STC2
Basic information
Region (hg38): 5:173314723-173328447
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 STC2 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 | 1 | |||||
| missense | 11 | 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 | 11 | 0 | 1 |
Variants in STC2
This is a list of pathogenic ClinVar variants found in the STC2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-173317951-T-C | not specified | Uncertain significance (Sep 28, 2021) | ||
| 5-173318025-T-C | not specified | Uncertain significance (Feb 28, 2025) | ||
| 5-173318038-C-G | not specified | Uncertain significance (Mar 07, 2025) | ||
| 5-173318056-G-A | not specified | Uncertain significance (Jun 22, 2024) | ||
| 5-173318208-T-G | not specified | Uncertain significance (Dec 08, 2023) | ||
| 5-173323220-C-T | not specified | Uncertain significance (Dec 16, 2023) | ||
| 5-173323262-C-G | not specified | Uncertain significance (Mar 07, 2025) | ||
| 5-173325905-A-G | not specified | Uncertain significance (Feb 02, 2022) | ||
| 5-173325948-C-T | not specified | Uncertain significance (Jul 25, 2023) | ||
| 5-173325963-C-T | not specified | Uncertain significance (Aug 11, 2024) | ||
| 5-173325979-G-A | Benign (Jan 08, 2018) | |||
| 5-173325984-C-T | not specified | Uncertain significance (Aug 26, 2024) | ||
| 5-173326010-G-A | not specified | Uncertain significance (Nov 14, 2024) | ||
| 5-173328171-T-G | not specified | Uncertain significance (Apr 27, 2023) | ||
| 5-173328190-A-C | not specified | Uncertain significance (Dec 06, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STC2 | protein_coding | protein_coding | ENST00000265087 | 4 | 14791 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.266 | 0.729 | 125741 | 0 | 5 | 125746 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.20 | 141 | 187 | 0.753 | 0.0000115 | 1980 |
| Missense in Polyphen | 36 | 70.79 | 0.50855 | 846 | ||
| Synonymous | 0.282 | 77 | 80.2 | 0.960 | 0.00000541 | 593 |
| Loss of Function | 2.42 | 3 | 12.1 | 0.248 | 7.69e-7 | 128 |
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 | 0.000143 | 0.000139 |
| European (Non-Finnish) | 0.00000880 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Has an anti-hypocalcemic action on calcium and phosphate homeostasis.;
- Pathway
- Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
(Consensus)
Recessive Scores
- pRec
- 0.162
Intolerance Scores
- loftool
- 0.0329
- rvis_EVS
- -0.54
- rvis_percentile_EVS
- 20.54
Haploinsufficiency Scores
- pHI
- 0.145
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.469
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.853
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Stc2
- Phenotype
- reproductive system phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- cellular calcium ion homeostasis;response to oxidative stress;embryo implantation;regulation of signaling receptor activity;negative regulation of gene expression;endoplasmic reticulum unfolded protein response;response to vitamin D;negative regulation of multicellular organism growth;response to peptide hormone;post-translational protein modification;cellular protein metabolic process;decidualization;regulation of hormone biosynthetic process;cellular response to hypoxia;regulation of store-operated calcium entry
- Cellular component
- extracellular space;endoplasmic reticulum;endoplasmic reticulum lumen;Golgi apparatus;perinuclear region of cytoplasm
- Molecular function
- hormone activity;enzyme binding;heme binding;protein homodimerization activity