SPTLC3
Basic information
Region (hg38): 20:13008972-13169103
Previous symbols: [ "C20orf38", "SPTLC2L" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (62 variants)
- not_provided (1 variants)
- Sensory_neuropathy (1 variants)
- Peripheral_neuropathy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPTLC3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018327.4. 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 | 61 | 64 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 61 | 2 | 0 |
Highest pathogenic variant AF is 0.000032636093
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SPTLC3 | protein_coding | protein_coding | ENST00000399002 | 12 | 157785 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.23e-7 | 0.985 | 125698 | 0 | 46 | 125744 | 0.000183 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.17 | 255 | 314 | 0.813 | 0.0000169 | 3608 |
| Missense in Polyphen | 101 | 133.01 | 0.75932 | 1503 | ||
| Synonymous | -0.955 | 127 | 114 | 1.11 | 0.00000645 | 1061 |
| Loss of Function | 2.25 | 15 | 27.8 | 0.540 | 0.00000151 | 341 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000912 | 0.0000911 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000335 | 0.000326 |
| Finnish | 0.000232 | 0.000231 |
| European (Non-Finnish) | 0.000233 | 0.000229 |
| Middle Eastern | 0.000335 | 0.000326 |
| South Asian | 0.000229 | 0.000229 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, while the SPTLC1-SPTLC3-SPTSSB has the ability to use a broader range of acyl-CoAs without apparent preference. {ECO:0000269|PubMed:19416851}.;
- Pathway
- Sphingolipid signaling pathway - Homo sapiens (human);Sphingolipid metabolism - Homo sapiens (human);Sphingolipid Metabolism;Metabolism of lipids;Metabolism;ceramide <i>de novo</i> biosynthesis;Sphingolipid de novo biosynthesis;Sphingolipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.128
Intolerance Scores
- loftool
- 0.252
- rvis_EVS
- -0.22
- rvis_percentile_EVS
- 37.43
Haploinsufficiency Scores
- pHI
- 0.105
- hipred
- N
- hipred_score
- 0.306
- ghis
- 0.507
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.520
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sptlc3
- Phenotype
Zebrafish Information Network
- Gene name
- sptlc3
- Affected structure
- motor neuron
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- sphingolipid biosynthetic process;sphingoid biosynthetic process
- Cellular component
- endoplasmic reticulum membrane;integral component of membrane;serine C-palmitoyltransferase complex
- Molecular function
- serine C-palmitoyltransferase activity;protein binding;pyridoxal phosphate binding