STC1
Basic information
Region (hg38): 8:23841929-23854806
Previous symbols: [ "STC" ]
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 STC1 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 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 |
Variants in STC1
This is a list of pathogenic ClinVar variants found in the STC1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-23844782-A-T | not specified | Likely benign (Apr 13, 2023) | ||
| 8-23844793-G-A | not specified | Uncertain significance (Feb 26, 2024) | ||
| 8-23844825-C-T | not specified | Uncertain significance (May 20, 2024) | ||
| 8-23844831-T-C | not specified | Uncertain significance (Jan 10, 2025) | ||
| 8-23844871-G-A | not specified | Uncertain significance (Jul 06, 2021) | ||
| 8-23844966-A-T | not specified | Uncertain significance (Jul 26, 2022) | ||
| 8-23845020-C-T | not specified | Uncertain significance (Dec 31, 2024) | ||
| 8-23845029-C-A | not specified | Uncertain significance (Feb 09, 2025) | ||
| 8-23851386-C-T | not specified | Uncertain significance (Dec 13, 2023) | ||
| 8-23851420-G-C | not specified | Uncertain significance (Oct 26, 2022) | ||
| 8-23851489-C-T | not specified | Uncertain significance (Nov 08, 2022) | ||
| 8-23852320-T-G | not specified | Uncertain significance (Aug 22, 2023) | ||
| 8-23852346-C-T | not specified | Uncertain significance (Nov 10, 2024) | ||
| 8-23854414-T-A | not specified | Uncertain significance (Jan 03, 2025) | ||
| 8-23854462-G-A | not specified | Uncertain significance (Sep 12, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STC1 | protein_coding | protein_coding | ENST00000290271 | 4 | 12893 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.204 | 0.788 | 125738 | 0 | 9 | 125747 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.67 | 87 | 143 | 0.608 | 0.00000814 | 1635 |
| Missense in Polyphen | 35 | 53.89 | 0.64948 | 607 | ||
| Synonymous | 0.264 | 55 | 57.5 | 0.956 | 0.00000330 | 485 |
| Loss of Function | 2.26 | 3 | 11.2 | 0.269 | 7.50e-7 | 110 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.0000266 | 0.0000264 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Stimulates renal phosphate reabsorption, and could therefore prevent hypercalcemia.;
- Pathway
- Ectoderm Differentiation
(Consensus)
Intolerance Scores
- loftool
- 0.181
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 42.88
Haploinsufficiency Scores
- pHI
- 0.861
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.493
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.655
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Stc1
- Phenotype
- reproductive system phenotype; normal phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- stc1l
- Affected structure
- NCC ionocyte
- Phenotype tag
- abnormal
- Phenotype quality
- increased amount
Gene ontology
- Biological process
- ossification;endothelial cell morphogenesis;growth plate cartilage axis specification;cellular calcium ion homeostasis;embryo implantation;regulation of signaling receptor activity;negative regulation of endothelial cell migration;negative regulation of cell migration;response to vitamin D;chondrocyte proliferation;regulation of anion transport;decidualization;negative regulation of calcium ion transport;bone development;cellular response to cAMP;cellular response to glucocorticoid stimulus;cellular response to hypoxia;regulation of cardiac muscle cell contraction;positive regulation of calcium ion import;negative regulation of renal phosphate excretion
- Cellular component
- extracellular space;nucleus;cytoplasm;apical plasma membrane
- Molecular function
- hormone activity