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

Gene ID: 8242, updated on 27-Nov-2024

Summary

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Official Symbol
KDM5Cprovided by HGNC
Official Full Name
lysine demethylase 5Cprovided by HGNC
Primary source
HGNC:HGNC:11114
See related
Ensembl:ENSG00000126012 MIM:314690; AllianceGenome:HGNC:11114
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
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Genomic context

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See KDM5C in Genome Data Viewer
Location:
Xp11.22
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (53176277..53225207, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (52462547..52511471, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (53205459..53254389, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene KANTR integral membrane protein Neighboring gene RNA, U7 small nuclear 37 pseudogene Neighboring gene actin gamma 1 pseudogene 10 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:53192545-53193079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29654 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29655 Neighboring gene microRNA 6895 Neighboring gene microRNA 6894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29656 Neighboring gene Sharpr-MPRA regulatory region 5919 Neighboring gene IQ motif and Sec7 domain ArfGEF 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:53285843-53286438 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:53309250-53309449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:53310370-53311197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:53317293-53318184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20858 Neighboring gene ribosomal protein SA pseudogene 62

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. DNA methylation fingerprint of monozygotic twins and their singleton sibling with intellectual disability carrying a novel KDM5C mutation. Guerra JVS, et al. Eur J Med Genet, 2020 Mar. PMID 31419599
  2. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders. Levy MA, et al. Hum Mutat, 2022 Nov. PMID 35904121
  3. Molecular and cellular events linking variants in the histone demethylase KDM5C to the intellectual disability disorder Claes-Jensen syndrome. Hatch HAM, et al. FEBS J, 2022 Dec. PMID 34536985, Free PMC Article
  4. Deficiency of the X-inactivation escaping gene KDM5C in clear cell renal cell carcinoma promotes tumorigenicity by reprogramming glycogen metabolism and inhibiting ferroptosis. Zheng Q, et al. Theranostics, 2021. PMID 34522206, Free PMC Article
  5. Caregiver-reported characteristics of children diagnosed with pathogenic variants in KDM5C. Hatch HAM, et al. Am J Med Genet A, 2021 Oct. PMID 34089235, Free PMC Article

See all (121) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Histone demethylase JARID1C/KDM5C regulates Th17 cells by increasing IL-6 expression in diabetic plasmacytoid dendritic cells.
    Title: Histone demethylase JARID1C/KDM5C regulates Th17 cells by increasing IL-6 expression in diabetic plasmacytoid dendritic cells.
  2. Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization.
    Title: Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization.
  3. KDM5C-Mediated Recruitment of BRD4 to Chromatin Regulates Enhancer Activation and BET Inhibitor Sensitivity.
    Title: KDM5C-Mediated Recruitment of BRD4 to Chromatin Regulates Enhancer Activation and BET Inhibitor Sensitivity.
  4. WNT signalling control by KDM5C during development affects cognition.
    Title: WNT signalling control by KDM5C during development affects cognition.
  5. Lysine demethylase 5C inhibits transcription of prefoldin subunit 5 to activate c-Myc signal transduction and colorectal cancer progression.
    Title: Lysine demethylase 5C inhibits transcription of prefoldin subunit 5 to activate c-Myc signal transduction and colorectal cancer progression.
  6. KDM5 family of demethylases promotes CD44-mediated chemoresistance in pancreatic adenocarcinomas.
    Title: KDM5 family of demethylases promotes CD44-mediated chemoresistance in pancreatic adenocarcinomas.
  7. The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system.
    Title: The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system.
  8. Elevated PSPC1 and KDM5C expression indicates poor prognosis in prostate cancer.
    Title: Elevated PSPC1 and KDM5C expression indicates poor prognosis in prostate cancer.
  9. The histone demethylase KDM5C controls female bone mass by promoting energy metabolism in osteoclasts.
    Title: The histone demethylase KDM5C controls female bone mass by promoting energy metabolism in osteoclasts.
  10. The histone demethylase KDM5C functions as a tumor suppressor in AML by repression of bivalently marked immature genes.
    Title: The histone demethylase KDM5C functions as a tumor suppressor in AML by repression of bivalently marked immature genes.
Submit: New GeneRIF Correction See all GeneRIFs (67)

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
Syndromic X-linked intellectual disability Claes-Jensen type
MedGen: C1845243 OMIM: 300534 GeneReviews: Not available
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Copy number response

Description
Copy number response
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2023-07-27)

ClinGen Genome Curation PagePubMed
Triplosensitivity

No evidence available (Last evaluated 2023-07-27)

ClinGen Genome Curation Page

Variation

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See Variation Viewer (GRCh37.p13)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K4 demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K4 demethylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone demethylase activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding 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 negative regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to toxic substance IEA
Inferred from Electronic Annotation
more info
  
involved_in rhythmic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol 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
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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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 H3]-trimethyl-L-lysine(4) demethylase 5C
histone demethylase JARID1C
lysine (K)-specific demethylase 5C
NP_001140174.1
NP_001269551.1
NP_001340907.1
NP_001340908.1
NP_001340910.1
NP_001340911.1
NP_001340913.1
NP_004178.2

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

  1. NG_008085.2 RefSeqGene

    Range
    5216..38265
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001146702.2 → NP_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/TrEMBL
    A0A6M4C8G8, A0A8I5KQR8
    Related
    ENSP00000445176.1, ENST00000452825.7
    Conserved Domains (7) summary
    smart00545
    Location:13 → 50
    JmjN; Small domain found in the jumonji family of transcription factors
    cd15604
    Location:259 → 304
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cl28902
    Location:51 → 103
    ARID; ARID/BRIGHT DNA binding domain family
    pfam02373
    Location:434 → 550
    JmjC; JmjC domain, hydroxylase
    pfam02928
    Location:640 → 692
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:705 → 1033
    PLU-1; PLU-1-like protein
    cl22851
    Location:1120 → 1180
    PHD_SF; PHD finger superfamily

  2. NM_001282622.3 → NP_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/TrEMBL
    A6N6J7
    Related
    ENSP00000385394.3, ENST00000404049.7
    Conserved Domains (7) summary
    smart00501
    Location:80 → 170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:13 → 54
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:500 → 616
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:325 → 370
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:1186 → 1246
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:706 → 758
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:771 → 1097
    PLU-1; PLU-1-like protein

  3. NM_001353978.3 → NP_001340907.1  lysine-specific demethylase 5C isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL139396
    Consensus CDS
    CCDS87747.1
    UniProtKB/TrEMBL
    A0A8I5KQR8
    Related
    ENSP00000364528.3, ENST00000375379.7
    Conserved Domains (7) summary
    smart00501
    Location:80 → 170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:13 → 54
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:501 → 617
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:326 → 371
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:1187 → 1247
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:707 → 759
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:772 → 1098
    PLU-1; PLU-1-like protein

  4. NM_001353979.2 → NP_001340908.1  lysine-specific demethylase 5C isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL139396
    UniProtKB/TrEMBL
    A6N6J7
    Related
    ENSP00000508806.1, ENST00000685423.1
    Conserved Domains (7) summary
    smart00501
    Location:80 → 170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:13 → 54
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:500 → 616
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:325 → 370
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:1186 → 1246
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:706 → 758
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:771 → 1097
    PLU-1; PLU-1-like protein

  5. NM_001353981.2 → NP_001340910.1  lysine-specific demethylase 5C isoform 6

    Status: REVIEWED

    Source sequence(s)
    AL139396
    Consensus CDS
    CCDS94610.1
    UniProtKB/TrEMBL
    A0A8I5KQR8, A0A8I5KTT1
    Related
    ENSP00000509818.1, ENST00000685641.2
    Conserved Domains (7) summary
    smart00501
    Location:80 → 170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:13 → 54
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:501 → 617
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:326 → 371
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:1187 → 1247
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:707 → 759
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:772 → 1098
    PLU-1; PLU-1-like protein

  6. NM_001353982.2 → NP_001340911.1  lysine-specific demethylase 5C isoform 7

    Status: REVIEWED

    Source sequence(s)
    AL139396
    UniProtKB/TrEMBL
    A0A8I5KQR8
    Conserved Domains (7) summary
    smart00501
    Location:80 → 170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:13 → 54
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:500 → 616
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:325 → 370
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:1186 → 1246
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:706 → 758
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:771 → 1097
    PLU-1; PLU-1-like protein

  7. NM_001353984.2 → NP_001340913.1  lysine-specific demethylase 5C isoform 8

    Status: REVIEWED

    Source sequence(s)
    AL139396
    Consensus CDS
    CCDS94611.1
    UniProtKB/TrEMBL
    A0A8I5KQR8, A0A8I5KYW1
    Related
    ENSP00000510430.1, ENST00000688699.1
    Conserved Domains (7) summary
    smart00501
    Location:80 → 170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:13 → 54
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:501 → 617
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:326 → 371
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:1187 → 1247
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:707 → 759
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:772 → 1098
    PLU-1; PLU-1-like protein

  8. NM_004187.5 → NP_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
    B0QZ44, B4E3I2, F5H3T1, P41229, Q5JUX3, Q5JUX4, Q5JUX5, Q7Z5S5
    UniProtKB/TrEMBL
    A6N6J7
    Related
    ENSP00000364550.4, ENST00000375401.8
    Conserved Domains (7) summary
    smart00501
    Location:80 → 170
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    smart00545
    Location:13 → 54
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:501 → 617
    JmjC; JmjC domain, hydroxylase
    cd15604
    Location:326 → 371
    PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    cd15608
    Location:1187 → 1247
    PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
    pfam02928
    Location:707 → 759
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:772 → 1098
    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
    Related
    ENST00000687695.1

  3. NR_148674.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL139396

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

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    53176277..53225207 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    52462547..52511471 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P41229.2 GenPept UniProtKB/Swiss-Prot:P41229

Gene LinkOut

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