SMC1A structural maintenance of chromosomes 1A [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMC1Aprovided by HGNC
Official Full Name: structural maintenance of chromosomes 1Aprovided by HGNC
Primary source: HGNC:HGNC:11111
See related: Ensembl:ENSG00000072501 MIM:300040; AllianceGenome:HGNC:11111
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: SMC1; SMCB; CDLS2; DEE85; SB1.8; EIEE85; SMC1L1; DXS423E; SMC1alpha
Summary: Proper cohesion of sister chromatids is a prerequisite for the correct segregation of chromosomes during cell division. The cohesin multiprotein complex is required for sister chromatid cohesion. This complex is composed partly of two structural maintenance of chromosomes (SMC) proteins, SMC3 and either SMC1B or the protein encoded by this gene. Most of the cohesin complexes dissociate from the chromosomes before mitosis, although those complexes at the kinetochore remain. Therefore, the encoded protein is thought to be an important part of functional kinetochores. In addition, this protein interacts with BRCA1 and is phosphorylated by ATM, indicating a potential role for this protein in DNA repair. This gene, which belongs to the SMC gene family, is located in an area of the X-chromosome that escapes X inactivation. Mutations in this gene result in Cornelia de Lange syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]
Expression: Ubiquitous expression in lymph node (RPKM 13.2), appendix (RPKM 13.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xp11.22

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (53374149..53422728, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (52660456..52709071, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (53401070..53449677, complement)

Chromosome X - NC_000023.11 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?

Structural Variants in the SMC1A Gene Associated With Near-Haploidy in Undifferentiated Pleomorphic Sarcomas.
Title: Structural Variants in the SMC1A Gene Associated With Near-Haploidy in Undifferentiated Pleomorphic Sarcomas.
AKT/FOXM1/STMN1 signaling pathway activation by SMC1A promotes tumor growth in breast cancer.
Title: AKT/FOXM1/STMN1 signaling pathway activation by SMC1A promotes tumor growth in breast cancer.
SMC1A facilitates gastric cancer cell proliferation, migration, and invasion via promoting SNAIL activated EMT.
Title: SMC1A facilitates gastric cancer cell proliferation, migration, and invasion via promoting SNAIL activated EMT.
PIK3R3 is upregulated in liver cancer and activates Akt signaling to control cancer growth by regulation of CDKN1C and SMC1A.
Title: PIK3R3 is upregulated in liver cancer and activates Akt signaling to control cancer growth by regulation of CDKN1C and SMC1A.
Phenotypes and Genotypes in Patients with SMC1A-Related Developmental and Epileptic Encephalopathy.
Title: Phenotypes and Genotypes in Patients with SMC1A-Related Developmental and Epileptic Encephalopathy.
Further Characterization of SMC1A Loss of Function Epilepsy Distinct From Cornelia de Lange Syndrome.
Title: Further Characterization of SMC1A Loss of Function Epilepsy Distinct From Cornelia de Lange Syndrome.
Cohesin promotes HSV-1 lytic transcription by facilitating the binding of RNA Pol II on viral genes.
Title: Cohesin promotes HSV-1 lytic transcription by facilitating the binding of RNA Pol II on viral genes.
Expansion of the phenotypic spectrum of SMC1A nonsense variants: a patient with cerebellar atrophy and review of the literature.
Title: Expansion of the phenotypic spectrum of SMC1A nonsense variants: a patient with cerebellar atrophy and review of the literature.
A novel mosaic variant on SMC1A reported in buccal mucosa cells, albeit not in blood, of a patient with Cornelia de Lange-like presentation.
Title: A novel mosaic variant on SMC1A reported in buccal mucosa cells, albeit not in blood, of a patient with Cornelia de Lange-like presentation.
Significant phenotypical behavioral differences between individuals with de Lange syndrome caused by SMC1A variants and those caused by NIPBL variants.
Title: Development, behaviour and autism in individuals with SMC1A variants.

Submit: New GeneRIF Correction See all GeneRIFs (71)

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
Congenital muscular hypertrophy-cerebral syndrome MedGen: C1802395 OMIM: 300590 GeneReviews: Cornelia de Lange Syndrome	Compare labs
Developmental and epileptic encephalopathy, 85, with or without midline brain defects MedGen: C5393312 OMIM: 301044 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2018-07-23) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2018-07-23) ClinGen Genome Curation PagePubMed

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
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify structural maintenance of chromosomes 1A (SMC1A), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify structural maintenance of chromosomes 1A (SMC1A), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify structural maintenance of chromosomes 1A (SMC1A), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify structural maintenance of chromosomes 1A (SMC1A), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Vpr	vpr	HIV-1 Vpr decreases the amount of Smc1 and Smc3 proteins in the chromatin	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

DXS423 (e-PCR)
- UniSTS:99130

DXS423 (e-PCR)
- UniSTS:99649

RH25393 (e-PCR)
- UniSTS:5466

STS-T70312 (e-PCR)
- UniSTS:23657

AL023613 (e-PCR)
- UniSTS:83320

RH26243 (e-PCR)
- UniSTS:85633

WI-13565 (e-PCR)
- UniSTS:4034

SMC1L1__1206 (e-PCR)
- UniSTS:277753

SMC1L1__v341 (e-PCR)
- UniSTS:277753

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 DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	HDA more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables mediator complex binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA repair	TAS Traceable Author Statement more info	PubMed
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in establishment of meiotic sister chromatid cohesion	NAS Non-traceable Author Statement more info	PubMed
involved_in establishment of mitotic sister chromatid cohesion	NAS Non-traceable Author Statement more info	PubMed
involved_in meiotic cell cycle	ISS Inferred from Sequence or Structural Similarity more info
involved_in mitotic sister chromatid cohesion	TAS Traceable Author Statement more info	PubMed
involved_in mitotic sister chromatid segregation	TAS Traceable Author Statement more info	PubMed
involved_in mitotic spindle assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to DNA damage checkpoint signaling	IDA Inferred from Direct Assay more info	PubMed
involved_in response to radiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in sister chromatid cohesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in sister chromatid cohesion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in somatic stem cell population maintenance	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromosome	TAS Traceable Author Statement more info
located_in chromosome, centromeric region	TAS Traceable Author Statement more info
part_of cohesin complex	IDA Inferred from Direct Assay more info	PubMed
part_of cohesin complex	TAS Traceable Author Statement more info	PubMed
located_in condensed nuclear chromosome	TAS Traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in kinetochore	IDA Inferred from Direct Assay more info	PubMed
part_of meiotic cohesin complex	IBA Inferred from Biological aspect of Ancestor more info
part_of meiotic cohesin complex	IDA Inferred from Direct Assay more info	PubMed
part_of meiotic cohesin complex	NAS Non-traceable Author Statement more info	PubMed
part_of mitotic cohesin complex	IPI Inferred from Physical Interaction more info	PubMed
part_of mitotic cohesin complex	ISS Inferred from Sequence or Structural Similarity more info
located_in mitotic spindle pole	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear matrix	IDA Inferred from Direct Assay 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
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: structural maintenance of chromosomes protein 1A

Names: SMC protein 1A; SMC-1-alpha; SMC1 (structural maintenance of chromosomes 1, yeast)-like 1; epididymis secretory sperm binding protein; segregation of mitotic chromosomes 1

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_006988.2 RefSeqGene

Range

4943..53522

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_773

mRNA and Protein(s)

NM_001281463.1 → NP_001268392.1 structural maintenance of chromosomes protein 1A isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AC233728

Consensus CDS

CCDS75985.1

UniProtKB/TrEMBL

A0A6Q8PHC3, G8JLG1

Related

ENSP00000364489.7, ENST00000375340.10

Conserved Domains (1) summary

pfam02463
Location:15 → 1188

SMC_N; RecF/RecN/SMC N terminal domain
NM_006306.4 → NP_006297.2 structural maintenance of chromosomes protein 1A isoform 1

See identical proteins and their annotated locations for NP_006297.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AC233728, BC080185, D80000

Consensus CDS

CCDS14352.1

UniProtKB/Swiss-Prot

O14995, Q14683, Q16351, Q2M228

UniProtKB/TrEMBL

A0A384MR33

Related

ENSP00000323421.3, ENST00000322213.9

Conserved Domains (1) summary

pfam02463
Location:3 → 1210

SMC_N; RecF/RecN/SMC N terminal domain