SLC22A4
solute carrier family 22 member 4, the group of Solute carrier family 22
Basic information
Region (hg38): 5:132294394-132344190
Previous symbols: [ "DFNB60" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (115 variants)
- not_specified (45 variants)
- SLC22A4-related_disorder (16 variants)
- Hereditary_hearing_loss_and_deafness (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC22A4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003059.3. 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 | 41 | 45 | ||||
| missense | 79 | 84 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 82 | 44 | 6 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC22A4 | protein_coding | protein_coding | ENST00000200652 | 10 | 49764 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.83e-8 | 0.864 | 125651 | 0 | 97 | 125748 | 0.000386 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.852 | 259 | 301 | 0.862 | 0.0000158 | 3553 |
| Missense in Polyphen | 57 | 65.647 | 0.86828 | 800 | ||
| Synonymous | -1.11 | 140 | 124 | 1.13 | 0.00000678 | 1162 |
| Loss of Function | 1.64 | 16 | 24.8 | 0.644 | 0.00000126 | 266 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000860 | 0.000843 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000653 | 0.000653 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000292 | 0.000290 |
| Middle Eastern | 0.000653 | 0.000653 |
| South Asian | 0.000915 | 0.000915 |
| Other | 0.000654 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Sodium-ion dependent, low affinity carnitine transporter. Probably transports one sodium ion with one molecule of carnitine. Also transports organic cations such as tetraethylammonium (TEA) without the involvement of sodium. Relative uptake activity ratio of carnitine to TEA is 1.78. A key substrate of this transporter seems to be ergothioneine (ET). {ECO:0000269|PubMed:10215651, ECO:0000269|PubMed:15795384}.;
- Disease
- DISEASE: Rheumatoid arthritis (RA) [MIM:180300]: An inflammatory disease with autoimmune features and a complex genetic component. It primarily affects the joints and is characterized by inflammatory changes in the synovial membranes and articular structures, widespread fibrinoid degeneration of the collagen fibers in mesenchymal tissues, and by atrophy and rarefaction of bony structures. {ECO:0000269|PubMed:14608356}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
- Pathway
- Choline metabolism in cancer - Homo sapiens (human);Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Organic cation transport;Organic cation/anion/zwitterion transport
(Consensus)
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- loftool
- 0.538
- rvis_EVS
- -0.71
- rvis_percentile_EVS
- 14.57
Haploinsufficiency Scores
- pHI
- 0.0720
- hipred
- N
- hipred_score
- 0.312
- ghis
- 0.550
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0217
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc22a4
- Phenotype
- homeostasis/metabolism phenotype; immune system phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- triglyceride metabolic process;sodium ion transport;body fluid secretion;carnitine metabolic process;organic cation transport;quaternary ammonium group transport;carnitine transport;carnitine transmembrane transport
- Cellular component
- mitochondrion;plasma membrane;integral component of plasma membrane;apical plasma membrane
- Molecular function
- nucleotide binding;protein binding;ATP binding;secondary active organic cation transmembrane transporter activity;carnitine transmembrane transporter activity;symporter activity;cation:cation antiporter activity;quaternary ammonium group transmembrane transporter activity;PDZ domain binding