SOCS2

suppressor of cytokine signaling 2, the group of Suppressors of cytokine signaling|SH2 domain containing

Basic information

Region (hg38): 12:93569813-93583487

Links

ENSG00000120833 ∙ NCBI:8835 ∙ OMIM:605117 ∙ HGNC:19382 ∙ Uniprot:O14508 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SOCS2 gene.

• Inborn genetic diseases (11 variants)

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			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	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
12-93572946-C-T		not specified	Uncertain significance (Jun 13, 2023)
12-93572974-C-T		not specified	Uncertain significance (Jun 21, 2021)
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)
12-93575159-G-A		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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