SPCS1
Basic information
Region (hg38): 3:52704955-52711148
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPCS1 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 | 0 | |||||
| missense | 10 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 1 | 0 |
Variants in SPCS1
This is a list of pathogenic ClinVar variants found in the SPCS1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-52706092-C-A | not specified | Uncertain significance (Dec 28, 2023) | ||
| 3-52706124-G-A | not specified | Uncertain significance (Sep 07, 2022) | ||
| 3-52706139-G-C | not specified | Likely benign (Oct 06, 2024) | ||
| 3-52706151-C-G | not specified | Uncertain significance (Jan 04, 2024) | ||
| 3-52706165-A-C | not specified | Uncertain significance (Feb 14, 2024) | ||
| 3-52706173-C-A | not specified | Uncertain significance (Jan 23, 2024) | ||
| 3-52706179-T-C | not specified | Likely benign (Aug 08, 2023) | ||
| 3-52706194-C-T | not specified | Uncertain significance (Apr 08, 2024) | ||
| 3-52706224-G-A | not specified | Uncertain significance (Nov 08, 2022) | ||
| 3-52706859-G-A | not specified | Uncertain significance (Feb 16, 2023) | ||
| 3-52707714-C-T | not specified | Uncertain significance (Oct 21, 2024) | ||
| 3-52707747-G-A | not specified | Uncertain significance (Oct 13, 2023) | ||
| 3-52707754-G-A | not specified | Uncertain significance (Aug 14, 2023) | ||
| 3-52707799-C-G | not specified | Uncertain significance (Mar 15, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SPCS1 | protein_coding | protein_coding | ENST00000233025 | 4 | 3212 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0139 | 0.878 | 125743 | 0 | 5 | 125748 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.462 | 85 | 97.9 | 0.869 | 0.00000476 | 1054 |
| Missense in Polyphen | 17 | 26.537 | 0.64061 | 317 | ||
| Synonymous | 0.466 | 37 | 40.8 | 0.907 | 0.00000205 | 348 |
| Loss of Function | 1.34 | 4 | 8.11 | 0.493 | 3.45e-7 | 91 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the microsomal signal peptidase complex which removes signal peptides from nascent proteins as they are translocated into the lumen of the endoplasmic reticulum. {ECO:0000250}.;
- Pathway
- Protein export - Homo sapiens (human);Biotin Metabolism;Multiple carboxylase deficiency, neonatal or early onset form;Biotinidase Deficiency;Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP);Incretin synthesis, secretion, and inactivation;Peptide hormone metabolism;SRP-dependent cotranslational protein targeting to membrane;Synthesis, secretion, and deacylation of Ghrelin;Translation;Metabolism of proteins;Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1)
(Consensus)
Recessive Scores
- pRec
- 0.116
Intolerance Scores
- loftool
- 0.495
- rvis_EVS
- 0.3
- rvis_percentile_EVS
- 71.81
Haploinsufficiency Scores
- pHI
- 0.189
- hipred
- Y
- hipred_score
- 0.581
- ghis
- 0.437
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.952
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Spcs1
- Phenotype
Gene ontology
- Biological process
- signal peptide processing;proteolysis;protein targeting to ER
- Cellular component
- signal peptidase complex;endoplasmic reticulum membrane;integral component of endoplasmic reticulum membrane;organelle membrane
- Molecular function
- molecular_function;protein binding;peptidase activity