SLC9A9 solute carrier family 9 member A9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC9A9provided by HGNC
Official Full Name: solute carrier family 9 member A9provided by HGNC
Primary source: HGNC:HGNC:20653
See related: Ensembl:ENSG00000181804 MIM:608396; AllianceGenome:HGNC:20653
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: NHE9; AUTS16
Summary: This gene encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein family. The encoded protein localizes the to the late recycling endosomes and may play an important role in maintaining cation homeostasis. Mutations in this gene are associated with autism susceptibility 16 and attention-deficit/hyperactivity disorder. [provided by RefSeq, Mar 2012]
Expression: Ubiquitous expression in lymph node (RPKM 3.2), esophagus (RPKM 3.0) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q24

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (143265222..143848468, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (146012562..146595091, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (142984064..143567310, complement)

Chromosome 3 - NC_000003.12 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Genes for endosomal pH regulators NHE6 and NHE9 are dysregulated in the substantia nigra in Parkinson's disease.
Title: Genes for endosomal pH regulators NHE6 and NHE9 are dysregulated in the substantia nigra in Parkinson's disease.
Structure and elevator mechanism of the mammalian sodium/proton exchanger NHE9.
Title: Structure and elevator mechanism of the mammalian sodium/proton exchanger NHE9.
Sodium hydrogen exchanger 9 NHE9 (SLC9A9) and its emerging roles in neuropsychiatric comorbidity.
Title: Sodium hydrogen exchanger 9 NHE9 (SLC9A9) and its emerging roles in neuropsychiatric comorbidity.
results provide a detailed understanding of the functions of protein NHE9 and its disrupted interactions, possibly underlying Attention Deficit Hyperactivity Disorder and Autism Spectrum Disorders.
Title: Effect of disease-associated SLC9A9 mutations on protein-protein interaction networks: implications for molecular mechanisms for ADHD and autism.
rs9828519 polymorphism is associated with differential expression of SLC9A9 in occipital cortex, intralobular white matter, and substantia nigra in patients with multiple sclerosis.
Title: Genetic Variants and Multiple Sclerosis Risk Gene SLC9A9 Expression in Distinct Human Brain Regions.
downregulation of miR-135a as a potential mechanism underlying the high NHE9 expression observed in subset of glioblastomas
Title: MicroRNA-135a regulates NHE9 to inhibit proliferation and migration of glioblastoma cells.
SLC9A9 is a sodium hydrogen exchanger present in the recycling endosome and highly expressed in the brain.
Title: SLC9A9 Co-expression modules in autism-associated brain regions.
SLC9A9 has an oncogenic function by being related to EGFR signaling, suggesting SLC9A9 may be a novel prognostic indicator and a therapeutic target in colorectal cancer
Title: Up-regulation of SLC9A9 Promotes Cancer Progression and Is Involved in Poor Prognosis in Colorectal Cancer.
Ectopic expression of NHE9 in human brain microvascular endothelial cells without external cues induced up-regulation of the transferrin receptor (TfR) and down-regulation of ferritin, leading to an increase in iron uptake
Title: Na(+)/H(+) Exchanger 9 Regulates Iron Mobilization at the Blood-Brain Barrier in Response to Iron Starvation.
Taken together, our findings demonstrate that NHE9 can be an effective predictor of chemoradiotherapy response in esophageal squamous cell carcinoma
Title: NHE9 induces chemoradiotherapy resistance in esophageal squamous cell carcinoma by upregulating the Src/Akt/β-catenin pathway and Bcl-2 expression.

Submit: New GeneRIF Correction See all GeneRIFs (21)

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

Associated conditions

Description	Tests
Autism, susceptibility to, 16 MedGen: C3150677 OMIM: 613410 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Family-based genome-wide association scan of attention-deficit/hyperactivity disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed
Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genomic association analysis identifies multiple loci influencing antihypertensive response to an angiotensin II receptor blocker. EBI GWAS Catalog EBI GWAS CatalogPubMed
Pharmacogenomics in Alzheimer's disease: a genome-wide association study of response to cholinesterase inhibitors. 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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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	EIPA, a potent and specific inhibitor of Na+/H+ exchanger activity, significantly inhibits the Nef internalization into M2-macrophages, indicating that Nef is imported by Na+/H+ exchanger (solute carrier family 9, subfamily A)	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

D3S3373 (e-PCR)
- UniSTS:11008

SHGC-143952 (e-PCR)
- UniSTS:174109

SHGC-81458 (e-PCR)
- UniSTS:103212

SHGC-146757 (e-PCR)
- UniSTS:175412

SHGC-106921 (e-PCR)
- UniSTS:183615

SHGC-143982 (e-PCR)
- UniSTS:172118

WI-11313 (e-PCR)
- UniSTS:11096

D3S1569 (e-PCR), detects polymorphism
- UniSTS:79960

D3S3599 (e-PCR), detects polymorphism
- UniSTS:49799

STS-AA029791 (e-PCR)
- UniSTS:655

SHGC-154454 (e-PCR)
- UniSTS:183708

SHGC-154961 (e-PCR)
- UniSTS:183723

SHGC-155079 (e-PCR)
- UniSTS:183729

SHGC-142017 (e-PCR)
- UniSTS:171196

G59487 (e-PCR)
- UniSTS:136651

SHGC-79506 (e-PCR)
- UniSTS:103637

SHGC-33458 (e-PCR)
- UniSTS:44767

SHGC-145424 (e-PCR)
- UniSTS:174568

RH16165 (e-PCR)
- UniSTS:70639

SHGC-148816 (e-PCR)
- UniSTS:176627

WI-11352 (e-PCR)
- UniSTS:69878

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables potassium:proton antiporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables potassium:proton antiporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sodium:proton antiporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables sodium:proton antiporter activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in defense response to bacterium	IEA Inferred from Electronic Annotation more info
involved_in monoatomic ion transport	TAS Traceable Author Statement more info
involved_in phagosome maturation	IEA Inferred from Electronic Annotation more info
involved_in potassium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in potassium ion transmembrane transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in proton transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of intracellular pH	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of intracellular pH	IDA Inferred from Direct Assay more info	PubMed
involved_in sodium ion import across plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome membrane	IEA Inferred from Electronic Annotation more info
located_in early phagosome	IEA Inferred from Electronic Annotation more info
located_in late endosome membrane	TAS Traceable Author Statement more info
located_in phagocytic vesicle membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in recycling endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in recycling endosome	IDA Inferred from Direct Assay more info	PubMed
located_in recycling endosome membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sodium/hydrogen exchanger 9

Names: Na(+)/H(+) exchanger 9; putative protein product of Nbla00118; sodium/proton exchanger NHE9; solute carrier family 9 (sodium/hydrogen exchanger); solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9

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_017077.2 RefSeqGene

Range

5064..588310

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_173653.4 → NP_775924.1 sodium/hydrogen exchanger 9

See identical proteins and their annotated locations for NP_775924.1

Status: REVIEWED

Source sequence(s)

AB089794, AI252807, AL832304, AY254100, DB285312

Consensus CDS

CCDS33872.1

UniProtKB/Swiss-Prot

A6NMQ9, Q3LIC2, Q5JPI6, Q5WA58, Q8IVB4, Q8NAB9

UniProtKB/TrEMBL

B2RCH0

Related

ENSP00000320246.6, ENST00000316549.11

Conserved Domains (1) summary

pfam00999
Location:128 → 486

Na_H_Exchanger; Sodium/hydrogen exchanger family

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_000003.12 Reference GRCh38.p14 Primary Assembly

Range

143265222..143848468 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017006203.2 → XP_016861692.1 sodium/hydrogen exchanger 9 isoform X2

UniProtKB/TrEMBL

B2RCH0
XM_011512703.4 → XP_011511005.1 sodium/hydrogen exchanger 9 isoform X3

Conserved Domains (1) summary

pfam00999
Location:2 → 270

Na_H_Exchanger; Sodium/hydrogen exchanger family
XM_017006202.3 → XP_016861691.1 sodium/hydrogen exchanger 9 isoform X1

UniProtKB/TrEMBL

B2RCH0
XM_011512704.4 → XP_011511006.1 sodium/hydrogen exchanger 9 isoform X4

Conserved Domains (1) summary

pfam00999
Location:128 → 334

Na_H_Exchanger; Sodium/hydrogen exchanger family

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

146012562..146595091 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054346248.1 → XP_054202223.1 sodium/hydrogen exchanger 9 isoform X2

UniProtKB/TrEMBL

B2RCH0
XM_054346249.1 → XP_054202224.1 sodium/hydrogen exchanger 9 isoform X3
XM_054346247.1 → XP_054202222.1 sodium/hydrogen exchanger 9 isoform X1

UniProtKB/TrEMBL

B2RCH0
XM_054346250.1 → XP_054202225.1 sodium/hydrogen exchanger 9 isoform X4