SMARCD2 SWI/SNF related BAF chromatin remodeling complex subunit D2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMARCD2provided by HGNC
Official Full Name: SWI/SNF related BAF chromatin remodeling complex subunit D2provided by HGNC
Primary source: HGNC:HGNC:11107
See related: Ensembl:ENSG00000108604 MIM:601736; AllianceGenome:HGNC:11107
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: SGD2; Rsc6p; BAF60B; CRACD2; PRO2451
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. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in skin (RPKM 24.5), esophagus (RPKM 18.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q23.3

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (63832081..63842685, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (64702930..64713532, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (61909441..61920045, complement)

Chromosome 17 - NC_000017.11 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?

Novel Frameshift Autosomal Recessive Loss-of-Function Mutation in SMARCD2 Encoding a Chromatin Remodeling Factor Mediates Granulopoiesis.
Title: Novel Frameshift Autosomal Recessive Loss-of-Function Mutation in SMARCD2 Encoding a Chromatin Remodeling Factor Mediates Granulopoiesis.
Defective neutrophil development and specific granule deficiency caused by a homozygous splice-site mutation in SMARCD2.
Title: Defective neutrophil development and specific granule deficiency caused by a homozygous splice-site mutation in SMARCD2.
Defective expression of SMARCD2 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily D, member 2) leads to transcriptional and chromatin changes in acute myeloid leukemia (AML) promyelocytic cells, suggesting SMARCD2 is a key factor controlling myelopoiesis and is a potential tumor suppressor in leukemia.
Title: Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes.
Data show that both CEBPE and SMARCD2 loss-of-function mutations identified in patients with neutrophil-specific granule deficiency (SGD) abolish the interaction with SWI/SNF and secondary granule gene expression, thus providing a molecular basis for this disease.
Title: SMARCD2 subunit of SWI/SNF chromatin-remodeling complexes mediates granulopoiesis through a CEBPɛ dependent mechanism.
the role of SMARCA4 and the two SWI/SNF subunits SMARCD2/BAF60B and DPF2/BAF45D in leukaemia, was investigated.
Title: SWI/SNF Subunits SMARCA4, SMARCD2 and DPF2 Collaborate in MLL-Rearranged Leukaemia Maintenance.
the Rac- and Unkempt-dependent process leading to BAF60b ubiquitination takes place in the nuclear compartment
Title: The SWI/SNF protein BAF60b is ubiquitinated through a signalling process involving Rac GTPase and the RING finger protein Unkempt.

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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
Specific granule deficiency 2 MedGen: C4479548 OMIM: 617475 GeneReviews: Not available	Compare labs

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

RH36133 (e-PCR)
- UniSTS:37130

RH36220 (e-PCR)
- UniSTS:37131

RH80844 (e-PCR)
- UniSTS:83987

MARC_26036-26037:1032447192:1 (e-PCR)
- UniSTS:268920

SMARCD2_2130 (e-PCR)
- UniSTS:281022

SGC30177 (e-PCR)
- UniSTS:12005

D17S1654 (e-PCR)
- UniSTS:153831

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
contributes_to nucleosomal DNA binding	HDA more info	PubMed
enables protein 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

Process	Evidence Code	Pubs
involved_in chromatin remodeling	HDA 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 nucleosome disassembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	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 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

Component	Evidence Code	Pubs
part_of RSC-type complex	NAS Non-traceable Author Statement more info	PubMed
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 bBAF complex	NAS Non-traceable Author Statement more info	PubMed
part_of brahma complex	NAS Non-traceable Author Statement more info	PubMed
located_in chromatin	HDA more info	PubMed
located_in chromatin	NAS Non-traceable Author Statement more info	PubMed
located_in kinetochore	NAS Non-traceable Author Statement more info	PubMed
located_in nuclear matrix	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
part_of protein-containing complex	HDA 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 2

Names: 60 kDa BRG-1/Brm-associated factor subunit B; BRG1-associated factor 60B; SWI/SNF complex 60 kDa subunit B; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2; Swp73-like protein; chromatin remodeling complex BAF60B subunit; mammalian chromatin remodeling complex BRG1-associated factor 60B

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_053004.1 RefSeqGene

Range

5307..15911

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001098426.2 → NP_001091896.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 isoform 1

See identical proteins and their annotated locations for NP_001091896.1

Status: REVIEWED

Source sequence(s)

AC015651

Consensus CDS

CCDS45756.1

UniProtKB/Swiss-Prot

A5PLL5, A6NNQ7, B4DV56, B4E1R6, Q7L2I6, Q92925, Q9UHZ1

UniProtKB/TrEMBL

A0A8V8TLC9

Related

ENSP00000392617.2, ENST00000448276.7

Conserved Domains (2) summary

PHA03201
Location:61 → 148

PHA03201; uracil DNA glycosylase; Provisional

cd17675
Location:307 → 386

SWIB_BAF60B; SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins
NM_001330439.1 → NP_001317368.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 isoform 2

Status: REVIEWED

Source sequence(s)

AK307944, AW375602, BQ670607

Consensus CDS

CCDS82187.1

UniProtKB/TrEMBL

A0A8V8TLC9, J3KMX2

Related

ENSP00000225742.9, ENST00000225742.13

Conserved Domains (1) summary

cd17675
Location:232 → 311

SWIB_BAF60B; SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins
NM_001330440.2 → NP_001317369.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 isoform 3

Status: REVIEWED

Source sequence(s)

AK303951, AW375602, BQ670607

Consensus CDS

CCDS82188.1

UniProtKB/TrEMBL

A0A8V8TLC9

Related

ENSP00000318451.10, ENST00000323347.14

Conserved Domains (2) summary

PHA03201
Location:10 → 100

PHA03201; uracil DNA glycosylase; Provisional

cd17675
Location:259 → 338

SWIB_BAF60B; SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

63832081..63842685 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

64702930..64713532 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_003077.3: Suppressed sequence

Description

NM_003077.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which aligns with non-consensus splice sites.