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SLC9C1 solute carrier family 9 member C1 [ Homo sapiens (human) ]

Gene ID: 285335, updated on 2-Nov-2024

Summary

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Official Symbol
SLC9C1provided by HGNC
Official Full Name
solute carrier family 9 member C1provided by HGNC
Primary source
HGNC:HGNC:31401
See related
Ensembl:ENSG00000172139 MIM:612738; AllianceGenome:HGNC:31401
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NHE; NHE-10; SLC9A10; sperm-NHE
Summary
Predicted to enable potassium:proton antiporter activity and sodium:proton antiporter activity. Predicted to be involved in potassium ion transmembrane transport; regulation of intracellular pH; and sodium ion import across plasma membrane. Predicted to act upstream of or within flagellated sperm motility. Predicted to be located in membrane and motile cilium. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in testis (RPKM 3.5) and skin (RPKM 0.5) See more
Orthologs
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Genomic context

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See SLC9C1 in Genome Data Viewer
Location:
3q13.2
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (112140898..112294216, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (114862010..115015274, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (111859745..112013063, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene chromosome 3 open reading frame 52 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20235 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:111845355-111845988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20237 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:111855415-111855934 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:111855935-111856453 Neighboring gene germinal center associated signaling and motility Neighboring gene TGF-beta induced lncRNA Neighboring gene uncharacterized LOC124909407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:111904045-111904638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:111904639-111905231 Neighboring gene INAVA pseudogene 1 Neighboring gene ubiquitination factor E4A (UFD2 homolog, yeast) pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14603 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:112020972-112021844 Neighboring gene uncharacterized LOC105374042 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112051670-112052627 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112052628-112053584 Neighboring gene NANOG hESC enhancer GRCh37_chr3:112054081-112054840 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:112073606-112074235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20238 Neighboring gene CD200 molecule Neighboring gene uncharacterized LOC105374041 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112109833-112110448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20239 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:112118629-112119141 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:112119142-112119653 Neighboring gene uncharacterized LOC124909408 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112119654-112120166

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. The sodium/proton exchanger SLC9C1 (sNHE) is essential for human sperm motility and fertility. Cavarocchi E, et al. Clin Genet, 2021 May. PMID 33462806
  2. Role of the Na(+)/H(+) exchanger on the development of diabetes mellitus and its chronic complications. Sun YM, et al. Biochem Biophys Res Commun, 2012 Oct 19. PMID 23000155
  3. A new sperm-specific Na+/H+ exchanger required for sperm motility and fertility. Wang D, et al. Nat Cell Biol, 2003 Dec. PMID 14634667
  4. Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs. Oduru S, et al. BMC Genomics, 2003 Jun 3. PMID 12783626, Free PMC Article
  5. Impaired plasma membrane localization of ubiquitin ligase complex underlies 3-M syndrome development. Wang P, et al. J Clin Invest, 2019 Jul 25. PMID 31343991, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The sodium/proton exchanger SLC9C1 (sNHE) is essential for human sperm motility and fertility.
    Title: The sodium/proton exchanger SLC9C1 (sNHE) is essential for human sperm motility and fertility.
  2. this review outlines the contribution of NHE to chronic complications of diabetes mellitus, such as diabetic nephropathy; diabetic cardiomyopathy.[review]
    Title: Role of the Na(+)/H(+) exchanger on the development of diabetes mellitus and its chronic complications.
  3. 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.
Submit: New GeneRIF Correction

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 Variation Viewer (GRCh37.p13)

Pathways from PubChem

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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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables monoatomic ion channel activity IEA
Inferred from Electronic Annotation
more info
  
enables potassium:proton antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables sodium:proton antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in flagellated sperm motility IEA
Inferred from Electronic Annotation
more info
  
involved_in potassium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
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 sodium ion import across plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in motile cilium IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
solute carrier family 9 member C1
Names
sodium/hydrogen exchanger 10
solute carrier family 9, member 10
solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1
sperm-specific Na(+)/H(+) exchanger
sperm-specific sodium proton exchanger

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.

mRNA and Protein(s)

  1. NM_001320531.2 → NP_001307460.1  solute carrier family 9 member C1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC128688, BC044801
    Consensus CDS
    CCDS82818.1
    UniProtKB/Swiss-Prot
    Q4G0N8
    Related
    ENSP00000420688.1, ENST00000487372.5
    Conserved Domains (4) summary
    COG0664
    Location:834 → 968
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:834 → 950
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    pfam00520
    Location:596 → 678
    Ion_trans; Ion transport protein
    cl01133
    Location:19 → 286
    Na_H_Exchanger; Sodium/hydrogen exchanger family

  2. NM_183061.3 → NP_898884.1  solute carrier family 9 member C1 isoform 1

    See identical proteins and their annotated locations for NP_898884.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC128688, AK128084, BC044801
    Consensus CDS
    CCDS33817.1
    UniProtKB/Swiss-Prot
    Q4G0N8, Q6ZRP4, Q7RTP2
    Related
    ENSP00000306627.5, ENST00000305815.10
    Conserved Domains (4) summary
    COG0664
    Location:882 → 1016
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:882 → 998
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    pfam00520
    Location:644 → 726
    Ion_trans; Ion transport protein
    cl01133
    Location:19 → 421
    Na_H_Exchanger; Sodium/hydrogen exchanger family

RNA

  1. NR_135297.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks multiple alternate internal exons, and uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5' most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC128688, BC044801, BC143774, DB068586, DB072593
    Related
    ENST00000471295.1

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

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    112140898..112294216 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011512718.2 → XP_011511020.1  solute carrier family 9 member C1 isoform X2

    Conserved Domains (4) summary
    COG0664
    Location:828 → 962
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:828 → 944
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    pfam00520
    Location:590 → 672
    Ion_trans; Ion transport protein
    cl01133
    Location:19 → 367
    Na_H_Exchanger; Sodium/hydrogen exchanger family

  2. XM_017006247.2 → XP_016861736.1  solute carrier family 9 member C1 isoform X4

  3. XM_017006248.2 → XP_016861737.1  solute carrier family 9 member C1 isoform X5

  4. XM_011512719.2 → XP_011511021.1  solute carrier family 9 member C1 isoform X3

    Conserved Domains (3) summary
    pfam00520
    Location:644 → 726
    Ion_trans; Ion transport protein
    cl00047
    Location:882 → 916
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    cl01133
    Location:19 → 421
    Na_H_Exchanger; Sodium/hydrogen exchanger family

  5. XM_017006246.2 → XP_016861735.1  solute carrier family 9 member C1 isoform X1

    Conserved Domains (4) summary
    COG0664
    Location:839 → 973
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:839 → 955
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    pfam00520
    Location:601 → 683
    Ion_trans; Ion transport protein
    cl01133
    Location:14 → 378
    Na_H_Exchanger; Sodium/hydrogen exchanger family

  6. XM_011512725.2 → XP_011511027.1  solute carrier family 9 member C1 isoform X9

    Conserved Domains (3) summary
    COG0664
    Location:413 → 547
    Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
    cd00038
    Location:413 → 529
    CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...
    pfam00520
    Location:175 → 257
    Ion_trans; Ion transport protein

  7. XM_011512724.2 → XP_011511026.1  solute carrier family 9 member C1 isoform X8

    Conserved Domains (2) summary
    pfam00520
    Location:644 → 726
    Ion_trans; Ion transport protein
    cl01133
    Location:19 → 421
    Na_H_Exchanger; Sodium/hydrogen exchanger family

  8. XM_047448022.1 → XP_047303978.1  solute carrier family 9 member C1 isoform X6

  9. XM_017006250.2 → XP_016861739.1  solute carrier family 9 member C1 isoform X7

  10. XM_011512727.3 → XP_011511029.1  solute carrier family 9 member C1 isoform X10

    Conserved Domains (1) summary
    cl01133
    Location:19 → 421
    Na_H_Exchanger; Sodium/hydrogen exchanger family

  11. XM_011512726.3 → XP_011511028.1  solute carrier family 9 member C1 isoform X11

    Conserved Domains (1) summary
    cl01133
    Location:19 → 421
    Na_H_Exchanger; Sodium/hydrogen exchanger family

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_019805492.1 Reference GRCh38.p14 PATCHES

    Range
    24188..186954 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332391.1 → XP_054188366.1  solute carrier family 9 member C1 isoform X8

  2. XM_054332390.1 → XP_054188365.1  solute carrier family 9 member C1 isoform X7

  3. XM_054332389.1 → XP_054188364.1  solute carrier family 9 member C1 isoform X6

  4. XM_054332392.1 → XP_054188367.1  solute carrier family 9 member C1 isoform X10

  5. XM_054332393.1 → XP_054188368.1  solute carrier family 9 member C1 isoform X11

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    114862010..115015274 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054346315.1 → XP_054202290.1  solute carrier family 9 member C1 isoform X2

  2. XM_054346317.1 → XP_054202292.1  solute carrier family 9 member C1 isoform X4

  3. XM_054346318.1 → XP_054202293.1  solute carrier family 9 member C1 isoform X5

  4. XM_054346316.1 → XP_054202291.1  solute carrier family 9 member C1 isoform X3

  5. XM_054346314.1 → XP_054202289.1  solute carrier family 9 member C1 isoform X1

  6. XM_054346322.1 → XP_054202297.1  solute carrier family 9 member C1 isoform X9

  7. XM_054346321.1 → XP_054202296.1  solute carrier family 9 member C1 isoform X8

  8. XM_054346320.1 → XP_054202295.1  solute carrier family 9 member C1 isoform X7

  9. XM_054346319.1 → XP_054202294.1  solute carrier family 9 member C1 isoform X6

  10. XM_054346323.1 → XP_054202298.1  solute carrier family 9 member C1 isoform X10

  11. XM_054346324.1 → XP_054202299.1  solute carrier family 9 member C1 isoform X11

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q4G0N8.2 GenPept UniProtKB/Swiss-Prot:Q4G0N8

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