SMARCAD1 SNF2 related chromatin remodeling ATPase with DExD box 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMARCAD1provided by HGNC
Official Full Name: SNF2 related chromatin remodeling ATPase with DExD box 1provided by HGNC
Primary source: HGNC:HGNC:18398
See related: Ensembl:ENSG00000163104 MIM:612761; AllianceGenome:HGNC:18398
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: HRZ; TYS; ETL1; HEL1; ADERM; BASNS
Summary: This gene encodes a member of the SNF subfamily of helicase proteins. The encoded protein plays a critical role in the restoration of heterochromatin organization and propagation of epigenetic patterns following DNA replication by mediating histone H3/H4 deacetylation. Mutations in this gene are associated with adermatoglyphia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
Expression: Ubiquitous expression in thyroid (RPKM 8.6), testis (RPKM 7.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q22.3

Exon count:: 32

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (94207608..94291292)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (97523080..97606799)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (95128759..95212443)

Chromosome 4 - NC_000004.12 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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Basan syndrome in a family from South India: a novel SMARCAD1 variant.
Title: Basan syndrome in a family from South India: a novel SMARCAD1 variant.
The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse.
Title: The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse.
MSH2-MSH3 promotes DNA end resection during homologous recombination and blocks polymerase theta-mediated end-joining through interaction with SMARCAD1 and EXO1.
Title: MSH2-MSH3 promotes DNA end resection during homologous recombination and blocks polymerase theta-mediated end-joining through interaction with SMARCAD1 and EXO1.
Huriez syndrome caused by a large deletion that abrogates the skin-specific isoform of SMARCAD1.
Title: Huriez syndrome caused by a large deletion that abrogates the skin-specific isoform of SMARCAD1.
SMARCAD1-mediated recruitment of the DNA mismatch repair protein MutLalpha to MutSalpha on damaged chromatin induces apoptosis in human cells.
Title: SMARCAD1-mediated recruitment of the DNA mismatch repair protein MutLα to MutSα on damaged chromatin induces apoptosis in human cells.
A structural model of the KAP1 RBCC domain-SMARCAD1 CUE1 domain complex is presented. SMARCAD1 CUE1 has higher affinity for KAP1 RBCC than monoubiquitin. CUE1 binds an exposed coiled-coil surface on KAP1, not a domain resembling ubiquitin.
Title: A Ubiquitin-Binding Domain that Binds a Structural Fold Distinct from that of Ubiquitin.
Whole-genome sequencing on DNA from affected individuals with Huriez syndrome from three families revealed three not previously reported SNPs in SMARCAD1 gene. Western blot experiments confirmed the reduced expression of Smarcad1 protein in keratinocytes and fibroblasts from patients compared with healthy controls. Study concluded that haploinsufficiency for the skin-specific SMARCAD1 isoform accounts for Huriez syndrome.
Title: SMARCAD1 Haploinsufficiency Underlies Huriez Syndrome and Associated Skin Cancer Susceptibility.
Data suggest that retention of SMARCAD1 in nucleus is dependent on interaction of CUE1 domain of SMARCAD1 with RBCC domain of KAP1; these studies were conducted with recombinant proteins expressed in mouse embryonic stem cell line and human somatic cell line. (SMARCAD1 = ATP-dependent helicase-1; KAP1 = KRAB-interacting protein-1)
Title: The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes.
SMARCAD1 knockdown resulted in a significant decrease in breast cancer cell proliferation and colony formation, leading to the significant inhibition of tumour growth in both the chick embryo and nude mouse xenograft models. This inhibition was due, at least in part, to a decrease in IKKbeta expression.
Title: SMARCAD1 in Breast Cancer Progression.
identifies Smarcad1/Fun30 as an accessory factor for the mismatch repair reaction
Title: Nucleosomes around a mismatched base pair are excluded via an Msh2-dependent reaction with the aid of SNF2 family ATPase Smarcad1.

Submit: New GeneRIF Correction See all GeneRIFs (18)

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
Adermatoglyphia MedGen: C1852150 OMIM: 136000 GeneReviews: Not available	Compare labs
Basan syndrome MedGen: C0406707 OMIM: 129200 GeneReviews: Not available	Compare labs
Keratoderma with scleroatrophy of the extremities MedGen: C0406767 OMIM: 181600 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of novel germline polymorphisms governing capecitabine sensitivity. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies four new loci associated with testicular germ cell tumor. EBI GWAS Catalog EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. 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

PMC33171P1 (e-PCR)
- UniSTS:273153

RH71145 (e-PCR)
- UniSTS:17687

WI-19794 (e-PCR)
- UniSTS:34591

SHGC-24763 (e-PCR)
- UniSTS:16684

SHGC-148190 (e-PCR)
- UniSTS:176249

SHGC-68143 (e-PCR)
- UniSTS:83842

SHGC-24039 (e-PCR)
- UniSTS:83659

SHGC-68102 (e-PCR)
- UniSTS:49378

SMARCAD1__1204 (e-PCR)
- UniSTS:277752

SMARCAD1__v340 (e-PCR)
- UniSTS:277752

G33505 (e-PCR)
- UniSTS:764

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent chromatin remodeler activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables forked DNA-dependent helicase activity	IEA Inferred from Electronic Annotation more info
enables four-way junction helicase activity	IEA Inferred from Electronic Annotation more info
enables nucleosome array spacer activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded 3'-5' DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA double-strand break processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA double-strand break processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	NAS Non-traceable Author Statement more info	PubMed
involved_in chromosome separation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of DNA recombination	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in heterochromatin	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear replication fork	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in site of double-strand break	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 A containing DEAD/H box 1

Names: ATP-dependent helicase 1; SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1; sclerotylosis

NP_001121901.1

EC 3.6.4.12

NP_001121902.1

EC 3.6.4.12

NP_001241878.1

EC 3.6.4.12

NP_001362784.1

EC 3.6.4.12

NP_001362785.1

EC 3.6.4.12

NP_001362786.1

EC 3.6.4.12

NP_001362787.1

EC 3.6.4.12

NP_001362788.1

EC 3.6.4.12

NP_064544.2

EC 3.6.4.12

XP_024309922.1

EC 3.6.4.12

XP_047271943.1

EC 3.6.4.12

XP_054206523.1

EC 3.6.4.12

XP_054206524.1

EC 3.6.4.12

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_031945.1 RefSeqGene

Range

5258..88685

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001128429.3 → NP_001121901.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform a

See identical proteins and their annotated locations for NP_001121901.1

Status: REVIEWED

Source sequence(s)

AB032948, AL704040, AY008271, BC045534

Consensus CDS

CCDS47101.1

UniProtKB/Swiss-Prot

Q9H4L7

Related

ENSP00000415576.2, ENST00000457823.6

Conserved Domains (2) summary

pfam03288
Location:318 → 362

Pox_D5; Poxvirus D5 protein-like

cl26465
Location:476 → 1000

SNF2_N; SNF2 family N-terminal domain
NM_001128430.2 → NP_001121902.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform a

See identical proteins and their annotated locations for NP_001121902.1

Status: REVIEWED

Source sequence(s)

AB032948, AY008271, DA798320

Consensus CDS

CCDS47101.1

UniProtKB/Swiss-Prot

Q9H4L7

Related

ENSP00000351947.4, ENST00000359052.8

Conserved Domains (2) summary

pfam03288
Location:318 → 362

Pox_D5; Poxvirus D5 protein-like

cl26465
Location:476 → 1000

SNF2_N; SNF2 family N-terminal domain
NM_001254949.2 → NP_001241878.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform c

See identical proteins and their annotated locations for NP_001241878.1

Status: REVIEWED

Source sequence(s)

AB032948, AK301668, AL359929, AY008271

Consensus CDS

CCDS58914.1

UniProtKB/Swiss-Prot

Q9H4L7

Related

ENSP00000423286.1, ENST00000509418.1

Conserved Domains (2) summary

PLN03142
Location:46 → 568

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:67 → 249

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
NM_001375855.1 → NP_001362784.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform b

Status: REVIEWED

Source sequence(s)

AC096746

Consensus CDS

CCDS3639.1

UniProtKB/Swiss-Prot

B7Z799, Q05D56, Q96SX1, Q9H017, Q9H4L7, Q9H860, Q9NPU9, Q9ULU7

Conserved Domains (2) summary

PLN03142
Location:476 → 998

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:497 → 679

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
NM_001375856.1 → NP_001362785.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform b

Status: REVIEWED

Source sequence(s)

AC096746

Consensus CDS

CCDS3639.1

UniProtKB/Swiss-Prot

B7Z799, Q05D56, Q96SX1, Q9H017, Q9H4L7, Q9H860, Q9NPU9, Q9ULU7

Conserved Domains (2) summary

PLN03142
Location:476 → 998

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:497 → 679

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
NM_001375857.1 → NP_001362786.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform d

Status: REVIEWED

Source sequence(s)

AC096746

Conserved Domains (2) summary

PLN03142
Location:475 → 997

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:496 → 678

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
NM_001375858.1 → NP_001362787.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform e

Status: REVIEWED

Source sequence(s)

AC096746

Conserved Domains (2) summary

PLN03142
Location:476 → 991

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:497 → 672

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
NM_001375859.1 → NP_001362788.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform f

Status: REVIEWED

Source sequence(s)

AC096746

Conserved Domains (2) summary

PLN03142
Location:46 → 570

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:67 → 249

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
NM_020159.5 → NP_064544.2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform b

See identical proteins and their annotated locations for NP_064544.2

Status: REVIEWED

Source sequence(s)

AB032948, AL704040, AY008271

Consensus CDS

CCDS3639.1

UniProtKB/Swiss-Prot

B7Z799, Q05D56, Q96SX1, Q9H017, Q9H4L7, Q9H860, Q9NPU9, Q9ULU7

Related

ENSP00000346217.4, ENST00000354268.9

Conserved Domains (2) summary

PLN03142
Location:476 → 998

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:497 → 679

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

RNA

NR_045644.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164722.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164723.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164724.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164725.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164726.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164727.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164728.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164729.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164730.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164731.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164732.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164733.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164734.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164735.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164736.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746
NR_164737.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC096746

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_000004.12 Reference GRCh38.p14 Primary Assembly

Range

94207608..94291292

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024454154.2 → XP_024309922.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X1

Conserved Domains (2) summary

pfam03288
Location:318 → 362

Pox_D5; Poxvirus D5 protein-like

cl26465
Location:476 → 1000

SNF2_N; SNF2 family N-terminal domain
XM_047415987.1 → XP_047271943.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X2

RNA

XR_007057943.1 RNA Sequence
XR_007057944.1 RNA Sequence
XR_007057945.1 RNA Sequence
XR_007057946.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060928.1 Alternate T2T-CHM13v2.0

Range

97523080..97606799

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054350548.1 → XP_054206523.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X1
XM_054350549.1 → XP_054206524.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X2