SGPP1
sphingosine-1-phosphate phosphatase 1, the group of Sphingosine-1-phosphate phosphatases
Basic information
Region (hg38): 14:63684216-63728065
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (59 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGPP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030791.4. 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 | 1 | |||||
| missense | 56 | 59 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 56 | 4 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SGPP1 | protein_coding | protein_coding | ENST00000247225 | 3 | 43826 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000139 | 0.868 | 125738 | 0 | 10 | 125748 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.646 | 193 | 220 | 0.877 | 0.0000104 | 2798 |
| Missense in Polyphen | 61 | 87.778 | 0.69494 | 1048 | ||
| Synonymous | -0.701 | 97 | 88.6 | 1.09 | 0.00000420 | 947 |
| Loss of Function | 1.38 | 8 | 13.5 | 0.595 | 7.26e-7 | 159 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000152 | 0.000152 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000361 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Specifically dephosphorylates sphingosine 1-phosphate (S1P), dihydro-S1P, and phyto-S1P. Does not act on ceramide 1- phoshate, lysophosphatidic acid or phosphatidic acid. Regulates the intracellular levels of the bioactive sphingolipid metabolite S1P that regulates diverse biological processes acting both as an extracellular receptor ligand or as an intracellular second messenger (PubMed:12815058, PubMed:11756451). Involved in efficient ceramide synthesis from exogenous sphingoid bases. Converts S1P to sphingosine, which is readily metabolized to ceramide via ceramide synthase. In concert with sphingosine kinase 2 (SphK2), recycles sphingosine into ceramide though a phosphorylation/dephosphorylation cycle. Regulates intracellular ceramide levels, which in turn regulate apoptosis (By similarity). Via S1P levels, modulates resting tone, intracellular Ca(2+) and myogenic vasoconstriction in resistance arteries (PubMed:18583713). Also involved in unfolded protein response (UPR) and ER stress-induced autophagy via regulation of intracellular S1P levels (PubMed:20798685). {ECO:0000250|UniProtKB:Q9JI99, ECO:0000269|PubMed:11756451, ECO:0000269|PubMed:12815058, ECO:0000269|PubMed:18583713, ECO:0000269|PubMed:20798685}.;
- Pathway
- Sphingolipid signaling pathway - Homo sapiens (human);Sphingolipid metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;Sphingolipid de novo biosynthesis;Sphingolipid metabolism;sphingosine and sphingosine-1-phosphate metabolism;Sphingosine 1-phosphate (S1P) pathway
(Consensus)
Recessive Scores
- pRec
- 0.139
Intolerance Scores
- loftool
- 0.146
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 28.93
Haploinsufficiency Scores
- pHI
- 0.341
- hipred
- Y
- hipred_score
- 0.642
- ghis
- 0.608
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.858
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sgpp1
- Phenotype
- growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands 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); homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- sphinganine-1-phosphate metabolic process;sphingosine metabolic process;dephosphorylation;sphingolipid biosynthetic process;extrinsic apoptotic signaling pathway;intrinsic apoptotic signaling pathway
- Cellular component
- nucleus;nucleoplasm;endoplasmic reticulum membrane;plasma membrane;integral component of membrane
- Molecular function
- sphingosine-1-phosphate phosphatase activity;dihydrosphingosine-1-phosphate phosphatase activity