SOCS2
suppressor of cytokine signaling 2, the group of Suppressors of cytokine signaling|SH2 domain containing
Basic information
Region (hg38): 12:93569814-93583487
Links
Phenotypes
GenCC
Source:
No genCC data.
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 SOCS2 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 | 15 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 2 | 0 |
Variants in SOCS2
This is a list of pathogenic ClinVar variants found in the SOCS2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-93572908-G-T | not specified | Uncertain significance (Mar 19, 2024) | ||
| 12-93572935-G-C | not specified | Likely benign (Apr 17, 2024) | ||
| 12-93572946-C-T | not specified | Uncertain significance (Jun 13, 2023) | ||
| 12-93572974-C-T | not specified | Uncertain significance (Jun 21, 2021) | ||
| 12-93573027-G-A | not specified | Likely benign (Mar 25, 2024) | ||
| 12-93573031-A-G | not specified | Uncertain significance (Sep 20, 2022) | ||
| 12-93574961-G-A | not specified | Uncertain significance (Jan 26, 2022) | ||
| 12-93574968-A-G | not specified | Uncertain significance (Apr 04, 2023) | ||
| 12-93574992-G-A | not specified | Uncertain significance (Dec 22, 2023) | ||
| 12-93575052-A-G | not specified | Uncertain significance (Jun 24, 2022) | ||
| 12-93575055-C-A | not specified | Uncertain significance (Jun 28, 2022) | ||
| 12-93575061-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
| 12-93575090-A-T | not specified | Uncertain significance (Feb 01, 2023) | ||
| 12-93575102-T-C | not specified | Uncertain significance (Jan 16, 2024) | ||
| 12-93575108-G-A | not specified | Uncertain significance (Aug 22, 2023) | ||
| 12-93575149-T-G | not specified | Uncertain significance (Sep 12, 2024) | ||
| 12-93575159-G-A | not specified | Uncertain significance (Jun 11, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SOCS2 | protein_coding | protein_coding | ENST00000340600 | 2 | 13674 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.630 | 0.364 | 125724 | 0 | 1 | 125725 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.37 | 71 | 112 | 0.635 | 0.00000592 | 1244 |
| Missense in Polyphen | 19 | 38.951 | 0.4878 | 471 | ||
| Synonymous | 0.718 | 42 | 48.4 | 0.869 | 0.00000271 | 403 |
| Loss of Function | 2.19 | 1 | 7.43 | 0.135 | 3.79e-7 | 91 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: SOCS family proteins form part of a classical negative feedback system that regulates cytokine signal transduction. SOCS2 appears to be a negative regulator in the growth hormone/IGF1 signaling pathway. Probable substrate recognition component of a SCF-like ECS (Elongin BC-CUL2/5-SOCS-box protein) E3 ubiquitin- protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins.;
- Pathway
- Type II diabetes mellitus - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Prolactin signaling pathway - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);IGF-Core;Leptin signaling pathway;Prolactin Signaling Pathway;JAK-STAT;Ectoderm Differentiation;Leptin Insulin Overlap;Growth hormone receptor signaling;Prolactin;Cytokine Signaling in Immune system;Post-translational protein modification;Metabolism of proteins;Growth hormone signaling;Immune System;Neddylation;IL3;IL2-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.482
Intolerance Scores
- loftool
- 0.406
- rvis_EVS
- 0.19
- rvis_percentile_EVS
- 66.57
Haploinsufficiency Scores
- pHI
- 0.564
- hipred
- Y
- hipred_score
- 0.733
- ghis
- 0.429
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.977
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Socs2
- Phenotype
- hematopoietic system phenotype; reproductive system phenotype; respiratory system phenotype; liver/biliary system phenotype; renal/urinary system phenotype; skeleton phenotype; immune system phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- regulation of cell growth;JAK-STAT cascade;lactation;regulation of signal transduction;positive regulation of signal transduction;protein ubiquitination;response to estradiol;cellular response to hormone stimulus;interleukin-7-mediated signaling pathway;negative regulation of multicellular organism growth;negative regulation of apoptotic process;regulation of phosphatidylinositol 3-kinase activity;post-translational protein modification;positive regulation of neuron differentiation;negative regulation of JAK-STAT cascade;negative regulation of insulin receptor signaling pathway;phosphatidylinositol phosphorylation;growth hormone receptor signaling pathway;mammary gland alveolus development
- Cellular component
- cytoplasm;cytosol;phosphatidylinositol 3-kinase complex
- Molecular function
- SH3/SH2 adaptor activity;growth hormone receptor binding;insulin-like growth factor receptor binding;protein binding;JAK pathway signal transduction adaptor activity;1-phosphatidylinositol-3-kinase regulator activity