SLC4A8
Basic information
Region (hg38): 12:51391317-51515763
Links
Phenotypes
GenCC
Source:
- schizophrenia (Limited), mode of inheritance: Unknown
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (51 variants)
- not_provided (7 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC4A8 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001039960.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 52 | 52 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 52 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC4A8 | protein_coding | protein_coding | ENST00000453097 | 25 | 117880 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.998 | 0.00151 | 125732 | 0 | 16 | 125748 | 0.0000636 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.06 | 319 | 598 | 0.533 | 0.0000315 | 7209 |
| Missense in Polyphen | 115 | 284.42 | 0.40433 | 3377 | ||
| Synonymous | 0.672 | 201 | 213 | 0.941 | 0.0000110 | 2105 |
| Loss of Function | 5.81 | 8 | 54.2 | 0.148 | 0.00000273 | 658 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000333 | 0.000333 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000705 | 0.0000703 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Mediates electroneutral sodium- and carbonate-dependent chloride-HCO3(-) exchange with a Na(+):HCO3(-) stoichiometry of 2:1. Plays a major role in pH regulation in neurons. May be involved in cell pH regulation by transporting HCO3(-) from blood to cell. Enhanced expression in severe acid stress could be important for cell survival by mediating the influx of HCO3(-) into the cells. Also mediates lithium-dependent HCO3(-) cotransport. May be regulated by osmolarity. {ECO:0000269|PubMed:10362779, ECO:0000269|PubMed:11133997}.;
- Pathway
- Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Bicarbonate transporters
(Consensus)
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- loftool
- 0.114
- rvis_EVS
- -0.8
- rvis_percentile_EVS
- 12.46
Haploinsufficiency Scores
- pHI
- 0.0706
- hipred
- Y
- hipred_score
- 0.785
- ghis
- 0.556
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.493
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc4a8
- Phenotype
- renal/urinary system phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- sodium ion transport;inorganic anion transport;bicarbonate transport;regulation of intracellular pH;anion transmembrane transport
- Cellular component
- plasma membrane;integral component of plasma membrane;neuronal cell body membrane;neuron projection
- Molecular function
- inorganic anion exchanger activity;sodium:bicarbonate symporter activity;anion:anion antiporter activity