SLC9C1
protein-codingsolute carrier family 9 member C1, the group of Solute carrier family 9
Gene 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, Jul 2025]
- SLC9A10
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~153.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC9C1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_183061.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 1 | 4 | |||
| missense | 139 | 14 | 153 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 139 | 17 | 1 | 157 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_898884.1 | 28 | MANE Select | |
| Ensembl | ENSP00000306627.5 | 28 | MANE Select | |
| RefSeq | NP_001307460.1 | 27 | Standard | |
| Ensembl | ENSP00000518751.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Stimuli-sensing channels
- Ion channel transport
- Transport of small molecules
Biological Process
- multicellular organism development
- spermatogenesis
- cell differentiation
- flagellated sperm motility
- regulation of intracellular pH
Molecular Function
- ion channel activity
- sodium:proton antiporter activity
- potassium:proton antiporter activity
Cellular Component
- plasma membrane
- integral component of membrane
- motile cilium
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000305815
- Coding exons
- 28
- Length
- 153372
- Individuals with no LoFs
- 125631
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 116
- Defined
- 125747
- p
- 0.000461
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0613 | 570 | 574 | 0.993 | 0.0000273 | 7753 |
| Missense (PolyPhen) | 128 | 158.77 | 0.80621 | 2338 | ||
| Synonymous | -0.146 | 193 | 190 | 1.01 | 0.00000960 | 2099 |
| Loss of Function | 3.01 | 33 | 57.7 | 0.572 | 0.00000261 | 824 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00070 | 0.00068 | rare |
| Latino/Admixed American | 0.00070 | 0.00064 | rare |
| Ashkenazi Jewish | 0.00035 | 0.00020 | rare |
| East Asian | 0.00047 | 0.00044 | rare |
| Finnish | 0.000048 | 0.000046 | rare |
| European (Non-Finnish) | 0.00052 | 0.00050 | rare |
| South Asian | 0.00036 | 0.00033 | rare |
| Other | 0.00085 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Sperm-specific sodium/hydrogen exchanger involved in intracellular pH regulation of spermatozoa. Required for sperm motility and fertility. Involved in sperm cell hyperactivation, a step needed for sperm motility which is essential late in the preparation of sperm for fertilization. Required for the expression and bicarbonate regulation of the soluble adenylyl cyclase (sAC) (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0520
Intolerance Scores
- RVIS EVS
- 1.63
- RVIS percentile EVS
- 96.07
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |