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SNX29 sorting nexin 29 [ Homo sapiens (human) ]

Gene ID: 92017, updated on 5-Mar-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, Apr 2022]
Expression
Ubiquitous expression in kidney (RPKM 5.6), lymph node (RPKM 3.2) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
16p13.13-p13.12
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (11976734..12574287)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (12012847..12611331)
105.20220307 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 contribution of genotype by environment interaction to variation of diabetes-related traits. Zheng JS, et al. PLoS One, 2013. PMID 24204828, Free PMC Article
  5. 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

See all (34) 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)

Genotypes

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_2023_10

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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