SOCS6

suppressor of cytokine signaling 6, the group of Suppressors of cytokine signaling|SH2 domain containing

Basic information

Region (hg38): 18:70289045-70330199

Previous symbols: [ "SOCS4" ]

Links

ENSG00000170677 ∙ NCBI:9306 ∙ OMIM:605118 ∙ HGNC:16833 ∙ Uniprot:O14544 ∙ 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 SOCS6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOCS6 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	1
missense			29	3		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	1

Variants in SOCS6

This is a list of pathogenic ClinVar variants found in the SOCS6 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-70324697-G-A		not specified	Uncertain significance (Apr 07, 2023)
18-70324820-T-C		not specified	Uncertain significance (Feb 13, 2025)
18-70324840-G-A		not specified	Likely benign (Sep 09, 2021)
18-70324857-C-T			Benign (Mar 29, 2018)
18-70324868-G-A		not specified	Uncertain significance (Sep 26, 2024)
18-70324883-G-A		not specified	Uncertain significance (Apr 18, 2023)
18-70324891-G-T		not specified	Uncertain significance (Dec 22, 2023)
18-70324934-G-T		not specified	Uncertain significance (Jul 05, 2023)
18-70324940-C-G		not specified	Likely benign (Mar 20, 2023)
18-70324966-G-A		not specified	Uncertain significance (Oct 21, 2024)
18-70324999-A-G		not specified	Uncertain significance (Nov 26, 2024)
18-70325019-A-C		not specified	Uncertain significance (Dec 10, 2024)
18-70325032-A-G		not specified	Uncertain significance (Jul 31, 2024)
18-70325041-A-G		not specified	Uncertain significance (Aug 08, 2022)
18-70325051-G-A		not specified	Uncertain significance (Jan 10, 2025)
18-70325075-C-T		not specified	Uncertain significance (May 15, 2024)
18-70325153-C-G		not specified	Uncertain significance (Nov 14, 2023)
18-70325168-C-A		not specified	Uncertain significance (Feb 14, 2024)
18-70325179-G-A		not specified	Uncertain significance (Jan 08, 2025)
18-70325222-A-T		not specified	Uncertain significance (Oct 26, 2024)
18-70325258-A-G		not specified	Uncertain significance (Jan 19, 2025)
18-70325261-A-G		not specified	Uncertain significance (Mar 21, 2024)
18-70325302-G-A		not specified	Uncertain significance (Jun 16, 2023)
18-70325387-A-G		not specified	Uncertain significance (Oct 01, 2024)
18-70325446-C-T		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOCS6	protein_coding	protein_coding	ENST00000397942	1	41300

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.989	0.0113	125743	0	1	125744	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.854	283	326	0.867	0.0000203	3518
Missense in Polyphen		49	88.354	0.55459		999
Synonymous	-0.370	135	130	1.04	0.00000880	1071
Loss of Function	3.40	0	13.5	0.00	5.68e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
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. 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 (By similarity). Regulates KIT degradation by ubiquitination of the tyrosine-phosphorylated receptor. {ECO:0000250, ECO:0000269|PubMed:21030588}.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Prolactin signaling pathway - Homo sapiens (human);Kit receptor signaling pathway;Signal Transduction;Post-translational protein modification;Metabolism of proteins;Regulation of KIT signaling;Neddylation;Signaling by SCF-KIT;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• loftool: 0.0293
• rvis_EVS: -1.02
• rvis_percentile_EVS: 7.94

Haploinsufficiency Scores

• pHI: 0.190
• hipred: Y
• hipred_score: 0.654
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.675

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Socs6
• Phenotype: growth/size/body region phenotype

Gene ontology

• Biological process: defense response;JAK-STAT cascade;negative regulation of signal transduction;proteasomal protein catabolic process;protein ubiquitination;regulation of growth;regulation of phosphatidylinositol 3-kinase activity;post-translational protein modification;phosphatidylinositol phosphorylation;negative regulation of T cell activation
• Cellular component: immunological synapse;cytoplasm;cytosol;phosphatidylinositol 3-kinase complex
• Molecular function: protein binding;1-phosphatidylinositol-3-kinase regulator activity