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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
KDM5C
lysine demethylase 5C
Chromosome X Β· Xp11.22
NCBI Gene: 8242Ensembl: ENSG00000126012.14HGNC: HGNC:11114UniProt: A0A6M4C8G8
126PubMed Papers
21Diseases
0Drugs
185Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
nucleoplasmprotein bindingzinc ion bindinghistone H3K4 demethylase activitysyndromic X-linked intellectual disability Claes-Jensen typeSyndromic X-linked intellectual disability due to JARID1C mutationclear cell renal carcinomaSpastic paraplegia
✦AI Summary

KDM5C is an X-linked histone demethylase that specifically removes methyl groups from histone H3 lysine 4 (H3K4me2/3), playing a central role in transcriptional regulation 1. The enzyme demethylates trimethylated and dimethylated, but not monomethylated H3K4, and participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST complexes at neuron-restrictive silencer elements 1. In neurodevelopment, KDM5C functions as a developmental safeguard controlling WNT signaling output to regulate the timely transition from primary to intermediate progenitor cells during neurogenesis 2. Disruption of this function leads to intellectual disability, with transient WNT pathway alterations sufficient to rescue cognitive deficits 2. In renal cell carcinoma, KDM5C mutations associate with altered angiogenesis and metabolic reprogramming 3. KDM5C regulates glucose-6-phosphate dehydrogenase and HIF-related genes, controlling glycogen metabolism and pentose phosphate pathway flux; loss of KDM5C increases ferroptosis resistance through enhanced NADPH/glutathione production 4. KDM5C is classified as a cancer driver tumor suppressor gene across multiple cancer types 5. Mutations in KDM5C occur in X-linked intellectual developmental disorder, Claes-Jensen type, and represent immunogenic targets in therapeutic neoantigen vaccination approaches 6.

Sources cited
1
KDM5C is a histone demethylase specific for H3K4; demethylates di- and trimethylated H3K4; participates in transcriptional repression via recruitment of HDACs and REST
PMID: 28262558
2
KDM5C controls WNT signaling during neurodevelopment to regulate progenitor cell transition and neurogenesis; mutations cause intellectual disability; WNT modulation rescues transcriptomic and behavioral deficits
PMID: 38383780
3
KDM5C mutations in renal cell carcinoma associate with high angiogenesis and AMPK/fatty acid oxidation gene expression
PMID: 33157048
4
KDM5C regulates glucose-6-phosphate dehydrogenase and HIF genes; loss of KDM5C increases glycogen accumulation and pentose phosphate pathway flux, conferring ferroptosis resistance
PMID: 34522206
5
KDM5C is identified as a cancer driver tumor suppressor gene in kidney renal clear cell carcinoma and pan-cancer analysis
PMID: 31221981
6
KDM5C mutations are immunogenic targets in neoantigen cancer vaccines for renal cell carcinoma; T cell responses generated against KDM5C driver mutations
PMID: 39910301
7
KDM5C undergoes multiple distinct and spatially separated inactivating mutations within single renal carcinoma tumors, suggesting convergent phenotypic evolution
PMID: 22397650
Disease Associationsβ“˜21
syndromic X-linked intellectual disability Claes-Jensen typeOpen Targets
0.81Strong
Syndromic X-linked intellectual disability due to JARID1C mutationOpen Targets
0.78Strong
clear cell renal carcinomaOpen Targets
0.62Moderate
Spastic paraplegiaOpen Targets
0.55Moderate
genetic disorderOpen Targets
0.55Moderate
Intellectual disabilityOpen Targets
0.52Moderate
renal cell carcinomaOpen Targets
0.44Moderate
multiple myelomaOpen Targets
0.37Weak
colorectal adenocarcinomaOpen Targets
0.37Weak
Endometrial Endometrioid AdenocarcinomaOpen Targets
0.37Weak
Fibrous MeningiomaOpen Targets
0.37Weak
skin basal cell carcinomaOpen Targets
0.37Weak
skin squamous cell carcinomaOpen Targets
0.37Weak
X-linked non-syndromic intellectual disabilityOpen Targets
0.37Weak
X-linked syndromic intellectual disabilityOpen Targets
0.37Weak
developmental disorder of mental healthOpen Targets
0.34Weak
Smith-Magenis syndromeOpen Targets
0.34Weak
HirsutismOpen Targets
0.33Weak
lung adenocarcinomaOpen Targets
0.33Weak
head and neck squamous cell carcinomaOpen Targets
0.31Weak
Intellectual developmental disorder, X-linked, syndromic, Claes-Jensen typeUniProt
Pathogenic Variants185
NM_004187.5(KDM5C):c.202C>T (p.Arg68Ter)Pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 68
NM_004187.5(KDM5C):c.2041C>T (p.Arg681Ter)Pathogenic
not provided|Spastic paraplegia|Syndromic X-linked intellectual disability Claes-Jensen type
β˜…β˜…β˜†β˜†2025β†’ Residue 681
NM_004187.5(KDM5C):c.1762C>T (p.Gln588Ter)Pathogenic
not provided|Spastic paraplegia
β˜…β˜…β˜†β˜†2025β†’ Residue 588
NM_004187.5(KDM5C):c.1843G>T (p.Val615Phe)Likely pathogenic
Syndromic X-linked intellectual disability Claes-Jensen type
β˜…β˜…β˜†β˜†2025β†’ Residue 615
NM_004187.5(KDM5C):c.2427_2430del (p.Glu810fs)Pathogenic
not provided|Syndromic X-linked intellectual disability Claes-Jensen type
β˜…β˜…β˜†β˜†2025β†’ Residue 810
NM_004187.5(KDM5C):c.1510G>A (p.Val504Met)Pathogenic
not provided|Syndromic X-linked intellectual disability Claes-Jensen type
β˜…β˜…β˜†β˜†2025β†’ Residue 504
NM_004187.5(KDM5C):c.1607G>A (p.Gly536Glu)Likely pathogenic
Syndromic X-linked intellectual disability Claes-Jensen type|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 536
NM_004187.5(KDM5C):c.994C>T (p.Arg332Ter)Pathogenic
Syndromic X-linked intellectual disability Claes-Jensen type|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 332
NM_004187.5(KDM5C):c.1243-2A>GPathogenic
not provided|Spastic paraplegia
β˜…β˜…β˜†β˜†2024
NM_004187.5(KDM5C):c.2785C>T (p.Arg929Ter)Pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2024β†’ Residue 929
NM_004187.5(KDM5C):c.2248C>T (p.Arg750Trp)Likely pathogenic
Syndromic X-linked intellectual disability Claes-Jensen type|Spastic paraplegia
β˜…β˜…β˜†β˜†2023β†’ Residue 750
NM_004187.5(KDM5C):c.1439C>T (p.Pro480Leu)Pathogenic
Syndromic X-linked intellectual disability Claes-Jensen type|not provided|Spastic paraplegia
β˜…β˜…β˜†β˜†2023β†’ Residue 480
NM_004187.5(KDM5C):c.974_975del (p.Tyr325fs)Pathogenic
Spastic paraplegia|Syndromic X-linked intellectual disability Claes-Jensen type
β˜…β˜…β˜†β˜†2023β†’ Residue 325
NM_004187.5(KDM5C):c.3058C>T (p.Gln1020Ter)Pathogenic
not provided|Inborn genetic diseases|Syndromic X-linked intellectual disability Claes-Jensen type
β˜…β˜…β˜†β˜†2023β†’ Residue 1020
NM_004187.5(KDM5C):c.2482C>T (p.Arg828Ter)Pathogenic
Syndromic X-linked intellectual disability Claes-Jensen type|Inborn genetic diseases|not provided|Developmental disorder
β˜…β˜…β˜†β˜†2023β†’ Residue 828
NM_004187.5(KDM5C):c.2908C>T (p.Gln970Ter)Pathogenic
Spastic paraplegia|Syndromic X-linked intellectual disability Claes-Jensen type
β˜…β˜…β˜†β˜†2023β†’ Residue 970
NM_004187.5(KDM5C):c.2332C>T (p.Arg778Ter)Pathogenic
not provided|Spastic paraplegia
β˜…β˜…β˜†β˜†2022β†’ Residue 778
NM_004187.5(KDM5C):c.1795C>T (p.Arg599Cys)Likely pathogenic
Syndromic X-linked intellectual disability Claes-Jensen type|not provided
β˜…β˜…β˜†β˜†2022β†’ Residue 599
NM_004187.5(KDM5C):c.3392_3393del (p.Glu1131fs)Pathogenic
not provided|Rare genetic intellectual disability|Spastic paraplegia|Inborn genetic diseases|Syndromic X-linked intellectual disability Claes-Jensen type
β˜…β˜…β˜†β˜†2022β†’ Residue 1131
NM_004187.5(KDM5C):c.2575C>T (p.Gln859Ter)Pathogenic
Inborn genetic diseases|Spastic paraplegia
β˜…β˜…β˜†β˜†2022β†’ Residue 859
View on ClinVar β†—
Related Genes
MSL1Shared pathway100%HDGFL1Shared pathway100%HIPK4Shared pathway100%HMGB4Shared pathway100%NAA40Shared pathway100%NSD1Shared pathway100%
Tissue Expression6 tissues
Ovary
100%
Lung
80%
Bone Marrow
77%
Liver
53%
Brain
53%
Heart
51%
Gene Interaction Network
Click a node to explore
KDM5CMSL1HDGFL1HIPK4HMGB4NAA40NSD1
PROTEIN STRUCTURE
Preparing viewer…
PDB5FWJ Β· 2.10 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.22Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.14 [0.10–0.22]
RankingsWhere KDM5C stands among ~20K protein-coding genes
  • #3,725of 20,598
    Most Researched126 Β· top quartile
  • #381of 5,498
    Most Pathogenic Variants185 Β· top 10%
  • #560of 17,882
    Most Constrained (LOEUF)0.22 Β· top 5%
Genes detectedKDM5C
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
PMID: 22397650
N Engl J Med Β· 2012
1.00
2
Molecular Subsets in Renal Cancer Determine Outcome to Checkpoint and Angiogenesis Blockade.
PMID: 33157048
Cancer Cell Β· 2020
0.90
3
Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma.
PMID: 32472114
Nat Med Β· 2020
0.80
4
METTL14-mediated N6-methyladenosine modification of SOX4 mRNA inhibits tumor metastasis in colorectal cancer.
PMID: 32552762
Mol Cancer Β· 2020
0.70
5
A neoantigen vaccine generates antitumour immunity in renal cell carcinoma.
PMID: 39910301
Nature Β· 2025
0.60