SPHK1
sphingosine kinase 1
Basic information
Region (hg38): 17:76376584-76387860
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (52 variants)
- not_provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPHK1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001142601.2. 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 | 3 | |||||
| missense | 47 | 49 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 47 | 2 | 4 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SPHK1 | protein_coding | protein_coding | ENST00000323374 | 6 | 11277 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.03e-7 | 0.328 | 125122 | 2 | 613 | 125737 | 0.00245 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.489 | 279 | 303 | 0.921 | 0.0000184 | 2930 |
| Missense in Polyphen | 45 | 56.979 | 0.78976 | 551 | ||
| Synonymous | -1.24 | 152 | 134 | 1.14 | 0.00000835 | 1052 |
| Loss of Function | 0.491 | 11 | 12.9 | 0.852 | 6.33e-7 | 150 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00214 | 0.00212 |
| Ashkenazi Jewish | 0.000995 | 0.000993 |
| East Asian | 0.0000606 | 0.0000544 |
| Finnish | 0.00163 | 0.00162 |
| European (Non-Finnish) | 0.00318 | 0.00317 |
| Middle Eastern | 0.0000606 | 0.0000544 |
| South Asian | 0.00425 | 0.00419 |
| Other | 0.00327 | 0.00326 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the phosphorylation of sphingosine to form sphingosine 1-phosphate (SPP), a lipid mediator with both intra- and extracellular functions. Also acts on D-erythro- sphingosine and to a lesser extent sphinganine, but not other lipids, such as D,L-threo-dihydrosphingosine, N,N- dimethylsphingosine, diacylglycerol, ceramide, or phosphatidylinositol. {ECO:0000269|PubMed:20577214, ECO:0000269|PubMed:23602659}.;
- Pathway
- Fc gamma R-mediated phagocytosis - Homo sapiens (human);VEGF signaling pathway - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Sphingolipid metabolism - Homo sapiens (human);Sphingolipid Metabolism;Signal Transduction of S1P Receptor;Metabolism of Spingolipids in ER and Golgi apparatus;Signal Transduction;phospholipids as signalling intermediaries;VEGFA-VEGFR2 Pathway;Metabolism of lipids;Metabolism of proteins;Chaperonin-mediated protein folding;Metabolism;Association of TriC/CCT with target proteins during biosynthesis;Fibroblast growth factor-1;Glycosphingolipid metabolism;Beta3 integrin cell surface interactions;Protein folding;Signaling by VEGF;Sphingolipid de novo biosynthesis;Sphingolipid metabolism;sphingosine and sphingosine-1-phosphate metabolism;Signaling by Receptor Tyrosine Kinases;Fc-epsilon receptor I signaling in mast cells;S1P1 pathway;PDGFR-beta signaling pathway;Sphingosine 1-phosphate (S1P) pathway;VEGFR2 mediated cell proliferation
(Consensus)
Recessive Scores
- pRec
- 0.236
Intolerance Scores
- loftool
- 0.821
- rvis_EVS
- -0.22
- rvis_percentile_EVS
- 37.54
Haploinsufficiency Scores
- pHI
- 0.134
- hipred
- Y
- hipred_score
- 0.505
- ghis
- 0.521
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sphk1
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; embryo phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); normal phenotype; endocrine/exocrine gland phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- sphk1
- Affected structure
- heart
- Phenotype tag
- abnormal
- Phenotype quality
- split bilaterally
Gene ontology
- Biological process
- blood vessel development;sphingosine-1-phosphate receptor signaling pathway;protein folding;sphingosine metabolic process;inflammatory response;signal transduction;brain development;positive regulation of peptidyl-threonine phosphorylation;regulation of tumor necrosis factor-mediated signaling pathway;calcium-mediated signaling;sphingolipid biosynthetic process;positive regulation of cell growth;positive regulation of cell migration;positive regulation of protein ubiquitination;regulation of interleukin-1 beta production;intracellular signal transduction;negative regulation of apoptotic process;positive regulation of angiogenesis;positive regulation of mitotic cell cycle;positive regulation of smooth muscle contraction;sphingosine biosynthetic process;sphingoid catabolic process;lipid phosphorylation;positive regulation of fibroblast proliferation;positive regulation of NF-kappaB transcription factor activity;positive regulation of NIK/NF-kappaB signaling
- Cellular component
- nucleus;cytoplasm;cytosol;plasma membrane
- Molecular function
- magnesium ion binding;DNA binding;NAD+ kinase activity;protein binding;calmodulin binding;ATP binding;sphinganine kinase activity;D-erythro-sphingosine kinase activity;sphingosine-1-phosphate receptor activity;protein phosphatase 2A binding