GeneBe

KDM5C

lysine demethylase 5C, the group of Lysine demethylases|MicroRNA protein coding host genes|AT-rich interaction domain containing|PHD finger proteins

Basic information

Region (hg38): X:53176277-53225422

Previous symbols: [ "SMCX", "JARID1C", "MRX13" ]

Links

ENSG00000126012 ∙ NCBI:8242 ∙ OMIM:314690 ∙ HGNC:11114 ∙ Uniprot:P41229 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 29.

Transcript IDProtein IDCoding exonsMANE SelectMANE Plus Clinical
NM_004187.5NP_004178.226yes-
ENST00000375401.8ENSP00000364550.426yes-
NM_001146702.2NP_001140174.124--
NM_001282622.3NP_001269551.126--

Phenotypes

GenCC

Source: genCC

  • syndromic X-linked intellectual disability Claes-Jensen type (Definitive), mode of inheritance: XL
  • X-linked syndromic intellectual disability (Definitive), mode of inheritance: XL
  • syndromic X-linked intellectual disability Claes-Jensen type (Strong), mode of inheritance: XL
  • syndromic X-linked intellectual disability Claes-Jensen type (Supportive), mode of inheritance: XL
  • syndromic X-linked intellectual disability Claes-Jensen type (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Intellectual developmental disorder, X-linked, syndromic, Claes-Jensen typeXLGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Genitourinary; Musculoskeletal; Neurologic10982473; 15586325; 16538222; 18697827; 18203167; 19826449; 21575681; 22326837; 22611640
Loading mutation effect viewer...

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KDM5C gene.

  • Spastic_paraplegia (470 variants)
  • not_provided (385 variants)
  • Syndromic_X-linked_intellectual_disability_Claes-Jensen_type (177 variants)
  • Inborn_genetic_diseases (132 variants)
  • not_specified (53 variants)
  • KDM5C-related_disorder (28 variants)
  • Intellectual_disability (14 variants)
  • See_cases (2 variants)
  • Neurodevelopmental_disorder (1 variants)
  • Kabuki_syndrome (1 variants)
  • X-linked_syndromic_intellectual_disability (1 variants)
  • Hirsutism (1 variants)
  • KDM5C-related_X-linked_syndromic_intellectual_disability (1 variants)
  • Multiple_myeloma (1 variants)
  • Rare_genetic_intellectual_disability (1 variants)
  • Smith-Magenis_Syndrome-like (1 variants)
  • Developmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM5C gene is commonly pathogenic or not. These statistics are base on transcript: NM_004187.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
36
clinvar
182
clinvar
30
clinvar
 248
missense
12
clinvar
40
clinvar
439
clinvar
52
clinvar
16
clinvar
 559
nonsense
37
clinvar
14
clinvar
20
clinvar
 71
start loss
1
1
frameshift
47
clinvar
21
clinvar
1
clinvar
 69
splice donor/acceptor (+/-2bp)
4
clinvar
17
clinvar
34
clinvar
 55
Total 100 93 530 234 46

Highest pathogenic variant AF is 0.000026458132

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KDM5Cprotein_codingprotein_codingENST00000375401 2634102
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
125742141257470.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense5.152936670.4390.000057210067
Missense in Polyphen43263.20.163374170
Synonymous-0.5822722601.050.00002013210
Loss of Function6.38455.10.07260.00000433846

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00007600.0000615
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001280.00000879
Middle Eastern0.000.00
South Asian0.0001580.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Histone demethylase that specifically demethylates 'Lys- 4' of histone H3, thereby playing a central role in histone code (PubMed:28262558). Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements. Represses the CLOCK-ARNTL/BMAL1 heterodimer- mediated transcriptional activation of the core clock component PER2 (By similarity). {ECO:0000250|UniProtKB:P41230, ECO:0000269|PubMed:17320160, ECO:0000269|PubMed:17320161, ECO:0000269|PubMed:17468742, ECO:0000269|PubMed:26645689, ECO:0000269|PubMed:28262558}.;
Disease
DISEASE: Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ) [MIM:300534]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRXSCJ patients manifest mental retardation associated with variable features such as slowly progressive spastic paraplegia, seizures, facial dysmorphism. {ECO:0000269|PubMed:15586325, ECO:0000269|PubMed:16538222, ECO:0000269|PubMed:16541399, ECO:0000269|PubMed:17320160, ECO:0000269|PubMed:17468742, ECO:0000269|PubMed:23356856, ECO:0000269|PubMed:25666439}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Pathways in clear cell renal cell carcinoma;HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

pRec
0.193

Intolerance Scores

loftool
0.0636
rvis_EVS
-1.51
rvis_percentile_EVS
3.5

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.730

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Zebrafish Information Network

Gene name
kdm5c
Affected structure
whole organism
Phenotype tag
abnormal
Phenotype quality
curved ventral

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;chromatin remodeling;histone H3-K4 demethylation;histone H3-K4 demethylation, trimethyl-H3-K4-specific;negative regulation of transcription, DNA-templated;rhythmic process;oxidation-reduction process
Cellular component
nucleus;nucleoplasm;cytosol;histone methyltransferase complex
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;zinc ion binding;histone demethylase activity;histone demethylase activity (H3-K4 specific);histone demethylase activity (H3-trimethyl-K4 specific);dioxygenase activity
Feedback | API | Annotate VCF | Sitemap | About | Privacy & Terms
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.