SMPD3
Basic information
Region (hg38): 16:68358327-68448508
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (92 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMPD3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018667.4. 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 | 0 | |||||
| missense | 90 | 92 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 90 | 2 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SMPD3 | protein_coding | protein_coding | ENST00000219334 | 7 | 90361 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.594 | 0.406 | 125723 | 0 | 12 | 125735 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.11 | 356 | 420 | 0.848 | 0.0000282 | 4181 |
| Missense in Polyphen | 96 | 156.71 | 0.61261 | 1588 | ||
| Synonymous | -1.34 | 228 | 204 | 1.12 | 0.0000156 | 1368 |
| Loss of Function | 3.66 | 5 | 24.6 | 0.203 | 0.00000140 | 254 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000166 | 0.0000905 |
| Ashkenazi Jewish | 0.000199 | 0.000198 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.0000445 | 0.0000440 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the hydrolysis of sphingomyelin to form ceramide and phosphocholine. Ceramide mediates numerous cellular functions, such as apoptosis and growth arrest, and is capable of regulating these 2 cellular events independently. Also hydrolyzes sphingosylphosphocholine. Regulates the cell cycle by acting as a growth suppressor in confluent cells. Probably acts as a regulator of postnatal development and participates in bone and dentin mineralization. {ECO:0000269|PubMed:10823942, ECO:0000269|PubMed:14741383, ECO:0000269|PubMed:15051724}.;
- Pathway
- Sphingolipid metabolism - Homo sapiens (human);Signal Transduction;Metabolism of lipids;sphingomyelin metabolism/ceramide salvage;Metabolism;Glycosphingolipid metabolism;TNFR1-mediated ceramide production;TNF signaling;Death Receptor Signalling;Glycosphingolipid metabolism;Sphingolipid metabolism;TNFalpha;Ceramide signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.183
Intolerance Scores
- loftool
- 0.152
- rvis_EVS
- -0.91
- rvis_percentile_EVS
- 10.12
Haploinsufficiency Scores
- pHI
- 0.351
- hipred
- Y
- hipred_score
- 0.687
- ghis
- 0.555
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.984
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Smpd3
- Phenotype
- endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; craniofacial 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); limbs/digits/tail phenotype; reproductive 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); respiratory system phenotype; skeleton phenotype;
Gene ontology
- Biological process
- hematopoietic progenitor cell differentiation;sphingomyelin metabolic process;sphingomyelin catabolic process;cell cycle;peptide hormone secretion;positive regulation of exosomal secretion;positive regulation of ceramide biosynthetic process
- Cellular component
- Golgi cis cisterna;Golgi membrane;cytoplasm;plasma membrane
- Molecular function
- sphingomyelin phosphodiesterase activity;protein binding;metal ion binding