SOCS5

suppressor of cytokine signaling 5, the group of Suppressors of cytokine signaling|SH2 domain containing

Basic information

Region (hg38): 2:46698952-46780245

Links

ENSG00000171150 ∙ ∙ OMIM:607094 ∙ HGNC:16852 ∙ Uniprot:O75159 ∙ 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 SOCS5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOCS5 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					3	3
missense			36	3		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	3	3

Variants in SOCS5

This is a list of pathogenic ClinVar variants found in the SOCS5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-46758547-A-G		not specified	Uncertain significance (Nov 19, 2024)
2-46758586-T-A		not specified	Uncertain significance (Jun 26, 2023)
2-46758587-C-T			Benign (May 31, 2018)
2-46758588-G-A		not specified	Likely benign (Apr 25, 2023)
2-46758588-G-C		not specified	Uncertain significance (Nov 17, 2022)
2-46758606-C-T		not specified	Uncertain significance (Nov 11, 2024)
2-46758624-A-G		not specified	Uncertain significance (May 09, 2023)
2-46758656-G-C		not specified	Uncertain significance (Nov 10, 2022)
2-46758681-A-G		not specified	Likely benign (Aug 12, 2021)
2-46758695-A-C		not specified	Uncertain significance (Jun 10, 2024)
2-46758702-C-A		not specified	Uncertain significance (Nov 12, 2021)
2-46758712-A-C		not specified	Uncertain significance (May 31, 2023)
2-46758745-C-T		not specified	Uncertain significance (Sep 27, 2024)
2-46758774-T-G		not specified	Uncertain significance (Oct 06, 2022)
2-46758813-G-A		not specified	Uncertain significance (Dec 21, 2022)
2-46758843-G-A		not specified	Uncertain significance (Jan 26, 2023)
2-46758877-G-T		not specified	Uncertain significance (May 17, 2024)
2-46758931-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-46758945-G-C		not specified	Uncertain significance (Dec 16, 2022)
2-46758963-A-G		not specified	Uncertain significance (Jul 13, 2022)
2-46759002-G-A		not specified	Uncertain significance (Dec 01, 2022)
2-46759002-G-C		not specified	Uncertain significance (Nov 17, 2022)
2-46759014-C-T		not specified	Uncertain significance (Nov 11, 2024)
2-46759029-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-46759032-T-G		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOCS5	protein_coding	protein_coding	ENST00000306503	1	64178

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.542	0.458	125719	0	23	125742	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.690	269	303	0.888	0.0000167	3545
Missense in Polyphen		84	124.81	0.67303		1542
Synonymous	-1.36	128	110	1.17	0.00000624	1016
Loss of Function	3.27	4	19.6	0.204	0.00000115	230

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000883	0.0000879
Middle Eastern	0.000163	0.000163
South Asian	0.0000980	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: SOCS family proteins form part of a classical negative feedback system that regulates cytokine signal transduction. May be a 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. Inhibits for instance EGF signaling by mediating the degradation of the EGF receptor/EGFR. Involved in the regulation of T-helper cell differentiation by inhibiting of the IL4 signaling pathway which promotes differentiation into the Th2 phenotype. Can also partially inhibit IL6 and LIF signaling. {ECO:0000269|PubMed:15590694}.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Prolactin signaling pathway - Homo sapiens (human);IL-4 Signaling Pathway;HDAC6 interactions;Interleukin-4 and 13 signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;Post-translational protein modification;Metabolism of proteins;Immune System;Neddylation;IL4-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.232

Intolerance Scores

• loftool: 0.472
• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.75

Haploinsufficiency Scores

• pHI: 0.685
• hipred: Y
• hipred_score: 0.783
• ghis: 0.655

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Socs5
• 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); endocrine/exocrine gland phenotype; normal phenotype; reproductive system phenotype

Gene ontology

• Biological process: epidermal growth factor receptor signaling pathway;negative regulation of epidermal growth factor-activated receptor activity;JAK-STAT cascade;negative regulation of signal transduction;protein ubiquitination;cytokine-mediated signaling pathway;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;negative regulation of interleukin-6 production;regulation of growth;regulation of phosphatidylinositol 3-kinase activity;post-translational protein modification;positive regulation of T-helper 1 cell differentiation;negative regulation of T-helper 2 cell differentiation;phosphatidylinositol phosphorylation;negative regulation of inflammatory response;cellular response to low-density lipoprotein particle stimulus;negative regulation of monocyte chemotactic protein-1 production;vascular endothelial cell response to fluid shear stress
• Cellular component: cytosol;phosphatidylinositol 3-kinase complex
• Molecular function: epidermal growth factor receptor binding;protein binding;receptor tyrosine kinase binding;1-phosphatidylinositol-3-kinase regulator activity