SMARCD3 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMARCD3provided by HGNC
Official Full Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3provided by HGNC
Primary source: HGNC:HGNC:11108
See related: Ensembl:ENSG00000082014 MIM:601737; AllianceGenome:HGNC:11108
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: Rsc6p; BAF60C; CRACD3
Summary: The protein encoded by this gene is a member of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI and has sequence similarity to the yeast Swp73 protein. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in brain (RPKM 23.8), heart (RPKM 18.1) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q36.1

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (151238780..151277149, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (152411900..152450299, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (150935866..150974235, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Myofiber Baf60c controls muscle regeneration by modulating Dkk3-mediated paracrine signaling.
Title: Myofiber Baf60c controls muscle regeneration by modulating Dkk3-mediated paracrine signaling.
Smarcd3 is an epigenetic modulator of the metabolic landscape in pancreatic ductal adenocarcinoma.
Title: Smarcd3 is an epigenetic modulator of the metabolic landscape in pancreatic ductal adenocarcinoma.
BAF60c prevents abdominal aortic aneurysm formation through epigenetic control of vascular smooth muscle cell homeostasis.
Title: BAF60c prevents abdominal aortic aneurysm formation through epigenetic control of vascular smooth muscle cell homeostasis.
SMARCD3 is a potential prognostic marker and therapeutic target in CAFs.
Title: SMARCD3 is a potential prognostic marker and therapeutic target in CAFs.
Data show that the combination of GATA binding protein 4 (Gata4), T-box transcription factor 5 (Tbx5) and BRG1-associated factor 60C protein (Baf60c) is sufficient for inducing adipose tissue-derived mesenchymal stem cells (ADMSCs) to form cardiomyocytes.
Title: Gata4, Tbx5 and Baf60c induce differentiation of adipose tissue-derived mesenchymal stem cells into beating cardiomyocytes.
Inhibition of Wnt5a by either RNAi knockdown or blocking antibody reversed Smarcd3 -induced epithelial-mesenchymal transition. Thus, Smarcd3 epigenetically regulates epithelial-mesenchymal transition by activating WNT signaling pathways.
Title: SWI/SNF chromatin-remodeling factor Smarcd3/Baf60c controls epithelial-mesenchymal transition by inducing Wnt5a signaling.
Deptor is induced by the Baf60c-Six4 transcriptional complex and mediates activation of Akt and glycolytic metabolism by Baf60c in a cell-autonomous manner
Title: Baf60c drives glycolytic metabolism in the muscle and improves systemic glucose homeostasis through Deptor-mediated Akt activation.
BAF60c promotes lipogenesis in vivo and increases triglyceride levels, demonstrating its role in metabolic adaption to activate the lipogenic program in response to feeding and insulin.
Title: Phosphorylation and recruitment of BAF60c in chromatin remodeling for lipogenesis in response to insulin.
Data show a combination of only five genes (-BCL6, T (BRACHYURY), c-MYC, MITF and BAF60C (SMARCD3) rapidly and efficiently convert postnatal chorion and decidual cells into chondrocytes.
Title: Placenta to cartilage: direct conversion of human placenta to chondrocytes with transformation by defined factors.
BAF60c phosphorylation on a conserved threonine is the signal that promotes incorporation of MyoD-BAF60c into a Brg1-based SWI/SNF complex, which remodels the chromatin & activates transcription of MyoD-target genes.
Title: Signal-dependent incorporation of MyoD-BAF60c into Brg1-based SWI/SNF chromatin-remodelling complex.

Submit: New GeneRIF Correction See all GeneRIFs (14)

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

EBI GWAS Catalog

Description
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D7S642 (e-PCR), detects polymorphism
- UniSTS:58138

RH66788 (e-PCR)
- UniSTS:15670

D7S2157E (e-PCR)
- UniSTS:151151

STS-R51978 (e-PCR)
- UniSTS:46708

GDB:4584943 (e-PCR)
- UniSTS:65969

RH91733 (e-PCR)
- UniSTS:91344

G33154 (e-PCR)
- UniSTS:67058

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables nuclear receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator activity	NAS Non-traceable Author Statement more info	PubMed
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription coregulator binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cardiac right ventricle formation	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IC Inferred by Curator more info	PubMed
involved_in chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	NAS Non-traceable Author Statement more info	PubMed
involved_in muscle cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
involved_in neural retina development	IEP Inferred from Expression Pattern more info	PubMed
involved_in nucleosome disassembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay 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 T cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of double-strand break repair	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of myoblast differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of neuroblast proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of smooth muscle cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in regulation of G0 to G1 transition	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of G1/S transition of mitotic cell cycle	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of mitotic metaphase/anaphase transition	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of nucleotide-excision repair	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
involved_in secondary heart field specification	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of SWI/SNF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SWI/SNF complex	IDA Inferred from Direct Assay more info	PubMed
part_of SWI/SNF complex	NAS Non-traceable Author Statement more info	PubMed
part_of brahma complex	NAS Non-traceable Author Statement more info	PubMed
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	NAS Non-traceable Author Statement more info	PubMed
part_of nBAF complex	ISS Inferred from Sequence or Structural Similarity more info
part_of nBAF complex	NAS Non-traceable Author Statement more info	PubMed
part_of npBAF complex	IDA Inferred from Direct Assay more info	PubMed
part_of npBAF complex	ISS Inferred from Sequence or Structural Similarity more info
part_of npBAF complex	NAS Non-traceable Author Statement more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3

Names: 60 kDa BRG-1/Brm-associated factor subunit C; BRG1-associated factor 60C; SWI/SNF complex 60 kDa subunit C; Swp73-like protein; chromatin remodeling complex BAF60C subunit; mammalian chromatin remodeling complex BRG1-associated factor 60C

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_029468.1 RefSeqGene

Range

33452..43366

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001003801.2 → NP_001003801.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform 2

See identical proteins and their annotated locations for NP_001003801.1

Status: REVIEWED

Description

Transcript Variant: This variant (3), also known as hBAF60c2, has an alternate 5' sequence, as compared to variant 1. The encoded isoform 2 has a longer and distinct N-terminus, as compared to isoform 1.

Source sequence(s)

AC005486, AC021097, AY450430

Consensus CDS

CCDS34780.1

UniProtKB/Swiss-Prot

D3DX10, Q2YD86, Q6STE5, Q75MJ2, Q75MR8, Q92926, Q9BUH1

UniProtKB/TrEMBL

B3KXL9

Related

ENSP00000262188.8, ENST00000262188.13

Conserved Domains (1) summary

cd17676
Location:265 → 338

SWIB_BAF60C; SWIB domain found in BRG1-associated factor 60C (BAF60C) and similar proteins
NM_001003802.2 → NP_001003802.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform 1

See identical proteins and their annotated locations for NP_001003802.1

Status: REVIEWED

Description

Transcript Variant: This variant (1), also known as hBAF60c1, encodes the shorter isoform (1). Both variants 1 and 2 encode the same isoform.

Source sequence(s)

AC021097, AY450431

Consensus CDS

CCDS5924.1

UniProtKB/TrEMBL

A0A090N8Z9, B3KXL9

Related

ENSP00000349254.2, ENST00000356800.6

Conserved Domains (2) summary

NF033761
Location:2 → 108

gliding_GltJ; adventurous gliding motility protein GltJ

cl38907
Location:252 → 325

SWIB-MDM2; SWIB/MDM2 domain family
NM_003078.4 → NP_003069.2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform 1

See identical proteins and their annotated locations for NP_003069.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an alternate 5' exon, but encodes the same isoform (1), as compared to variant 1.

Source sequence(s)

AC005486, AC021097, BC002628, BI598614, U66619

Consensus CDS

CCDS5924.1

UniProtKB/TrEMBL

A0A090N8Z9, B3KXL9

Related

ENSP00000376558.2, ENST00000392811.6

Conserved Domains (2) summary

NF033761
Location:2 → 108

gliding_GltJ; adventurous gliding motility protein GltJ

cl38907
Location:252 → 325

SWIB-MDM2; SWIB/MDM2 domain family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

151238780..151277149 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047420758.1 → XP_047276714.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X2
XM_047420757.1 → XP_047276713.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X1

RNA

XR_007060146.1 RNA Sequence
XR_927518.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

152411900..152450299 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054358860.1 → XP_054214835.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X4
XM_054358861.1 → XP_054214836.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X5
XM_054358859.1 → XP_054214834.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X3