SOCS4

suppressor of cytokine signaling 4, the group of Suppressors of cytokine signaling|SH2 domain containing

Basic information

Region (hg38): 14:55027230-55049489

Previous symbols: [ "SOCS7" ]

Links

ENSG00000180008 ∙ NCBI:122809 ∙ OMIM:616337 ∙ HGNC:19392 ∙ Uniprot:Q8WXH5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autoimmune disease (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SOCS4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOCS4 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					2	2
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	2

Variants in SOCS4

This is a list of pathogenic ClinVar variants found in the SOCS4 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-55043101-G-A			Benign (Jun 26, 2018)
14-55043103-G-A		not specified	Uncertain significance (Jul 05, 2022)
14-55043141-G-A		not specified	Uncertain significance (Aug 27, 2024)
14-55043181-C-T		not specified	Uncertain significance (Dec 04, 2024)
14-55043212-A-T		not specified	Uncertain significance (Dec 13, 2023)
14-55043216-G-A		not specified	Uncertain significance (Nov 07, 2023)
14-55043223-C-A		not specified	Uncertain significance (Dec 05, 2024)
14-55043226-T-C		not specified	Uncertain significance (Jun 11, 2021)
14-55043336-G-A		not specified	Uncertain significance (Feb 16, 2023)
14-55043342-C-A		not specified	Uncertain significance (Nov 12, 2021)
14-55043414-A-C		not specified	Uncertain significance (Feb 08, 2023)
14-55043430-A-G		not specified	Uncertain significance (Oct 12, 2022)
14-55043480-A-G		not specified	Uncertain significance (Apr 11, 2023)
14-55043511-A-C		not specified	Uncertain significance (Nov 07, 2022)
14-55043532-C-G		not specified	Uncertain significance (Oct 26, 2021)
14-55043566-G-A			Benign (Jun 26, 2018)
14-55043583-T-C		not specified	Uncertain significance (Sep 12, 2024)
14-55043606-T-C		not specified	Uncertain significance (Nov 10, 2024)
14-55043616-A-G		not specified	Likely benign (Jul 14, 2021)
14-55043624-C-T		not specified	Uncertain significance (Sep 16, 2021)
14-55043640-C-A		not specified	Uncertain significance (Sep 27, 2022)
14-55043662-A-T		not specified	Uncertain significance (Oct 05, 2023)
14-55043703-A-C		not specified	Uncertain significance (Mar 01, 2023)
14-55043720-G-C		not specified	Uncertain significance (Jan 06, 2023)
14-55043744-C-G		not specified	Uncertain significance (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOCS4	protein_coding	protein_coding	ENST00000395472	1	22259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000142	0.861	125717	0	27	125744	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.637	208	236	0.883	0.0000125	2930
Missense in Polyphen		78	97.771	0.79779		1225
Synonymous	0.285	83	86.4	0.961	0.00000479	815
Loss of Function	1.43	10	16.2	0.617	0.00000119	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
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. 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 EGF signaling by mediating the degradation of the Tyr-phosphorylated EGF receptor/EGFR. {ECO:0000269|PubMed:15590694, ECO:0000269|PubMed:17997974}.
• 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);Type II diabetes mellitus;Transcriptional regulation by RUNX1;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;RUNX1 regulates transcription of genes involved in differentiation of keratinocytes;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.160

Intolerance Scores

• loftool: 0.780
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

• pHI: 0.157
• hipred: Y
• hipred_score: 0.675
• ghis: 0.665

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.922

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Socs4

Gene ontology

• Biological process: negative regulation of epidermal growth factor-activated receptor activity;protein ubiquitination;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;intracellular signal transduction;regulation of growth
• Molecular function: protein binding