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

Gene ID: 285195, updated on 4-Feb-2024

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
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Genomic context

See SLC9A9 in Genome Data Viewer
Location:
3q24
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (143265222..143848468, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (146012562..146595091, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (142984064..143567310, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374137 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:142861418-142861941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20652 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:142947064-142947564 Neighboring gene PBX homeobox 2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20653 Neighboring gene SLC9A9 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20654 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:143148743-143149263 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:143162319-143163518 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64869 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:143236449-143236979 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20655 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:143262071-143262249 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 47 Neighboring gene uncharacterized LOC124906294 Neighboring gene ST13, Hsp70 interacting protein pseudogene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20656 Neighboring gene uncharacterized LOC102724120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:143366803-143367304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:143367305-143367804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20657 Neighboring gene UBTD2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20659 Neighboring gene ribosomal protein S17 pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20660 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:143689971-143690551 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:143690552-143691132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20663 Neighboring gene divergent protein kinase domain 2A

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

HIV-1 interactions

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

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ35613

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

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

  1. NG_017077.2 RefSeqGene

    Range
    5064..588310
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_173653.4NP_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:128486
    Na_H_Exchanger; Sodium/hydrogen exchanger family

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    143265222..143848468 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    B2RCH0
  2. XM_011512703.4XP_011511005.1  sodium/hydrogen exchanger 9 isoform X3

    Conserved Domains (1) summary
    pfam00999
    Location:2270
    Na_H_Exchanger; Sodium/hydrogen exchanger family
  3. XM_017006202.3XP_016861691.1  sodium/hydrogen exchanger 9 isoform X1

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

    Conserved Domains (1) summary
    pfam00999
    Location:128334
    Na_H_Exchanger; Sodium/hydrogen exchanger family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    146012562..146595091 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    B2RCH0
  2. XM_054346249.1XP_054202224.1  sodium/hydrogen exchanger 9 isoform X3

  3. XM_054346247.1XP_054202222.1  sodium/hydrogen exchanger 9 isoform X1

    UniProtKB/TrEMBL
    B2RCH0
  4. XM_054346250.1XP_054202225.1  sodium/hydrogen exchanger 9 isoform X4