Kdm5c MGI Mouse Gene Detail - MGI:99781 - lysine demethylase 5C

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Kdm5c Gene Detail

Symbol

Kdm5c
Name

lysine demethylase 5C
Synonyms

D930009K15Rik, Jarid1c, mKIAA0234, Smcx

Feature Type

protein coding gene
IDs

MGI:99781
NCBI Gene: 20591
Alliance

genome feature page
Transcription Start Sites

4 TSS
Candidate for QTL

3 QTL

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Sequence Map

ChrX:151016016-151057531 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome X, 68.46 cM, cytoband F2-F4
Mapping Data

16 experiments

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SNPs within 2kb

749 from dbSNP Build 142
Strain Annotations

19
RFLP

2

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates	Select Strains
C57BL/6J	MGI_C57BL6J_99781	protein coding gene	ChrX:151015698-151062098 (+)
129S1/SvImJ	ENSMUSG00200031334	protein coding gene	ChrX:127822423-127863940 (+)
A/J	ENSMUSG00195020607	protein coding gene	ChrX:132820512-132862023 (+)
AKR/J	ENSMUSG00220031291	protein coding gene	ChrX:124831245-124872736 (+)
BALB/cJ	ENSMUSG00180038276	protein coding gene	ChrX:128196304-128237813 (+)
C3H/HeJ	ENSMUSG00175028541	protein coding gene	ChrX:132731062-132772578 (+)
C57BL/6NJ	ENSMUSG00215021063	protein coding gene	ChrX:128496204-128537720 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0033500	protein coding gene	ChrX:140873370-140914963 (+)
CAST/EiJ	ENSTCUG00005033442	protein coding gene	ChrX:130520112-130561775 (+)
CBA/J	ENSMUSG00210031510	protein coding gene	ChrX:130208393-130249910 (+)
DBA/2J	ENSMUSG00185042539	protein coding gene	ChrX:145029884-145071399 (+)
FVB/NJ	ENSMUSG00205016601	protein coding gene	ChrX:128777745-128819257 (+)
JF1/MsJ	ENSUMUG00000039265	protein coding gene	ChrX:165229563-165271354 (+)
LP/J	ENSMUSG00230013202	protein coding gene	ChrX:151831764-151873279 (+)
NOD/ShiLtJ	ENSMUSG00190026968	protein coding gene	ChrX:129314798-129356302 (+)
NZO/HlLtJ	ENSMUSG00225042128	protein coding gene	ChrX:155328772-155370287 (+)
PWK/PhJ	ENSLUMG00010032202	protein coding gene	ChrX:126753552-126795276 (+)
SPRET/EiJ	ENSMSPG00010037333	protein coding gene	ChrX:131615331-131656812 (+)
WSB/EiJ	ENSIUOG00005038309	protein coding gene	ChrX:129785743-129827252 (+)

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Human Ortholog

KDM5C, lysine demethylase 5C

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

KDM5C, lysine demethylase 5C
Synonyms

DXS1272E, JARID1C, MRX13, MRXJ, MRXS16, MRXSCJ, MRXSJ, SMCX, XE169
Links

HGNC:11114

NCBI Gene ID: 8242

UniProt: P41229
Chr Location

Xp11.22; chrX:53176277-53225422 (-) GRCh38

MGI Vertebrate Homology

Kdm5c stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: KDM5C
Gene Tree

Kdm5c

more

Diseases

1 with Kdm5c mouse models; 2 with human KDM5C associations

Human Disease

Mouse Models

Human and Mouse genes associated with disease

Human and Mouse genes associated with disease

syndromic X-linked intellectual disability Claes-Jensen type

IDs

View 1 model

Human gene associated with disease

descending colon cancer

IDs

Click on a disease name to see all genes associated with that disease.

Mutations/Alleles

1 with disease annotations

References

1 with disease annotations

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Phenotype Summary

22 phenotypes from 4 alleles in 4 genetic backgrounds
13 images
26 phenotype references

Phenotype Overview

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

38
Endonuclease-mediated

7
Gene trapped

24
Targeted

7
Find Mice (IMSR)

22 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Male chimeras hemizygous for a gene trapped allele exhibit posterior patterning defects and abnormal heart morphology at E9.5. Chimeras hemizygous for a different gene trapped allele appear normal at E10.5.

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All GO Annotations

28
GO References

12

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

727
Tissues

73
cDNA Data

29
Literature Summary

23

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase kdm5c

ZFIN kdm5c

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All Sequences

95
RefSeq

23
UniProt

5
CCDS

CCDS41178.1

Ensembl

ENSMUSG00000025332 (Evidence)
NCBI Gene

20591

Representative Sequences				Length	Strain/Species	Flank
	genomic	ENSMUSG00000025332	Ensembl Gene Model \| MGI Sequence Detail	41516	C57BL/6J	± kb
	transcript	ENSMUST00000112584	Ensembl \| MGI Sequence Detail	5900	Not Applicable
	polypeptide	ENSMUSP00000108203	Ensembl \| MGI Sequence Detail	1554	Not Applicable

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UniProt

5 Sequences
Protein Ontology

PR:000009206 lysine-specific demethylase 5C

(term hierarchy)
EC

1.14.11.67
InterPro Domains

IPR001606 ARID DNA-binding domain

IPR036431 ARID DNA-binding domain superfamily

IPR003347 JmjC domain

IPR003349 JmjN domain

IPR048615 Lysine-specific demethylase 5, C-terminal helical domain

IPR013637 Lysine-specific demethylase-like domain

IPR004198 Zinc finger, C5HC2-type

IPR011011 Zinc finger, FYVE/PHD-type

IPR019787 Zinc finger, PHD-finger

IPR001965 Zinc finger, PHD-type

IPR019786 Zinc finger, PHD-type, conserved site

IPR013083 Zinc finger, RING/FYVE/PHD-type
GlyGen

P41230 1 site, 1 N-linked glycan (1 site)

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All nucleic 43

Genomic 4

cDNA 32

Primer pair 5

Other 2

Antibodies 1

Microarray probesets 8

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MGD-MRK-16567, MGI:3026968

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Summaries

All 117

Developmental Gene Expression 23

Diseases 1

Gene Ontology 12

Phenotypes 26
Earliest

J:18900 Agulnik AI, et al., A mouse Y chromosome gene encoded by a region essential for spermatogenesis and expression of male-specific minor histocompatibility antigens. Hum Mol Genet. 1994 Jun;3(6):873-8
Latest

J:390091 Peeters S, et al., Escape from X-chromosome inactivation at KDM5C is driven by promoter-proximal DNA elements and enhanced by domain context. Hum Mol Genet. 2025 May 17;34(11):978-989

TSS for Kdm5c:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr162388	ChrX:151016224-151016256 (+)	224 bp
Tssr162389	ChrX:151018950-151018953 (+)	2,936 bp
Tssr162390	ChrX:151034272-151034276 (+)	18,258 bp
Tssr162391	ChrX:151056884-151056888 (+)	40,870 bp

Kdm5c is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Bw19	ChrX, 24.88 cM	ChrX:46376920-52412327	J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome X, Atp6ap1 (29.8 cM), Flna (29.8 cM), and Gdi1 (29.8 cM) all show differential expression between A/a and A/A animals on the restricted diet. Diabesity QTLs Bw19 (26.4 cM) and C10bw6 (32 cM) map near these candidate genes. Jarid1c (64 cM) shows differential expression between the restricted and unrestricted diets on the A/A background. Diabesity QTL Dob7 (59.5 cM) maps near Jarid1c.
C10bw6	ChrX, 30.84 cM		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome X, Atp6ap1 (29.8 cM), Flna (29.8 cM), and Gdi1 (29.8 cM) all show differential expression between A/a and A/A animals on the restricted diet. Diabesity QTLs Bw19 (26.4 cM) and C10bw6 (32 cM) map near these candidate genes. Jarid1c (64 cM) shows differential expression between the restricted and unrestricted diets on the A/A background. Diabesity QTL Dob7 (59.5 cM) maps near Jarid1c.
Dob7	ChrX, 57.38 cM		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome X, Atp6ap1 (29.8 cM), Flna (29.8 cM), and Gdi1 (29.8 cM) all show differential expression between A/a and A/A animals on the restricted diet. Diabesity QTLs Bw19 (26.4 cM) and C10bw6 (32 cM) map near these candidate genes. Jarid1c (64 cM) shows differential expression between the restricted and unrestricted diets on the A/A background. Diabesity QTL Dob7 (59.5 cM) maps near Jarid1c.

*cM position of peak correlated region/marker

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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