TEQ0, Q9HA26
      Related
      ENSP00000456480.1, ENST00000566228.6
      Conserved Domains (3) summary
      TIGR01843
      Location:438 → 636
      type_I_hlyD; type I secretion membrane fusion protein, HlyD family
      cd07277
      Location:658 → 775
      PX_RUN; The phosphoinositide binding Phox Homology domain of uncharacterized proteins containing PX and RUN domains
      pfam02759
      Location:44 → 177
      RUN; RUN domain

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      11976734..12574287
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017023874.2 → XP_016879363.1  sorting nexin-29 isoform X10

    2. XM_047434881.1 → XP_047290837.1  sorting nexin-29 isoform X4

    3. XM_047434884.1 → XP_047290840.1  sorting nexin-29 isoform X13

    4. XM_047434883.1 → XP_047290839.1  sorting nexin-29 isoform X9

    5. XM_047434887.1 → XP_047290843.1  sorting nexin-29 isoform X18

    6. XM_011522738.4 → XP_011521040.1  sorting nexin-29 isoform X2

      Conserved Domains (3) summary
      cd07277
      Location:668 → 820
      PX_RUN; The phosphoinositide binding Phox Homology domain of uncharacterized proteins containing PX and RUN domains
      pfam02759
      Location:54 → 189
      RUN; RUN domain
      pfam10211
      Location:487 → 552
      Ax_dynein_light; Axonemal dynein light chain

    7. XM_047434879.1 → XP_047290835.1  sorting nexin-29 isoform X1

    8. XM_047434880.1 → XP_047290836.1  sorting nexin-29 isoform X3

    9. XM_011522743.4 → XP_011521045.1  sorting nexin-29 isoform X8

      Conserved Domains (3) summary
      cd07277
      Location:668 → 821
      PX_RUN; The phosphoinositide binding Phox Homology domain of uncharacterized proteins containing PX and RUN domains
      pfam02759
      Location:54 → 189
      RUN; RUN domain
      pfam10211
      Location:487 → 552
      Ax_dynein_light; Axonemal dynein light chain

    10. XM_011522741.4 → XP_011521043.1  sorting nexin-29 isoform X5

      Conserved Domains (3) summary
      cd07277
      Location:668 → 822
      PX_RUN; The phosphoinositide binding Phox Homology domain of uncharacterized proteins containing PX and RUN domains
      pfam02759
      Location:54 → 189
      RUN; RUN domain
      pfam10211
      Location:487 → 552
      Ax_dynein_light; Axonemal dynein light chain

    11. XM_047434882.1 → XP_047290838.1  sorting nexin-29 isoform X6

    12. XM_017023873.3 → XP_016879362.1  sorting nexin-29 isoform X7

    13. XM_005255683.5 → XP_005255740.1  sorting nexin-29 isoform X16

      Conserved Domains (1) summary
      pfam02759
      Location:54 → 189
      RUN; RUN domain

    14. XM_011522744.4 → XP_011521046.1  sorting nexin-29 isoform X12

      Conserved Domains (3) summary
      cd07277
      Location:668 → 784
      PX_RUN; The phosphoinositide binding Phox Homology domain of uncharacterized proteins containing PX and RUN domains
      pfam02759
      Location:54 → 189
      RUN; RUN domain
      pfam10211
      Location:487 → 552
      Ax_dynein_light; Axonemal dynein light chain

    15. XM_017023876.3 → XP_016879365.1  sorting nexin-29 isoform X17

    16. XM_005255682.5 → XP_005255739.1  sorting nexin-29 isoform X11

      Conserved Domains (3) summary
      cd07277
      Location:668 → 785
      PX_RUN; The phosphoinositide binding Phox Homology domain of uncharacterized proteins containing PX and RUN domains
      pfam02759
      Location:54 → 189
      RUN; RUN domain
      pfam10211
      Location:487 → 552
      Ax_dynein_light; Axonemal dynein light chain

    17. XM_047434886.1 → XP_047290842.1  sorting nexin-29 isoform X15

    18. XM_047434885.1 → XP_047290841.1  sorting nexin-29 isoform X14

    19. XM_047434888.1 → XP_047290844.1  sorting nexin-29 isoform X19

    20. XM_047434889.1 → XP_047290845.1  sorting nexin-29 isoform X20

    RNA

    1. XR_001752024.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      12012847..12611331
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314341.1 → XP_054170316.1  sorting nexin-29 isoform X22

    2. XM_054314345.1 → XP_054170320.1  sorting nexin-29 isoform X10

    3. XM_054314348.1 → XP_054170323.1  sorting nexin-29 isoform X13

    4. XM_054314353.1 → XP_054170328.1  sorting nexin-29 isoform X18

    5. XM_054314339.1 → XP_054170314.1  sorting nexin-29 isoform X2

    6. XM_054314340.1 → XP_054170315.1  sorting nexin-29 isoform X21

    7. XM_054314344.1 → XP_054170319.1  sorting nexin-29 isoform X8

    8. XM_054314342.1 → XP_054170317.1  sorting nexin-29 isoform X5

    9. XM_054314343.1 → XP_054170318.1  sorting nexin-29 isoform X7

    10. XM_054314351.1 → XP_054170326.1  sorting nexin-29 isoform X16

    11. XM_054314347.1 → XP_054170322.1  sorting nexin-29 isoform X12

    12. XM_054314352.1 → XP_054170327.1  sorting nexin-29 isoform X17

    13. XM_054314346.1 → XP_054170321.1  sorting nexin-29 isoform X11

    14. XM_054314350.1 → XP_054170325.1  sorting nexin-29 isoform X15

    15. XM_054314349.1 → XP_054170324.1  sorting nexin-29 isoform X23

    16. XM_054314354.1 → XP_054170329.1  sorting nexin-29 isoform X19

    17. XM_054314355.1 → XP_054170330.1  sorting nexin-29 isoform X24

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001009607.1: Suppressed sequence

      Description
      NM_001009607.1: This RefSeq was permanently suppressed because the CDS was partial.

    2. NM_001080530.2: Suppressed sequence

      Description
      NM_001080530.2: This RefSeq was permanently suppressed because the CDS was partial.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TEQ0.3 GenPept UniProtKB/Swiss-Prot:Q8TEQ0

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