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KDM5C lysine demethylase 5C [ Homo sapiens (human) ]

Gene ID: 8242, updated on 1-Jun-2020

Summary

Official Symbol
KDM5Cprovided by HGNC
Official Full Name
lysine demethylase 5Cprovided by HGNC
Primary source
HGNC:HGNC:11114
See related
Ensembl:ENSG00000126012 MIM:314690
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
MRXJ; SMCX; MRX13; MRXSJ; XE169; MRXSCJ; JARID1C; DXS1272E
Summary
This gene is a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one JmjN domain and two PHD-type zinc fingers. The DNA-binding motifs suggest this protein is involved in the regulation of transcription and chromatin remodeling. Mutations in this gene have been associated with X-linked cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
Expression
Ubiquitous expression in endometrium (RPKM 14.4), lymph node (RPKM 13.5) and 25 other tissues See more
Orthologs

Genomic context

See KDM5C in Genome Data Viewer
Location:
Xp11.22
Exon count:
29
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (53176277..53225422, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (53220503..53254604, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene KDM5C adjacent transcript Neighboring gene RNA, U7 small nuclear 37 pseudogene Neighboring gene actin gamma 1 pseudogene 10 Neighboring gene microRNA 6895 Neighboring gene microRNA 6894 Neighboring gene Sharpr-MPRA regulatory region 5919 Neighboring gene IQ motif and Sec7 domain ArfGEF 2 Neighboring gene ribosomal protein SA pseudogene 62

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Mental retardation, syndromic, Claes-Jensen type, X-linked
MedGen: C1845243 OMIM: 300534 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-08-23)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-08-23)

ClinGen Genome Curation PagePubMed

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity (H3-K4 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-K4 specific) IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone demethylase activity (H3-trimethyl-K4 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H3-K4 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K4 demethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone H3-K4 demethylation, trimethyl-H3-K4-specific IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
histone methyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
lysine-specific demethylase 5C
Names
JmjC domain-containing protein SMCX
Jumonji, AT rich interactive domain 1C (RBP2-like)
Jumonji/ARID domain-containing protein 1C
Smcx homolog, X chromosome
Smcy homolog, X-linked
histone demethylase JARID1C
lysine (K)-specific demethylase 5C

NCBI Reference Sequences (RefSeq)

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

  1. NG_008085.2 RefSeqGene

    Range
    5216..39102
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001146702.2NP_001140174.1  lysine-specific demethylase 5C isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, 3' UTR, and coding region compared to variant 1, resulting in a protein (isoform 2) that maintains the reading frame but is shorter at both the N- and C-termini, compared to isoform 1.
    Source sequence(s)
    AL139396
    Consensus CDS
    CCDS55417.1
    UniProtKB/Swiss-Prot
    P41229
    Related
    ENSP00000445176.1, ENST00000452825.7
    Conserved Domains (7) summary
    smart00545
    Location:1350
    JmjN; Small domain found in the jumonji family of transcription factors
    smart01014
    Location:2598
    ARID; ARID/BRIGHT DNA binding domain
    pfam02373
    Location:434550
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:259304
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:640692
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7051031
    PLU-1; PLU-1-like protein
    cl22851
    Location:11201180
    PHD_SF; PHD finger superfamily
  2. NM_001282622.3NP_001269551.1  lysine-specific demethylase 5C isoform 3

    See identical proteins and their annotated locations for NP_001269551.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AL139396, BC054499, L25270
    Consensus CDS
    CCDS65269.1
    UniProtKB/Swiss-Prot
    P41229
    Related
    ENSP00000385394.3, ENST00000404049.7
    Conserved Domains (7) summary
    smart00501
    Location:80170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:500616
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:325370
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:11861246
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:706758
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7711097
    PLU-1; PLU-1-like protein
  3. NM_001353978.3NP_001340907.1  lysine-specific demethylase 5C isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL139396
    Consensus CDS
    CCDS87747.1
    Related
    ENSP00000364528.3, ENST00000375379.7
    Conserved Domains (7) summary
    smart00501
    Location:80170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:501617
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:326371
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:11871247
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:707759
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7721098
    PLU-1; PLU-1-like protein
  4. NM_001353979.2NP_001340908.1  lysine-specific demethylase 5C isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL139396
    Conserved Domains (7) summary
    smart00501
    Location:80170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:500616
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:325370
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:11861246
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:706758
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7711097
    PLU-1; PLU-1-like protein
  5. NM_001353981.2NP_001340910.1  lysine-specific demethylase 5C isoform 6

    Status: REVIEWED

    Source sequence(s)
    AL139396
    Conserved Domains (7) summary
    smart00501
    Location:80170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:501617
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:326371
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:11871247
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:707759
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7721098
    PLU-1; PLU-1-like protein
  6. NM_001353982.2NP_001340911.1  lysine-specific demethylase 5C isoform 7

    Status: REVIEWED

    Source sequence(s)
    AL139396
    Conserved Domains (7) summary
    smart00501
    Location:80170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:500616
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:325370
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:11861246
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:706758
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7711097
    PLU-1; PLU-1-like protein
  7. NM_001353984.1NP_001340913.1  lysine-specific demethylase 5C isoform 8

    Status: REVIEWED

    Source sequence(s)
    AL139396
    Conserved Domains (7) summary
    smart00501
    Location:80170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:501617
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:326371
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:11871247
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:707759
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7721098
    PLU-1; PLU-1-like protein
  8. NM_004187.5NP_004178.2  lysine-specific demethylase 5C isoform 1

    See identical proteins and their annotated locations for NP_004178.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL139396, BC047751, BC054499, L25270
    Consensus CDS
    CCDS14351.1
    UniProtKB/Swiss-Prot
    P41229
    Related
    ENSP00000364550.3, ENST00000375401.7
    Conserved Domains (7) summary
    smart00501
    Location:80170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:1354
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:501617
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:326371
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:11871247
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:707759
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7721098
    PLU-1; PLU-1-like protein

RNA

  1. NR_148672.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL139396
  2. NR_148673.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL139396
  3. NR_148674.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL139396

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    53176277..53225422 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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