MYSM1 Myb like, SWIRM and MPN domains 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: MYSM1provided by HGNC
Official Full Name: Myb like, SWIRM and MPN domains 1provided by HGNC
Primary source: HGNC:HGNC:29401
See related: Ensembl:ENSG00000162601 MIM:612176; AllianceGenome:HGNC:29401
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: 2ADUB; BMFS4; 2A-DUB
Summary: Enables histone binding activity; peptidase activity; and transcription coactivator activity. Involved in several processes, including chromatin remodeling; monoubiquitinated histone H2A deubiquitination; and positive regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm. Part of protein-containing complex. Implicated in diabetic retinopathy. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in bone marrow (RPKM 8.9), lymph node (RPKM 7.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p32.1

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (58654743..58700062, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (58532658..58578032, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (59120415..59165734, complement)

Chromosome 1 - NC_000001.11 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?

MYSM1 attenuates DNA damage signals triggered by physiologic and genotoxic DNA breaks.
Title: MYSM1 attenuates DNA damage signals triggered by physiologic and genotoxic DNA breaks.
Deubiquitinase catalytic activity of MYSM1 is essential in vivo for hematopoiesis and immune cell development.
Title: Deubiquitinase catalytic activity of MYSM1 is essential in vivo for hematopoiesis and immune cell development.
MYSM1 inhibits human colorectal cancer tumorigenesis by activating miR-200 family members/CDH1 and blocking PI3K/AKT signaling.
Title: MYSM1 inhibits human colorectal cancer tumorigenesis by activating miR-200 family members/CDH1 and blocking PI3K/AKT signaling.
MYSM1 Represses Innate Immunity and Autoimmunity through Suppressing the cGAS-STING Pathway.
Title: MYSM1 Represses Innate Immunity and Autoimmunity through Suppressing the cGAS-STING Pathway.
Interaction of Deubiquitinase 2A-DUB/MYSM1 with DNA Repair and Replication Factors.
Title: Interaction of Deubiquitinase 2A-DUB/MYSM1 with DNA Repair and Replication Factors.
MYSM1-AR complex-mediated repression of Akt/c-Raf/GSK-3beta signaling impedes castration-resistant prostate cancer growth.
Title: MYSM1-AR complex-mediated repression of Akt/c-Raf/GSK-3β signaling impedes castration-resistant prostate cancer growth.
differentiation of B cells to plasma cells was inhibited after the overexpression of MYSM1
Title: [Deubiquitinase MYSM1 Regulates Differentiation of Human B Cells to Plasma Cells].
Data indicate a pathway MYSM1/miR-150/FLT3 that inhibits proliferation of B1a cells, which may be involved in the pathogenesis of systemic lupus erythematosus (SLE).
Title: MYSM1/miR-150/FLT3 inhibits B1a cell proliferation.
this study shows that MYSM1 deficiency is associated with developmental aberrations, progressive bone marrow failure with myelodysplastic features, and increased susceptibility to genotoxic stress
Title: Myb-like, SWIRM, and MPN domains 1 (MYSM1) deficiency: Genotoxic stress-associated bone marrow failure and developmental aberrations.
data suggested that expression of MYSM1 was associated with the progression of CRC and might be a potential biomarker for clinical prognosis
Title: Expression of MYSM1 is associated with tumor progression in colorectal cancer.

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

Associated conditions

Description	Tests
Bone marrow failure syndrome 4 MedGen: C4748257 OMIM: 618116 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of diabetic retinopathy in a Taiwanese population. 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

WI-14224 (e-PCR)
- UniSTS:83271

D1S2251 (e-PCR)
- UniSTS:50010

SHGC-107489 (e-PCR)
- UniSTS:170377

SHGC-78793 (e-PCR)
- UniSTS:95682

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables histone H2A deubiquitinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables metal-dependent deubiquitinase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription coactivator activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in immune system process	IEA Inferred from Electronic Annotation more info
involved_in pigmentation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell migration	IEA Inferred from Electronic Annotation more info
involved_in regulation of hair follicle development	IEA Inferred from Electronic Annotation more info
involved_in regulation of hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IDA Inferred from Direct Assay 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
part_of protein-containing complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: deubiquitinase MYSM1

Names: histone H2A deubiquitinase MYSM1; myb-like, SWIRM and MPN domain-containing protein 1

NP_001078956.1

EC 3.1.2.15

XP_006710377.1

EC 3.1.2.15

XP_011538875.1

EC 3.1.2.15

XP_011538876.1

EC 3.1.2.15

XP_047299673.1

EC 3.1.2.15

XP_047299674.1

EC 3.1.2.15

XP_047299675.1

EC 3.1.2.15

XP_047299676.1

EC 3.1.2.15

XP_054190070.1

EC 3.1.2.15

XP_054190071.1

EC 3.1.2.15

XP_054190072.1

EC 3.1.2.15

XP_054190073.1

EC 3.1.2.15

XP_054190074.1

EC 3.1.2.15

XP_054190075.1

EC 3.1.2.15

XP_054190076.1

EC 3.1.2.15

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_065323.2 RefSeqGene

Range

5016..50335

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GenBank, FASTA, Sequence Viewer (Graphics), LRG_1411

mRNA and Protein(s)

NM_001085487.3 → NP_001078956.1 deubiquitinase MYSM1

See identical proteins and their annotated locations for NP_001078956.1

Status: VALIDATED

Source sequence(s)

AL035411, AL450024

Consensus CDS

CCDS41343.1

UniProtKB/Swiss-Prot

A8KA54, B3KX65, Q5VVJ2, Q68DD3, Q6AI53, Q7Z3G8, Q96PX3

UniProtKB/TrEMBL

A0A8V8TKW8

Related

ENSP00000418734.1, ENST00000472487.6

Conserved Domains (4) summary

cd08067
Location:571 → 753

MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase

smart00717
Location:120 → 164

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

pfam00249
Location:120 → 162

Myb_DNA-binding; Myb-like DNA-binding domain

pfam04433
Location:382 → 461

SWIRM; SWIRM domain

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_000001.11 Reference GRCh38.p14 Primary Assembly

Range

58654743..58700062 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006710314.4 → XP_006710377.1 deubiquitinase MYSM1 isoform X1

UniProtKB/TrEMBL

A0A8V8TKW8

Conserved Domains (4) summary

cd08067
Location:571 → 753

MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase

smart00717
Location:120 → 164

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

pfam00249
Location:120 → 162

Myb_DNA-binding; Myb-like DNA-binding domain

pfam04433
Location:382 → 461

SWIRM; SWIRM domain
XM_011540573.4 → XP_011538875.1 deubiquitinase MYSM1 isoform X2

UniProtKB/TrEMBL

A0A8V8TKW8

Conserved Domains (4) summary

cd08067
Location:504 → 686

MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase

smart00717
Location:53 → 97

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

pfam00249
Location:53 → 95

Myb_DNA-binding; Myb-like DNA-binding domain

pfam04433
Location:315 → 394

SWIRM; SWIRM domain
XM_047443719.1 → XP_047299675.1 deubiquitinase MYSM1 isoform X4
XM_047443717.1 → XP_047299673.1 deubiquitinase MYSM1 isoform X4

Related

ENST00000493821.6
XM_011540574.3 → XP_011538876.1 deubiquitinase MYSM1 isoform X3

UniProtKB/TrEMBL

A0A8V8TKW8

Conserved Domains (4) summary

cd08067
Location:482 → 664

MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase

smart00717
Location:31 → 75

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

pfam00249
Location:31 → 73

Myb_DNA-binding; Myb-like DNA-binding domain

pfam04433
Location:293 → 372

SWIRM; SWIRM domain
XM_047443718.1 → XP_047299674.1 deubiquitinase MYSM1 isoform X4
XM_047443720.1 → XP_047299676.1 deubiquitinase MYSM1 isoform X5

UniProtKB/TrEMBL

A0A590UJW2

Related

ENSP00000499586.1, ENST00000665648.1