SLC9B1

gene
On this page

Also known as NHA1

Summary

SLC9B1 (solute carrier family 9 member B1, HGNC:24244) is a protein-coding gene on chromosome 4q24, encoding Sodium/hydrogen exchanger 9B1 (Q4ZJI4). Sperm-specific Na(+)/H(+) exchanger involved in intracellular pH regulation of spermatozoa. It is a selective cancer dependency (DepMap: 15.5% of cell lines).

The protein encoded by this gene is a sodium/hydrogen exchanger and transmembrane protein. Highly conserved orthologs of this gene have been found in other mammalian species. The expression of this gene may be limited to testis. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 150159 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 77 total — 1 pathogenic, 1 likely-pathogenic
  • Cancer dependency (DepMap): dependent in 15.5% of screened cell lines
  • MANE Select transcript: NM_139173

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24244
Approved symbolSLC9B1
Namesolute carrier family 9 member B1
Location4q24
Locus typegene with protein product
StatusApproved
AliasesNHA1
Ensembl geneENSG00000164037
Ensembl biotypeprotein_coding
OMIM611527
Entrez150159

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 6 protein_coding, 4 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000296422, ENST00000394789, ENST00000503584, ENST00000504216, ENST00000509614, ENST00000510243, ENST00000510559, ENST00000511253, ENST00000512651, ENST00000514340, ENST00000514972, ENST00000916167

RefSeq mRNA: 2 — MANE Select: NM_139173 NM_001100874, NM_139173

CCDS: CCDS34041, CCDS47119

Canonical transcript exons

ENST00000296422 — 12 exons

ExonStartEnd
ENSE00001652192102991643102991712
ENSE00001735298102989800102989941
ENSE00001803968102949257102949427
ENSE00002085617103019599103019705
ENSE00002456940102945193102945320
ENSE00002484120102946647102946789
ENSE00002487384102900928102901332
ENSE00003527699102910439102910588
ENSE00003552563102905514102905650
ENSE00003567788102932124102932299
ENSE00003572492102906536102906644
ENSE00003651197102911431102911537

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 92.46.

FANTOM5 (CAGE): breadth broad, TPM avg 2.3376 / max 159.6841, expressed in 802 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
534312.3376802

Top tissues by expression

246 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
spermCL:000001992.46silver quality
left testisUBERON:000453391.98gold quality
right testisUBERON:000453491.28gold quality
testisUBERON:000047389.66gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.02gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.46gold quality
calcaneal tendonUBERON:000370172.83gold quality
islet of LangerhansUBERON:000000669.08gold quality
stromal cell of endometriumCL:000225568.44gold quality
adrenal tissueUBERON:001830368.00gold quality
C1 segment of cervical spinal cordUBERON:000646966.37gold quality
right adrenal glandUBERON:000123365.44gold quality
left adrenal gland cortexUBERON:003582565.03gold quality
ventricular zoneUBERON:000305365.01gold quality
lymph nodeUBERON:000002964.95gold quality
right coronary arteryUBERON:000162564.88gold quality
left adrenal glandUBERON:000123464.84gold quality
granulocyteCL:000009464.82gold quality
embryoUBERON:000092264.77gold quality
ganglionic eminenceUBERON:000402364.77gold quality
tibial nerveUBERON:000132364.57gold quality
left ovaryUBERON:000211964.57gold quality
right adrenal gland cortexUBERON:003582764.05gold quality
spinal cordUBERON:000224064.00gold quality
adrenal glandUBERON:000236963.82gold quality
corpus callosumUBERON:000233663.79gold quality
cerebellar hemisphereUBERON:000224563.74gold quality
Brodmann (1909) area 9UBERON:001354063.62gold quality
cerebellar cortexUBERON:000212963.52gold quality
right hemisphere of cerebellumUBERON:001489063.15gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-CURD-112yes6.96
E-ANND-3yes5.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

13 targeting SLC9B1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-4692100.0067.322066
HSA-MIR-451499.9967.101870
HSA-MIR-1213699.9872.815713
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-4690-5P99.6566.24813
HSA-MIR-4743-3P99.6268.122095
HSA-MIR-318299.4068.152454
HSA-MIR-6507-3P99.3567.321059
HSA-MIR-664A-3P99.2271.082696
HSA-MIR-319897.8465.64579
HSA-MIR-430997.8465.45588
HSA-MIR-215-3P97.0268.011209

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 15.5% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

  • cloning and characterization of a novel NHEDC1 (Na+/H+ exchanger like domain containing 1) gene; it was mapped to chromosome 4p24; molecular weight of NHEDC1 is about 56 KDa; it is exclusively expressed in the testis (PMID:16850186)
  • Results identified multiple cis-acting DNA regulatory elements in the 5 end of the SLC9B1 gene and shown that DNA methylation at these elements could provide mechanisms by which SLC9B1 expression is restricted to male germ cells. (PMID:25701605)
  • DNA methylation patterns in maternal blood at four CpG sites in SLC9B1 are predictive of fetal intolerance of labor during the late second and early third trimester. (PMID:29235940)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_rerioSLC9B2ENSDARG00000052700
mus_musculusSlc9b1ENSMUSG00000050150
rattus_norvegicusSlc9b1ENSRNOG00000069829
drosophila_melanogasterNha1FBGN0031865
drosophila_melanogasterNha2FBGN0263390
caenorhabditis_elegansWBGENE00009617
caenorhabditis_elegansWBGENE00009618
caenorhabditis_elegansWBGENE00010214

Paralogs (1): SLC9B2 (ENSG00000164038)

Protein

Protein identifiers

Sodium/hydrogen exchanger 9B1Q4ZJI4 (reviewed: Q4ZJI4)

Alternative names: Na(+)/H(+) exchanger-like domain-containing protein 1, Sodium/hydrogen exchanger-like domain-containing protein 1, Solute carrier family 9, subfamily B member 1

All UniProt accessions (6): D6RA80, D6RFK4, D6RGI9, D6RHJ0, H0Y9Z0, Q4ZJI4

UniProt curated annotations — full annotation on UniProt →

Function. Sperm-specific Na(+)/H(+) exchanger involved in intracellular pH regulation of spermatozoa. Involved in sperm motility and fertility.

Subcellular location. Cell projection. Cilium. Flagellum membrane.

Tissue specificity. Expressed only in the testis.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the monovalent cation:proton antiporter 1 (CPA1) transporter (TC 2.A.36) family.

Isoforms (4)

UniProt IDNamesCanonical?
Q4ZJI4-11yes
Q4ZJI4-22
Q4ZJI4-33
Q4ZJI4-54

RefSeq proteins (2): NP_001094344, NP_631912* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006153Cation/H_exchanger_TMDomain
IPR038770Na+/solute_symporter_sfHomologous_superfamily
IPR051843CPA1_transporterFamily

Pfam: PF00999

UniProt features (23 total): transmembrane region 13, splice variant 4, compositionally biased region 2, chain 1, region of interest 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q4ZJI4-F179.200.39

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-2672351Stimuli-sensing channels
R-HSA-382551Transport of small molecules
R-HSA-983712Ion channel transport

MSigDB gene sets: 75 (showing top): GOBP_SINGLE_FERTILIZATION, chr4q24, GOBP_SODIUM_ION_TRANSMEMBRANE_TRANSPORT, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_CILIUM_MOVEMENT, WTGAAAT_UNKNOWN, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOMF_PROTON_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOBP_REGULATION_OF_PH, GOBP_MONOATOMIC_ION_HOMEOSTASIS, GOBP_FERTILIZATION, GOBP_TRANSMEMBRANE_TRANSPORT

GO Biological Process (11): single fertilization (GO:0007338), flagellated sperm motility (GO:0030317), monoatomic ion transmembrane transport (GO:0034220), regulation of intracellular pH (GO:0051453), obsolete inorganic cation transmembrane transport (GO:0098662), monoatomic ion transport (GO:0006811), monoatomic cation transport (GO:0006812), sodium ion transport (GO:0006814), sodium ion transmembrane transport (GO:0035725), transmembrane transport (GO:0055085), proton transmembrane transport (GO:1902600)

GO Molecular Function (2): sodium:proton antiporter activity (GO:0015385), antiporter activity (GO:0015297)

GO Cellular Component (6): plasma membrane (GO:0005886), sperm principal piece (GO:0097228), cilium (GO:0005929), membrane (GO:0016020), motile cilium (GO:0031514), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Ion channel transport1
Transport of small molecules1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
monoatomic ion transport2
transport2
monoatomic cation transmembrane transport2
fertilization1
cilium-dependent cell motility1
cilium movement involved in cell motility1
sperm motility1
transmembrane transport1
regulation of pH1
intracellular monoatomic cation homeostasis1
regulation of biological quality1
metal ion transport1
sodium ion transport1
cellular process1
sodium ion transmembrane transporter activity1
metal cation:proton antiporter activity1
secondary active transmembrane transporter activity1
membrane1
cell periphery1
sperm flagellum1
intraciliary transport particle1
membrane-bounded organelle1
plasma membrane bounded cell projection1
cilium1

Protein interactions and networks

STRING

584 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLC9B1SLC9C1Q4G0N8707
SLC9B1SLC9C2Q5TAH2634
SLC9B1SLC9A5Q14940616
SLC9B1SLC9A9Q8IVB4603
SLC9B1SLC9A6Q92581599
SLC9B1SLC9A8Q9Y2E8597
SLC9B1SLC9A1P19634592
SLC9B1CPA2P48052585
SLC9B1BCCIPQ9P287541
SLC9B1GARIN2Q8N9W8531
SLC9B1SLC9A2Q9UBY0522
SLC9B1SLC9A4Q6AI14496
SLC9B1CPA1P15085494
SLC9B1CATSPER1Q8NEC5474
SLC9B1WBP2NLQ6ICG8461

IntAct

3 interactions, top by confidence:

ABTypeScore
AMFRSLC9B1psi-mi:“MI:0915”(physical association)0.400
SLC9B1CFTRpsi-mi:“MI:0915”(physical association)0.370

BioGRID (2): SLC9B1 (PCA), AMFR (Affinity Capture-MS)

ESM2 similar proteins: A0A2K2BF92, A0A6P3HVI0, A1L3P4, A2VDL4, A4IHB9, B9H7I1, D3ZJ25, D4A7H1, E7EXX2, F7B113, O00341, O35874, O54902, O57321, P24942, P31596, P31597, P43003, P43004, P43005, P43006, P46411, P48763, P49281, P49282, P50482, P51906, P51907, P51912, P56564, Q0D7E4, Q3ZAS0, Q4R7S2, Q4ZJI4, Q5BKR2, Q5M7K3, Q5R6B8, Q6DFC0, Q86UD5, Q8BLV3

Diamond homologs: A0A6P3HVI0, A4IHB9, A6NJY1, Q4R7S2, Q4ZJI4, Q5BKR2, Q5R6B8, Q86UD5, Q8C0X2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

77 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic1
Likely pathogenic1
Uncertain significance52
Likely benign12
Benign1

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
2503084NM_139173.4(SLC9B1):c.1338_1339del (p.Leu447fs)Pathogenic
1703532GRCh37/hg19 4q24(chr4:102851823-104641864)Likely pathogenic

SpliceAI

2687 predictions. Top by Δscore:

VariantEffectΔscore
4:102887339:A:AGacceptor_gain1.0000
4:102887340:G:GGacceptor_gain1.0000
4:102906645:C:CCacceptor_gain1.0000
4:102932119:TTTA:Tdonor_loss1.0000
4:102932120:TTACC:Tdonor_loss1.0000
4:102932121:TACCT:Tdonor_loss1.0000
4:102932122:A:Tdonor_loss1.0000
4:102932123:C:CCdonor_loss1.0000
4:102932185:A:ACdonor_gain1.0000
4:102932186:C:CCdonor_gain1.0000
4:102932219:T:TAdonor_gain1.0000
4:102932295:CAAAA:Cacceptor_gain1.0000
4:102932296:AAAA:Aacceptor_gain1.0000
4:102932297:AAA:Aacceptor_gain1.0000
4:102932298:AA:Aacceptor_gain1.0000
4:102932300:C:CCacceptor_gain1.0000
4:102934919:C:CTdonor_gain1.0000
4:102934920:T:TTdonor_gain1.0000
4:102934932:C:CTdonor_gain1.0000
4:102934933:T:TTdonor_gain1.0000
4:102934937:T:TAdonor_gain1.0000
4:102991637:TTTTA:Tdonor_loss1.0000
4:102991638:TTTA:Tdonor_loss1.0000
4:102991639:TTACC:Tdonor_loss1.0000
4:102991640:TA:Tdonor_loss1.0000
4:102991642:C:CTdonor_loss1.0000
4:102991709:CATG:Cacceptor_gain1.0000
4:102991711:TG:Tacceptor_gain1.0000
4:102991713:C:CCacceptor_gain1.0000
4:103019602:CAA:Cdonor_gain1.0000

AlphaMissense

3338 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:102906588:A:CF381L0.997
4:102906588:A:TF381L0.997
4:102906590:A:GF381L0.997
4:102905527:T:AK440I0.995
4:102932155:G:CF266L0.994
4:102932155:G:TF266L0.994
4:102932157:A:GF266L0.994
4:102945209:A:GW213R0.994
4:102945209:A:TW213R0.994
4:102905514:C:AQ444H0.993
4:102905514:C:GQ444H0.993
4:102905526:T:AK440N0.993
4:102905526:T:GK440N0.993
4:102932185:A:CS256R0.993
4:102932185:A:TS256R0.993
4:102932187:T:GS256R0.993
4:102945194:C:GG218R0.993
4:102945193:C:TG218D0.991
4:102901223:G:TA481D0.990
4:102901323:C:GG448R0.990
4:102906614:A:GW373R0.990
4:102906614:A:TW373R0.990
4:102932188:G:CS255R0.990
4:102932188:G:TS255R0.990
4:102932190:T:GS255R0.990
4:102905611:C:GR412P0.989
4:102906612:C:AW373C0.989
4:102906612:C:GW373C0.989
4:102945247:G:TA200D0.988
4:102901322:C:TG448D0.987

dbSNP variants (sampled 300 via entrez): RS1000026364 (4:103007153 G>A), RS1000041969 (4:102903026 T>C), RS1000072864 (4:102903599 G>A), RS1000095625 (4:102994089 C>A,T), RS1000113193 (4:103000831 C>G), RS1000122566 (4:103019760 A>G), RS1000175984 (4:103013134 G>T), RS1000223629 (4:102894704 C>T), RS1000261050 (4:102993956 T>C), RS1000279528 (4:102912397 G>T), RS10003326 (4:102948193 C>G,T), RS1000355223 (4:102887951 A>C), RS1000392197 (4:103000790 C>A,T), RS1000403139 (4:102986771 A>G), RS1000409806 (4:102938789 A>G)

Disease associations

OMIM: gene MIM:611527 | disease phenotypes: MIM:604928, MIM:616576, MIM:276900

GenCC curated gene-disease

Mondo (3): Wolfram syndrome 2 (MONDO:0011502), immunodeficiency, common variable, 12 (MONDO:0014697), Usher syndrome (MONDO:0019501)

Orphanet (4): Wolfram syndrome (Orphanet:3463), OBSOLETE: Common variable immunodeficiency (Orphanet:1572), NFKB1-related immune dysregulation (Orphanet:696874), Usher syndrome (Orphanet:886)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

9 associations (top):

StudyTraitp-value
GCST004946_70Schizophrenia3.000000e-08
GCST006061_22Atrial fibrillation2.000000e-12
GCST006061_23Atrial fibrillation4.000000e-11
GCST006414_85Atrial fibrillation4.000000e-08
GCST007201_466Schizophrenia4.000000e-08
GCST008919_4Asthma and attention deficit hyperactivity disorder3.000000e-08
GCST009379_265Type 2 diabetes2.000000e-10
GCST009597_14Multiple sclerosis7.000000e-16
GCST90013406_237Liver enzyme levels (alkaline phosphatase)2.000000e-15

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004533alkaline phosphatase measurement

MeSH disease descriptors (2)

DescriptorNameTree numbers
D052245Usher SyndromesC09.218.458.341.186.500.500; C09.218.458.341.887.886; C10.597.751.418.341.186.500.500; C10.597.751.418.341.887.886; C10.597.751.941.162.625.500; C11.768.585.658.500.813; C11.966.075.375.500; C16.131.077.299.500; C16.320.290.684.500; C23.888.592.763.393.341.887.886
C565733Wolfram Syndrome 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — SLC9 family of sodium/hydrogen exchangers

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, decreases methylation2
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
benzo(e)pyreneincreases methylation1
bisphenol Sdecreases expression1
Acetaminophenincreases expression1
Benzo(a)pyreneincreases methylation1
Methapyrileneincreases methylation1
Oxygenincreases expression1
Polystyrenesdecreases expression1
Tobacco Smoke Pollutionincreases expression1
2,4-Dichlorophenoxyacetic Aciddecreases expression1
Aflatoxin B1decreases methylation1
Cadmium Chloridedecreases expression1
Permethrinincreases expression1

Clinical trials (associated diseases)

18 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT07290530PHASE3NOT_YET_RECRUITING24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
NCT02065011PHASE2ACTIVE_NOT_RECRUITINGA Study to Determine the Long-Term Safety, Tolerability and Biological Activity of SAR421869 in Patients With Usher Syndrome Type 1B
NCT01505062PHASE1/PHASE2TERMINATEDStudy of SAR421869 in Participants With Retinitis Pigmentosa Associated With Usher Syndrome Type 1B
NCT04355689PHASE1/PHASE2ACTIVE_NOT_RECRUITINGSafety and Efficacy of NPI-001 Tablets for RP Associated With Usher Syndrome
NCT06789445PHASE1/PHASE2RECRUITINGA Study to Investigate the Safety of OpCT-001 in Adults Who Have Primary Photoreceptor Disease (CLARICO)
NCT00004345Not specifiedTERMINATEDStudy of Dietary N-3 Fatty Acids in Patients With Retinitis Pigmentosa and Usher Syndrome
NCT00016471Not specifiedCOMPLETEDA Genetic Analysis of Usher Syndrome in Ashkenazi Jews
NCT00106743Not specifiedCOMPLETEDNatural History and Genetic Studies of Usher Syndrome
NCT01954953Not specifiedUNKNOWNClinical and Genetic Examination of Usher Syndrome Patients’ Cohort in Europe
NCT02435940Not specifiedRECRUITINGInherited Retinal Degenerative Disease Registry
NCT03319524Not specifiedCOMPLETEDClinical and Genetic Testing of Patients With Usher Syndrome
NCT03901391Not specifiedCOMPLETEDProspective Open Clinical and Genetic Study of Patients With Retinitis Pigmentosa
NCT03990727Not specifiedUNKNOWNPhenotype Correlates Genotype of Inherited Retina Dystrophies, Retinitis Pigmentosa, Con>Rod Dystrophies.
NCT04665726Not specifiedRECRUITINGNatural History Study of Usher Syndrome ( Light4Deaf )
NCT04906135Not specifiedCOMPLETEDAuditory Neural Function in Implanted Patients With Usher Syndrome
NCT05355415Not specifiedRECRUITINGAdaptive Optics Imaging of Outer Retinal Diseases
NCT07278843Not specifiedRECRUITINGNatural History of Photoreceptor Degeneration in USH1B: Clinical Parameters and Validation of Functional Vision Tests in MYO7A
NCT07548944Not specifiedRECRUITINGObservational Study to Investigate the Short-term Effects of Transcorneal Electrical Stimulation on Visual Performance