SIN3A SIN3 transcription regulator family member A [Homo sapiens (human)] - Gene

Summary

Official Symbol: SIN3Aprovided by HGNC
Official Full Name: SIN3 transcription regulator family member Aprovided by HGNC
Primary source: HGNC:HGNC:19353
See related: Ensembl:ENSG00000169375 MIM:607776; AllianceGenome:HGNC:19353
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: WITKOS; DEL15Q24; CHR15DELq24
Summary: The protein encoded by this gene is a transcriptional regulatory protein. It contains paired amphipathic helix (PAH) domains, which are important for protein-protein interactions and may mediate repression by the Mad-Max complex. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 15.9), thyroid (RPKM 12.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q24.2

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (75369379..75455815, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (73239476..73331180, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (75661720..75748156, complement)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Coordination of cross-talk between metabolism and epigenetic regulation by the SIN3 complex.
Title: Coordination of cross-talk between metabolism and epigenetic regulation by the SIN3 complex.
Inherited 15q24 microdeletion syndrome in twins and their father with phenotypic variability
Title: Inherited 15q24 microdeletion syndrome in twins and their father with phenotypic variability.
DNA methylation episignature for Witteveen-Kolk syndrome due to SIN3A haploinsufficiency.
Title: DNA methylation episignature for Witteveen-Kolk syndrome due to SIN3A haploinsufficiency.
Suppression of SIN3A by miR-183 Promotes Breast Cancer Metastasis.
Title: Suppression of SIN3A by miR-183 Promotes Breast Cancer Metastasis.
The Sin3A/MAD1 Complex, through Its PAH2 Domain, Acts as a Second Repressor of Retinoic Acid Receptor Beta Expression in Breast Cancer Cells.
Title: The Sin3A/MAD1 Complex, through Its PAH2 Domain, Acts as a Second Repressor of Retinoic Acid Receptor Beta Expression in Breast Cancer Cells.
miR-138-5p inhibits proliferation and invasion in kidney renal clear cell carcinoma by targeting SINA3 and regulation of the Notch signaling pathway.
Title: miR-138-5p inhibits proliferation and invasion in kidney renal clear cell carcinoma by targeting SINA3 and regulation of the Notch signaling pathway.
Comprehensive study of 28 individuals with SIN3A-related disorder underscoring the associated mild cognitive and distinctive facial phenotype.
Title: Comprehensive study of 28 individuals with SIN3A-related disorder underscoring the associated mild cognitive and distinctive facial phenotype.
Structural Insight into the Binding of TGIF1 to SIN3A PAH2 Domain through a C-Terminal Amphipathic Helix.
Title: Structural Insight into the Binding of TGIF1 to SIN3A PAH2 Domain through a C-Terminal Amphipathic Helix.
Regulation of the Methylation and Expression Levels of the BMPR2 Gene by SIN3a as a Novel Therapeutic Mechanism in Pulmonary Arterial Hypertension.
Title: Regulation of the Methylation and Expression Levels of the BMPR2 Gene by SIN3a as a Novel Therapeutic Mechanism in Pulmonary Arterial Hypertension.
Transcription Repressor Protein ZBTB25 Associates with HDAC1-Sin3a Complex in Mycobacterium tuberculosis-Infected Macrophages, and Its Inhibition Clears Pathogen by Autophagy.
Title: Transcription Repressor Protein ZBTB25 Associates with HDAC1-Sin3a Complex in Mycobacterium tuberculosis-Infected Macrophages, and Its Inhibition Clears Pathogen by Autophagy.

Submit: New GeneRIF Correction See all GeneRIFs (60)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
SIN3A-related intellectual disability syndrome due to a point mutation MedGen: C4310804 OMIM: 613406 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2020-01-13) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2020-01-13) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	The SIN3/HDAC complex, composed of SIN3A, SAP30, SAP18, HDAC-1 AND -2 and RbAp46/48 except SAP30, are identified to interact with HIV-1 Tat in Jurkat cell	PubMed
integrase	gag-pol	HIV-1 IN and INI1/hSNF5 bind SAP18 and selectively recruit components of Sin3a-HDAC1 complex into HIV-1 virions. HIV-1 virion-associated HDAC1 is required for efficient early post-entry events	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH44902 (e-PCR)
- UniSTS:41484

D11S1301 (e-PCR)
- UniSTS:52496

RH102482 (e-PCR)
- UniSTS:96816

RH101985 (e-PCR)
- UniSTS:96319

D15S735E (e-PCR)
- UniSTS:151629

RH91923 (e-PCR)
- UniSTS:90724

D10S16 (e-PCR)
- UniSTS:155756

SIN3A_8019 (e-PCR)
- UniSTS:471761

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
enables transcription corepressor activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription corepressor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription regulator inhibitor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
involved_in activation of innate immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to dopamine	IEA Inferred from Electronic Annotation more info
involved_in cellular response to glucose stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to tert-butyl hydroperoxide	IEA Inferred from Electronic Annotation more info
involved_in cerebral cortex neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in hematopoietic progenitor cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell migration	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of circadian rhythm	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of protein localization to nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of stem cell population maintenance	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of transforming growth factor beta receptor signaling pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of G2/M transition of mitotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of defense response to virus by host	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of stem cell population maintenance	NAS Non-traceable Author Statement more info	PubMed
involved_in protein localization	IEA Inferred from Electronic Annotation more info
involved_in regulation of axon extension	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of hormone levels	IEA Inferred from Electronic Annotation more info
involved_in response to methylglyoxal	IEA Inferred from Electronic Annotation more info
involved_in rhythmic process	IEA Inferred from Electronic Annotation more info
involved_in type I interferon-mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of Sin3-type complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Sin3-type complex	IDA Inferred from Direct Assay more info	PubMed
part_of Sin3-type complex	NAS Non-traceable Author Statement more info	PubMed
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
part_of histone deacetylase complex	IDA Inferred from Direct Assay more info	PubMed
located_in kinetochore	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
part_of transcription repressor complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: paired amphipathic helix protein Sin3a

Names: SIN3 homolog A, transcription regulator; histone deacetylase complex subunit Sin3a; transcriptional co-repressor Sin3A; transcriptional corepressor Sin3a; transcriptional regulator, SIN3A

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_052855.1 RefSeqGene

Range

9094..91405

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001145357.2 → NP_001138829.1 paired amphipathic helix protein Sin3a

See identical proteins and their annotated locations for NP_001138829.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

AC068338, AC105137, AF418569, AL832463, BM676304

Consensus CDS

CCDS10279.1

UniProtKB/Swiss-Prot

B2RNS5, Q8N8N4, Q8NC83, Q8WV18, Q96L98, Q96ST3, Q9UFQ1

UniProtKB/TrEMBL

A0A994J7C7

Related

ENSP00000353622.4, ENST00000360439.8

Conserved Domains (1) summary

COG5602
Location:5 → 1213

Sin3; Histone deacetylase complex, regulatory component SIN3 [Chromatin structure and dynamics]
NM_001145358.2 → NP_001138830.1 paired amphipathic helix protein Sin3a

See identical proteins and their annotated locations for NP_001138830.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

AC068338, AF418569, AK096477, BM676304

Consensus CDS

CCDS10279.1

UniProtKB/Swiss-Prot

B2RNS5, Q8N8N4, Q8NC83, Q8WV18, Q96L98, Q96ST3, Q9UFQ1

UniProtKB/TrEMBL

A0A994J7C7

Related

ENSP00000378402.3, ENST00000394947.8

Conserved Domains (1) summary

COG5602
Location:5 → 1213

Sin3; Histone deacetylase complex, regulatory component SIN3 [Chromatin structure and dynamics]
NM_015477.3 → NP_056292.1 paired amphipathic helix protein Sin3a

See identical proteins and their annotated locations for NP_056292.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

AC068338, AC105137, AF418569, BC041047, BM676304

Consensus CDS

CCDS10279.1

UniProtKB/Swiss-Prot

B2RNS5, Q8N8N4, Q8NC83, Q8WV18, Q96L98, Q96ST3, Q9UFQ1

UniProtKB/TrEMBL

A0A994J7C7

Related

ENSP00000378403.4, ENST00000394949.8

Conserved Domains (1) summary

COG5602
Location:5 → 1213

Sin3; Histone deacetylase complex, regulatory component SIN3 [Chromatin structure and dynamics]