SIN3B

SIN3 transcription regulator family member B, the group of EMSY complex|SIN3 histone deacetylase complex subunits

Basic information

Region (hg38): 19:16829397-16880353

Links

ENSG00000127511 ∙ NCBI:23309 ∙ OMIM:607777 ∙ HGNC:19354 ∙ Uniprot:O75182 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• SIN3A-related intellectual disability syndrome due to a point mutation (Supportive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SIN3B gene.

• Inborn genetic diseases (36 variants)
• not provided (32 variants)
• SIN3B-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIN3B 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	1	3
missense			60	1	1	62
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					1	1
non coding			1			1
Total	0	0	62	4	2

Variants in SIN3B

This is a list of pathogenic ClinVar variants found in the SIN3B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-16829436-G-A		not specified	Uncertain significance (Dec 08, 2023)
19-16829451-A-C		not specified	Uncertain significance (Jan 22, 2024)
19-16829457-G-T		not specified	Uncertain significance (Aug 12, 2021)
19-16829467-C-T			Uncertain significance (Jun 25, 2021)
19-16829512-C-T			Uncertain significance (Sep 06, 2023)
19-16829807-C-G		not specified	Uncertain significance (Jun 21, 2023)
19-16829873-T-C			Uncertain significance (Apr 06, 2023)
19-16831524-C-G			Likely benign (Jul 05, 2018)
19-16831537-C-T		not specified	Uncertain significance (Oct 05, 2023)
19-16831547-C-G		not specified	Uncertain significance (May 25, 2022)
19-16831552-C-T			Uncertain significance (Dec 02, 2022)
19-16831557-T-G		not specified	Uncertain significance (Jun 01, 2023)
19-16831628-A-G			Uncertain significance (Oct 04, 2022)
19-16831631-C-T		SIN3B-related disorder	Likely benign (Feb 11, 2022)
19-16831643-G-A			Uncertain significance (Jan 23, 2022)
19-16831648-G-A			Uncertain significance (Jul 27, 2022)
19-16841807-A-C		not specified	Uncertain significance (Feb 05, 2024)
19-16841852-G-C		not specified	Uncertain significance (Aug 12, 2022)
19-16841879-G-A			Uncertain significance (Jul 01, 2022)
19-16841962-G-A		SIN3B-related disorder	Likely benign (Jul 30, 2019)
19-16846986-C-A			Uncertain significance (Aug 31, 2022)
19-16851416-C-G		SIN3B-related disorder	Uncertain significance (Oct 03, 2022)
19-16851427-C-T		not specified	Uncertain significance (May 18, 2023)
19-16851441-C-G		not specified	Uncertain significance (Dec 09, 2023)
19-16851444-C-T		SIN3B-related disorder	Likely benign (Feb 14, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIN3B	protein_coding	protein_coding	ENST00000379803	20	50954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000117	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.87	454	752	0.603	0.0000525	7619
Missense in Polyphen		44	176.97	0.24863		1813
Synonymous	0.175	321	325	0.988	0.0000247	2253
Loss of Function	6.18	5	54.0	0.0927	0.00000240	629

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000301	0.0000301
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000959	0.0000924
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor. Interacts with MXI1 to repress MYC responsive genes and antagonize MYC oncogenic activities. Interacts with MAD-MAX heterodimers by binding to MAD. The heterodimer then represses transcription by tethering SIN3B to DNA. Also forms a complex with FOXK1 which represses transcription. With FOXK1, regulates cell cycle progression probably by repressing cell cycle inhibitor genes expression. {ECO:0000250|UniProtKB:Q62141}.
• Pathway: NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);mets affect on macrophage differentiation;Generic Transcription Pathway;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Metabolism of lipids;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;Metabolism;Transcriptional regulation by RUNX1;Regulation of Telomerase;Signaling events mediated by HDAC Class I;Hedgehog signaling events mediated by Gli proteins;Regulation of nuclear SMAD2/3 signaling (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.233
• rvis_EVS: -1.37
• rvis_percentile_EVS: 4.51

Haploinsufficiency Scores

• pHI: 0.338
• hipred: Y
• hipred_score: 0.745
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.944

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sin3b
• Phenotype: growth/size/body region phenotype; cellular phenotype; immune system phenotype; liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; hematopoietic system phenotype; skeleton phenotype

Zebrafish Information Network

• Gene name: sin3b
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased behavioural activity

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;histone deacetylation;regulation of lipid metabolic process
• Cellular component: chromatin;X chromosome;Y chromosome;XY body;nucleus;nucleoplasm;cytoplasm;Sin3 complex;autosome
• Molecular function: chromatin binding;transcription corepressor activity;histone deacetylase activity;protein binding