ATG9B autophagy related 9B [Homo sapiens (human)] - Gene

Summary

Official Symbol: ATG9Bprovided by HGNC
Official Full Name: autophagy related 9Bprovided by HGNC
Primary source: HGNC:HGNC:21899
See related: Ensembl:ENSG00000181652 MIM:612205; AllianceGenome:HGNC:21899
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: SONE; APG9L2; NOS3AS
Summary: This gene functions in the regulation of autophagy, a lysosomal degradation pathway. This gene also functions as an antisense transcript in the posttranscriptional regulation of the endothelial nitric oxide synthase 3 gene, which has 3' overlap with this gene on the opposite strand. Mutations in this gene and disruption of the autophagy process have been associated with multiple cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2012]
Expression: Broad expression in skin (RPKM 9.1), placenta (RPKM 8.7) and 15 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q36.1

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (151012209..151024499, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (152185332..152201351, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (150709297..150721586, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Depletion of CPNE7 sensitizes colorectal cancer to 5-fluorouracil by downregulating ATG9B expression.
Title: Depletion of CPNE7 sensitizes colorectal cancer to 5-fluorouracil by downregulating ATG9B expression.
ATG9B is a tissue-specific homotrimeric lipid scramblase that can compensate for ATG9A.
Title: ATG9B is a tissue-specific homotrimeric lipid scramblase that can compensate for ATG9A.
Contribution of NOS3AS Variants to Susceptibility to Essential Hypertension: A Study in Kermanshah Province, Western Iran.
Title: Contribution of NOS3AS Variants to Susceptibility to Essential Hypertension: A Study in Kermanshah Province, Western Iran.
Aging is associated with a decline in Atg9b-mediated autophagosome formation and appearance of enlarged mitochondria in the heart.
Title: Aging is associated with a decline in Atg9b-mediated autophagosome formation and appearance of enlarged mitochondria in the heart.
This study highlights the transcriptional inactivation mechanisms of ATG2B, ATG4D, ATG9A and ATG9B promoter methylation status and the possible origin of autophagy signal pathway repression in invasive ductal carcinomas.
Title: Aberrant methylation of ATG2B, ATG4D, ATG9A and ATG9B CpG island promoter is associated with decreased mRNA expression in sporadic breast carcinoma.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Polymorphisms in innate immunity genes and risk of childhood leukemia.
The role of Atg9 trafficking in yeast and mammalian autophagy, is summarised.
Title: New insights into the function of Atg9.
Observational study of gene-disease association, gene-gene interaction, gene-environment interaction, and genetic testing. (HuGE Navigator)
Title: Integrative predictive model of coronary artery calcification in atherosclerosis.
Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Genetic polymorphisms in nitric oxide synthase genes modify the relationship between vegetable and fruit intake and risk of non-Hodgkin lymphoma.

Submit: New GeneRIF Correction See all GeneRIFs (12)

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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Macrophage exposure to infectious or AT-2 inactivated HIV-1 increases expression of the TFEB targets ATG9B, UVRAG (both autophagy genes) and MCOLN1 (a lysosomal gene) at 24 hours post-exposure.	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH99113 (e-PCR)
- UniSTS:87829

GDB:4585743 (e-PCR)
- UniSTS:16746

RH45385 (e-PCR)
- UniSTS:50879

D7S2866 (e-PCR)
- UniSTS:64495

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables phospholipid scramblase activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within autophagosome assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in bone morphogenesis	ISS Inferred from Sequence or Structural Similarity 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 plasma membrane phospholipid scrambling	IEA Inferred from Electronic Annotation more info
involved_in programmed necrotic cell death	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to phagophore assembly site	IBA Inferred from Biological aspect of Ancestor more info
involved_in reticulophagy	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in autophagosome	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in phagophore assembly site	IBA Inferred from Biological aspect of Ancestor more info
located_in phagophore assembly site membrane	IEA Inferred from Electronic Annotation more info
located_in recycling endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in trans-Golgi network	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: autophagy-related protein 9B

Names: APG9-like 2; ATG9 autophagy related 9 homolog B; autophagy 9-like 2 protein; endothelial nitric oxide synthase antisense; nitric oxide synthase 3-overlapping antisense gene protein

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

NG_030317.1 RefSeqGene

Range

5006..14349

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001317056.2 → NP_001303985.1 autophagy-related protein 9B

Status: REVIEWED

Source sequence(s)

AC010973, AY515311, BM821239, BU741121, BX380863, BX420361

Consensus CDS

CCDS83242.1

UniProtKB/Swiss-Prot

A1A5D3, Q674R7, Q6JRW5, Q8N8I8

Related

ENSP00000491504.1, ENST00000639579.2

Conserved Domains (1) summary

pfam04109
Location:323 → 679

APG9; Autophagy protein Apg9

RNA

NR_073169.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) has alternate 5' exon structure, lacks an internal exon in the central region, and uses alternate exons in the 3' region, compared to variant 3. This variant is represented as non-coding because use of the expected translational start codon, as used in variant 1, results in a significantly truncated ORF and renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AI221785, AI243432, AY515311, BC128587
NR_133652.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (1) uses an alternate 3' structure compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC010973, AY515311

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

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

151012209..151024499 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011516065.3 → XP_011514367.3 autophagy-related protein 9B isoform X1

UniProtKB/Swiss-Prot

A1A5D3, Q674R7, Q6JRW5, Q8N8I8

Related

ENSP00000475737.2, ENST00000605952.5

RNA

XR_007060009.1 RNA Sequence
XR_002956421.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

152185332..152201351 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054357935.1 → XP_054213910.1 autophagy-related protein 9B isoform X2
XM_054357938.1 → XP_054213913.1 autophagy-related protein 9B isoform X2
XM_054357936.1 → XP_054213911.1 autophagy-related protein 9B isoform X2
XM_054357937.1 → XP_054213912.1 autophagy-related protein 9B isoform X2
XM_054357939.1 → XP_054213914.1 autophagy-related protein 9B isoform X1

UniProtKB/Swiss-Prot

A1A5D3, Q674R7, Q6JRW5, Q8N8I8