TM9SF2 transmembrane 9 superfamily member 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TM9SF2provided by HGNC
Official Full Name: transmembrane 9 superfamily member 2provided by HGNC
Primary source: HGNC:HGNC:11865
See related: Ensembl:ENSG00000125304 MIM:604678; AllianceGenome:HGNC:11865
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: P76; Lnc-PCIR
Summary: This gene encodes a member of the transmembrane 9 superfamily. The encoded 76 kDa protein localizes to early endosomes in human cells. The encoded protein possesses a conserved and highly hydrophobic C-terminal domain which contains nine transmembrane domains. The protein may play a role in small molecule transport or act as an ion channel. A pseudogene associated with this gene is located on the X chromosome. [provided by RefSeq, Oct 2012]
Expression: Ubiquitous expression in thyroid (RPKM 79.3), colon (RPKM 75.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q32.3

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (99501472..99564048)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (98712365..98774941)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (100153726..100216302)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Identification of sulfur metabolism-related gene signature in osteoarthritis and TM9SF2's sustenance effect on M2 macrophages' phagocytic activity.
Title: Identification of sulfur metabolism-related gene signature in osteoarthritis and TM9SF2's sustenance effect on M2 macrophages' phagocytic activity.
LINC01232 exerts oncogenic activities in pancreatic adenocarcinoma via regulation of TM9SF2.
Title: LINC01232 exerts oncogenic activities in pancreatic adenocarcinoma via regulation of TM9SF2.
Study validated EXT1, TM9SF2, and TMED10 as important host factors for vaccinia virus infection.
Title: A Genome-Wide Haploid Genetic Screen Identifies Heparan Sulfate-Associated Genes and the Macropinocytosis Modulator TMED10 as Factors Supporting Vaccinia Virus Infection.
TM9SF2 is identified as novel oncogene in colorectal cancer (CRC). TM9SF2 is potentially regulated by the Ets-family transcription factor ELF1, and TM9SF2 is upregulated in approximately one-third of human CRC samples. Transcriptome analysis of TM9SF2 knockout cells revealed a potential role for TM9SF2 in cell cycle progression, oxidative phosphorylation, and ceramide signaling.
Title: Transposon mutagenesis screen in mice identifies TM9SF2 as a novel colorectal cancer oncogene.
Among the genes enriched in this screening, the authors found that TM9SF2 is critical for N-sulfation of heparan sulfate and therefore for chikungunya virus infection because it is involved in the proper localization and stability of NDST1.
Title: Genome-Wide Screening Uncovers the Significance of N-Sulfation of Heparan Sulfate as a Host Cell Factor for Chikungunya Virus Infection.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

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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
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

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
Knockdown of transmembrane 9 superfamily member 2 (TM9SF2) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl 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

RH102724 (e-PCR)
- UniSTS:97058

D13S508E (e-PCR)
- UniSTS:153205

SGC32863 (e-PCR)
- UniSTS:26367

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in ceramide metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in glycosphingolipid biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of heparan sulfate proteoglycan biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in endosome	TAS Traceable Author Statement more info	PubMed
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in microtubule organizing center	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: transmembrane 9 superfamily member 2

Names: 76 kDa membrane protein; LncRNA Positively Correlated with Inflammatory Responses; dinucleotide oxidase disulfide thiol exchanger 3 superfamily member 2; epididymis secretory sperm binding protein; transmembrane protein 9 superfamily member 2

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.