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

Summary

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, Dec 2024]
Expression: Biased expression in testis (RPKM 3.5) and skin (RPKM 0.5) See more
Orthologs: mouse all
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Genomic context

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

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.
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.
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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S1215 (e-PCR), detects polymorphism
- UniSTS:18044

RH65506 (e-PCR)
- UniSTS:84359

NIB1965 (e-PCR)
- UniSTS:26516

SHGC-87656 (e-PCR)
- UniSTS:84433

AFM290yg5 (e-PCR)
- UniSTS:9715

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)

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
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

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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

112140898..112294216 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_017006247.2 → XP_016861736.1 solute carrier family 9 member C1 isoform X4
XM_017006248.2 → XP_016861737.1 solute carrier family 9 member C1 isoform X5
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
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
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
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
XM_047448022.1 → XP_047303978.1 solute carrier family 9 member C1 isoform X6
XM_017006250.2 → XP_016861739.1 solute carrier family 9 member C1 isoform X7
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
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