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

Gene ID: 401548, updated on 5-Mar-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 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. Predicted to be involved in protein transport. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in kidney (RPKM 13.0), lung (RPKM 12.9) and 24 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (112749723..112885769)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (124920960..125057645)
105.20220307 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 (22) 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)

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

  • 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 autophagy of mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endocytic recycling 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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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_2023_10

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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