SLC14A1
Basic information
Region (hg38): 18:45687024-45752520
Previous symbols: [ "JK" ]
Links
Phenotypes
GenCC
Source:
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Blood group, Kidd | BG | Hematologic | Variants associated with a blood group may be important in specific situations (eg, related to transfusion); Jk deficiency may be associated with a urine concentration defect | Hematologic | 1498276; 9215669; 11807016 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (16 variants)
- not provided (5 variants)
- SLC14A1-related condition (2 variants)
- Jk-null variant (1 variants)
- BLOOD GROUP--KIDD SYSTEM (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC14A1 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 14 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 1 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 2 | 15 | 1 | 5 |
Highest pathogenic variant AF is 0.000460
Variants in SLC14A1
This is a list of pathogenic ClinVar variants found in the SLC14A1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC14A1 | protein_coding | protein_coding | ENST00000436407 | 9 | 28394 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 5.77e-14 | 0.0154 | 125489 | 1 | 258 | 125748 | 0.00103 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.00926 | 246 | 246 | 1.00 | 0.0000135 | 2887 |
| Missense in Polyphen | 62 | 62.166 | 0.99732 | 789 | ||
| Synonymous | -0.103 | 96 | 94.7 | 1.01 | 0.00000590 | 909 |
| Loss of Function | -0.127 | 20 | 19.4 | 1.03 | 8.54e-7 | 235 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000543 | 0.000543 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0109 | 0.0109 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.000255 | 0.000255 |
| Middle Eastern | 0.0109 | 0.0109 |
| South Asian | 0.000327 | 0.000327 |
| Other | 0.00114 | 0.00114 |
dbNSFP
Source:
- Function
- FUNCTION: Urea channel that facilitates transmembrane urea transport down a concentration gradient. A constriction of the transmembrane channel functions as selectivity filter through which urea is expected to pass in dehydrated form. The rate of urea conduction is increased by hypotonic stress. Plays an important role in the kidney medulla collecting ducts, where it allows rapid equilibration between the lumen of the collecting ducts and the interstitium, and thereby prevents water loss driven by the high concentration of urea in the urine. Facilitates urea transport across erythrocyte membranes. May also play a role in transmembrane water transport, possibly by indirect means.;
- Pathway
- Amine compound SLC transporters;Purine metabolism;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules
(Consensus)
Recessive Scores
- pRec
- 0.281
Intolerance Scores
- loftool
- 0.982
- rvis_EVS
- 0.55
- rvis_percentile_EVS
- 81.55
Haploinsufficiency Scores
- pHI
- 0.0543
- hipred
- N
- hipred_score
- 0.144
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.200
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Slc14a1
- Phenotype
- homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; renal/urinary system 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); reproductive system phenotype; hematopoietic system phenotype;
Zebrafish Information Network
- Gene name
- slc14a2
- Affected structure
- urea transport
- Phenotype tag
- abnormal
- Phenotype quality
- decreased rate
Gene ontology
- Biological process
- water transport;urea transport;transmembrane transport;urea transmembrane transport
- Cellular component
- nucleolus;plasma membrane;integral component of plasma membrane;basolateral plasma membrane;intracellular membrane-bounded organelle
- Molecular function
- water transmembrane transporter activity;urea transmembrane transporter activity;urea channel activity