KDM1A lysine demethylase 1A [Homo sapiens (human)] - Gene

Summary

Official Symbol: KDM1Aprovided by HGNC
Official Full Name: lysine demethylase 1Aprovided by HGNC
Primary source: HGNC:HGNC:29079
See related: Ensembl:ENSG00000004487 MIM:609132; AllianceGenome:HGNC:29079
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: AOF2; CPRF; KDM1; LSD1; BHC110
Summary: This gene encodes a nuclear protein containing a SWIRM domain, a FAD-binding motif, and an amine oxidase domain. This protein is a component of several histone deacetylase complexes, though it silences genes by functioning as a histone demethylase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
Expression: Broad expression in testis (RPKM 45.8), endometrium (RPKM 15.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p36.12

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (23019468..23083689)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (22845130..22909357)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (23345961..23410182)

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?

GFI1B and LSD1 repress myeloid traits during megakaryocyte differentiation.
Title: GFI1B and LSD1 repress myeloid traits during megakaryocyte differentiation.
Histone demethylase KDM1A promotes hepatic steatosis and inflammation by increasing chromatin accessibility in NAFLD.
Title: Histone demethylase KDM1A promotes hepatic steatosis and inflammation by increasing chromatin accessibility in NAFLD.
TERRA-LSD1 phase separation promotes R-loop formation for telomere maintenance in ALT cancer cells.
Title: TERRA-LSD1 phase separation promotes R-loop formation for telomere maintenance in ALT cancer cells.
RNF20 contributes to epigenetic immunosuppression through CDK9-dependent LSD1 stabilization.
Title: RNF20 contributes to epigenetic immunosuppression through CDK9-dependent LSD1 stabilization.
DUSP4 maintains the survival and LSD1 protein stability in esophageal squamous cell carcinoma cells by inhibiting JNK signaling-dependent autophagy.
Title: DUSP4 maintains the survival and LSD1 protein stability in esophageal squamous cell carcinoma cells by inhibiting JNK signaling-dependent autophagy.
LSD1 Regulates Neurogenesis in Human Neural Stem Cells Through the Repression of Human-Enriched Extracellular Matrix and Cell Adhesion Genes.
Title: LSD1 Regulates Neurogenesis in Human Neural Stem Cells Through the Repression of Human-Enriched Extracellular Matrix and Cell Adhesion Genes.
Study of KDM1A and VEGF changes as the responsible genes in the angiogenesis of breast cancer.
Title: Study of KDM1A and VEGF changes as the responsible genes in the angiogenesis of breast cancer.
Uncovering New Conformational States of the Substrate Binding Pocket of LSD1 Potential for Inhibitor Design via Funnel Metadynamics.
Title: Uncovering New Conformational States of the Substrate Binding Pocket of LSD1 Potential for Inhibitor Design via Funnel Metadynamics.
FBXO24 Suppresses Breast Cancer Tumorigenesis by Targeting LSD1 for Ubiquitination.
Title: FBXO24 Suppresses Breast Cancer Tumorigenesis by Targeting LSD1 for Ubiquitination.
LSD1 interacting with HSP90 promotes skin wound healing by inducing metabolic reprogramming of hair follicle stem cells through the c-MYC/LDHA axis.
Title: LSD1 interacting with HSP90 promotes skin wound healing by inducing metabolic reprogramming of hair follicle stem cells through the c-MYC/LDHA axis.

Submit: New GeneRIF Correction See all GeneRIFs (342)

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
Palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome MedGen: C4225229 OMIM: 616728 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)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	LSD1/KDM1 demethylates HIV-1 Tat at position K51 in vitro and in cells	PubMed
	tat	LSD1 interacts with CTIP2 and co-localizes with HIV-1 Tat. LSD1 is required for CTIP2 recruitment at the HIV-1 proximal promoter to repress HIV-1 replication and transcription	PubMed
	tat	LSD1/KDM1 and CoREST proteins are recruited to the HIV-1 LTR in response to HIV-1 Tat and formation of the LSD1/KDM1/CoREST complex functions as a co-activator of HIV-1 transcription	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

SHGC-74372 (e-PCR)
- UniSTS:46110

RH69757 (e-PCR)
- UniSTS:70176

AL009553 (e-PCR)
- UniSTS:61987

SHGC-74369 (e-PCR)
- UniSTS:75311

SHGC-33968 (e-PCR)
- UniSTS:59695

G63383 (e-PCR)
- UniSTS:140347

AL009905 (e-PCR)
- UniSTS:67172

SHGC-33933 (e-PCR)
- UniSTS:16262

AFMa129zb5 (e-PCR)
- UniSTS:75695

RH98397 (e-PCR)
- UniSTS:84706

RH63847 (e-PCR)
- UniSTS:40435

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	IDA Inferred from Direct Assay more info	PubMed
enables FAD-dependent H3K4me/H3K4me3 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables MRF binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables flavin adenine dinucleotide binding	IBA Inferred from Biological aspect of Ancestor more info
enables flavin adenine dinucleotide binding	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K4 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9 demethylase activity	TAS Traceable Author Statement more info
enables histone demethylase activity	EXP Inferred from Experiment more info	PubMed
enables histone demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone demethylase activity	TAS Traceable Author Statement more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables nuclear androgen receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables nuclear receptor coactivator activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables oxidoreductase activity	IBA Inferred from Biological aspect of Ancestor more info
enables oxidoreductase activity	IDA Inferred from Direct Assay more info	PubMed
enables p53 binding	IPI Inferred from Physical Interaction more info	PubMed
enables promoter-specific chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
NOT enables telomeric DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables telomeric repeat-containing RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription coactivator activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription coactivator activity	ISS Inferred from Sequence or Structural Similarity more info
enables transcription factor binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA repair-dependent chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within cellular response to UV	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to cAMP	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to gamma radiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cerebral cortex development	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in guanine metabolic process	IEA Inferred from Electronic Annotation more info
involved_in muscle cell development	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in negative regulation of DNA binding	IC Inferred by Curator more info	PubMed
involved_in negative regulation of DNA damage response, signal transduction by p53 class mediator	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein binding	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron maturation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell size	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of neural precursor cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of neuroblast proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neuron projection development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of protein ubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of stem cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein demethylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA methylation-dependent heterochromatin formation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of androgen receptor signaling pathway	TAS Traceable Author Statement more info
acts_upstream_of_or_within regulation of double-strand break repair via homologous recombination	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of protein localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to fungicide	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of DNA repair complex	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in chromosome, telomeric region	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	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of transcription regulator complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: lysine-specific histone demethylase 1A

Names: BRAF35-HDAC complex protein BHC110; FAD-binding protein BRAF35-HDAC complex, 110 kDa subunit; [histone H3]-dimethyl-L-lysine(4) FAD-dependent demethylase 1A; amine oxidase (flavin containing) domain 2; flavin-containing amine oxidase domain-containing protein 2; lysine (K)-specific demethylase 1A; lysine-specific histone demethylase 1

NP_001009999.1

EC 1.14.99.66

NP_001350583.1

EC 1.14.99.66

NP_001397691.1

EC 1.14.99.66

NP_001397692.1

EC 1.14.99.66

NP_055828.2

EC 1.14.99.66

XP_005245843.1

EC 1.14.99.66

XP_006710536.1

EC 1.14.99.66

XP_016856205.1

EC 1.14.99.66

XP_047305633.1

EC 1.14.99.66

XP_054191226.1

EC 1.14.99.66

XP_054191227.1

EC 1.14.99.66

XP_054191228.1

EC 1.14.99.66

XP_054191229.1

EC 1.14.99.66

XP_054191230.1

EC 1.14.99.66

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_047129.1 RefSeqGene

Range

5026..69247

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001009999.3 → NP_001009999.1 lysine-specific histone demethylase 1A isoform a

See identical proteins and their annotated locations for NP_001009999.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

BC025362, BC040194, BC048134, BG717076

Consensus CDS

CCDS53278.1

UniProtKB/TrEMBL

A0A8I5QKM3

Related

ENSP00000383042.5, ENST00000400181.9

Conserved Domains (4) summary

pfam01593
Location:308 → 849

Amino_oxidase; Flavin containing amine oxidoreductase

pfam04433
Location:197 → 284

SWIRM; SWIRM domain

pfam13450
Location:303 → 361

NAD_binding_8; NAD(P)-binding Rossmann-like domain

cl21568
Location:391 → 495

SurA_N_3; SurA N-terminal domain
NM_001363654.2 → NP_001350583.1 lysine-specific histone demethylase 1A isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks two alternate in-frame exons and uses an alternate in-frame splice for a 3' exon, compared to variant 1. The encoded protein (isoform c) is shorter than isoform a.

Source sequence(s)

AL031428

Consensus CDS

CCDS85939.1

UniProtKB/TrEMBL

A0A8I5QJJ5, R4GMQ1

Related

ENSP00000473297.2, ENST00000465864.2

Conserved Domains (2) summary

cl27535
Location:183 → 831

Amino_oxidase; Flavin containing amine oxidoreductase

cl27975
Location:23 → 98

EBV-NA3; Epstein-Barr virus nuclear antigen 3 (EBNA-3)
NM_001410762.1 → NP_001397691.1 lysine-specific histone demethylase 1A isoform d

Status: REVIEWED

Source sequence(s)

AL031428

Consensus CDS

CCDS90880.1

UniProtKB/TrEMBL

A0A8I5KXU4

Related

ENSP00000509257.1, ENST00000685102.1
NM_001410763.1 → NP_001397692.1 lysine-specific histone demethylase 1A isoform e

Status: REVIEWED

Source sequence(s)

AL031428

Consensus CDS

CCDS90881.1

UniProtKB/TrEMBL

A0A8I5KSH0

Related

ENSP00000509679.1, ENST00000691682.1
NM_015013.4 → NP_055828.2 lysine-specific histone demethylase 1A isoform b

See identical proteins and their annotated locations for NP_055828.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks two alternate in-frame exons, compared to variant 1. The encoded protein (isoform b) is shorter than isoform a.

Source sequence(s)

AB011173, BC025362, BG717076

Consensus CDS

CCDS30627.1

UniProtKB/Swiss-Prot

A8MWP9, O60341, Q5TH94, Q5TH95, Q86VT7, Q8IXK4, Q8NDP6, Q8TAZ3, Q96AW4

UniProtKB/TrEMBL

A0A8I5QJJ5

Related

ENSP00000349049.3, ENST00000356634.7

Conserved Domains (2) summary

PLN02328
Location:183 → 825

PLN02328; lysine-specific histone demethylase 1 homolog

PHA03378
Location:23 → 98

PHA03378; EBNA-3B; Provisional

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

23019468..23083689

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006710473.4 → XP_006710536.1 lysine-specific histone demethylase 1A isoform X2

UniProtKB/TrEMBL

A0A8I5KV76

Conserved Domains (4) summary

smart00150
Location:430 → 532

SPEC; Spectrin repeats

pfam01593
Location:308 → 809

Amino_oxidase; Flavin containing amine oxidoreductase

pfam04433
Location:197 → 284

SWIRM; SWIRM domain

pfam13450
Location:303 → 361

NAD_binding_8; NAD(P)-binding Rossmann-like domain
XM_017000716.2 → XP_016856205.1 lysine-specific histone demethylase 1A isoform X3

UniProtKB/TrEMBL

A0A8I5KV76

Related

ENSP00000509252.1, ENST00000691404.1
XM_005245786.3 → XP_005245843.1 lysine-specific histone demethylase 1A isoform X1

See identical proteins and their annotated locations for XP_005245843.1

UniProtKB/TrEMBL

A0A8I5QKM3

Related

ENSP00000508820.1, ENST00000690627.1

Conserved Domains (2) summary

PLN02328
Location:203 → 845

PLN02328; lysine-specific histone demethylase 1 homolog

PHA03378
Location:23 → 98

PHA03378; EBNA-3B; Provisional
XM_047449677.1 → XP_047305633.1 lysine-specific histone demethylase 1A isoform X4

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

22845130..22909357

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054335252.1 → XP_054191227.1 lysine-specific histone demethylase 1A isoform X2
XM_054335253.1 → XP_054191228.1 lysine-specific histone demethylase 1A isoform X3
XM_054335251.1 → XP_054191226.1 lysine-specific histone demethylase 1A isoform X1
XM_054335254.1 → XP_054191229.1 lysine-specific histone demethylase 1A isoform X4
XM_054335255.1 → XP_054191230.1 lysine-specific histone demethylase 1A isoform X5