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    SNX30 sorting nexin family member 30 [ Homo sapiens (human) ]

    Gene ID: 401548, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SNX30provided by HGNC
    Official Full Name
    sorting nexin family member 30provided by HGNC
    Primary source
    HGNC:HGNC:23685
    See related
    Ensembl:ENSG00000148158 MIM:620955; AllianceGenome:HGNC:23685
    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
    ATG24A
    Summary
    Predicted to enable phosphatidylinositol binding activity. Involved in positive regulation of autophagosome assembly and protein transport. Is active in early endosome. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in kidney (RPKM 13.0), lung (RPKM 12.9) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SNX30 in Genome Data Viewer
    Location:
    9q32
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (112749723..112885769)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (124920960..125057645)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (115513040..115637267)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene HSDL2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20192 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20193 Neighboring gene KIAA1958 Neighboring gene Sharpr-MPRA regulatory region 4745 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:115309395-115309946 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:115309947-115310499 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:115310500-115311051 Neighboring gene Sharpr-MPRA regulatory region 8480 Neighboring gene NANOG hESC enhancer GRCh37_chr9:115313867-115314374 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:115357836-115358025 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:115380828-115381410 Neighboring gene MPRA-validated peak7319 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28828 Neighboring gene INTS3 and NABP interacting protein Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:115512887-115513808 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:115513809-115514728 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:115516859-115517473 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:115517474-115518087 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:115518123-115518802 Neighboring gene SNX30 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 12854 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:115565661-115566288 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:115566289-115566914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:115572830-115573740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28830 Neighboring gene MPRA-validated peak7321 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20197 Neighboring gene NANOG hESC enhancer GRCh37_chr9:115608506-115609059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:115609080-115609580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:115610366-115610938 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:115628995-115629496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28831 Neighboring gene solute carrier family 46 member 2 Neighboring gene major urinary protein, pseudogene Neighboring gene zinc finger protein 883

    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. A heterodimeric SNX4--SNX7 SNX-BAR autophagy complex coordinates ATG9A trafficking for efficient autophagosome assembly. Antón Z, et al. J Cell Sci, 2020 Jul 15. PMID 32513819, Free PMC Article
    2. Molecular basis for SNX-BAR-mediated assembly of distinct endosomal sorting tubules. van Weering JR, et al. EMBO J, 2012 Nov 28. PMID 23085988, Free PMC Article
    3. Identification of preferred protein interactions by phage-display of the human Src homology-3 proteome. Kärkkäinen S, et al. EMBO Rep, 2006 Feb. PMID 16374509, Free PMC Article
    4. Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate. Letra A, et al. Am J Med Genet A, 2010 Jul. PMID 20583170, Free PMC Article
    5. Comprehensive analysis of interactions between the Src-associated protein in mitosis of 68 kDa and the human Src-homology 3 proteome. Asbach B, et al. PLoS One, 2012. PMID 22745667, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate.
    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ26481, FLJ34280, FLJ35589, FLJ44686, FLJ45069, FLJ46877

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endocytic recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in piecemeal microautophagy of the nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of autophagosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in reticulophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in early endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in phagophore assembly site IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    sorting nexin-30

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001012994.2 → NP_001013012.1  sorting nexin-30

      See identical proteins and their annotated locations for NP_001013012.1

      Status: VALIDATED

      Source sequence(s)
      AA401207, AK127013, AL139041, AL360235, AL390067, BG699098, BX367137
      Consensus CDS
      CCDS43865.1
      UniProtKB/Swiss-Prot
      Q5VWJ9
      Related
      ENSP00000363349.3, ENST00000374232.8
      Conserved Domains (2) summary
      cd06860
      Location:91 → 206
      PX_SNX7_30_like; The phosphoinositide binding Phox Homology domain of Sorting Nexins 7 and 30
      cd07667
      Location:190 → 429
      BAR_SNX30; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 30

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      112749723..112885769
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423393.1 → XP_047279349.1  sorting nexin-30 isoform X1

    2. XM_047423395.1 → XP_047279351.1  sorting nexin-30 isoform X2

    RNA

    1. XR_007061307.1 RNA Sequence

    2. XR_007061301.1 RNA Sequence

    3. XR_007061302.1 RNA Sequence

    4. XR_007061303.1 RNA Sequence

    5. XR_007061304.1 RNA Sequence

    6. XR_007061305.1 RNA Sequence

    7. XR_007061306.1 RNA Sequence

    8. XR_007061308.1 RNA Sequence

    9. XR_007061309.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      124920960..125057645
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362972.1 → XP_054218947.1  sorting nexin-30 isoform X1

    2. XM_054362973.1 → XP_054218948.1  sorting nexin-30 isoform X2

    RNA

    1. XR_008488030.1 RNA Sequence

    2. XR_008488024.1 RNA Sequence

    3. XR_008488025.1 RNA Sequence

    4. XR_008488026.1 RNA Sequence

    5. XR_008488027.1 RNA Sequence

    6. XR_008488028.1 RNA Sequence

    7. XR_008488029.1 RNA Sequence

    8. XR_008488031.1 RNA Sequence

    9. XR_008488032.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VWJ9.1 GenPept UniProtKB/Swiss-Prot:Q5VWJ9

    Gene LinkOut

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

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