Capn3 MGI Mouse Gene Detail - MGI:107437 - calpain 3

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Capn3 Gene Detail

Symbol

Capn3
Name

calpain 3
Synonyms

Capa-3, Capa3, Lp82, p94

Feature Type

protein coding gene
IDs

MGI:107437
NCBI Gene: 12335
Alliance

genome feature page
Transcription Start Sites

18 TSS
Candidate for QTL

1 QTL

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Sequence Map

Chr2:120294074-120335400 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 60.31 cM
Mapping Data

6 experiments

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SNPs within 2kb

1181 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates	Select Strains
C57BL/6J	MGI_C57BL6J_107437	protein coding gene	Chr2:120294053-120335400 (+)
129S1/SvImJ	ENSMUSG00200046091	protein coding gene	Chr2:117240767-117282241 (+)
A/J	ENSMUSG00195023997	protein coding gene	Chr2:117279950-117321361 (+)
AKR/J	ENSMUSG00220039997	protein coding gene	Chr2:117205000-117246489 (+)
BALB/cJ	ENSMUSG00180040536	protein coding gene	Chr2:117080585-117122019 (+)
C3H/HeJ	ENSMUSG00175026478	protein coding gene	Chr2:117554029-117598184 (+)
C57BL/6NJ	ENSMUSG00215010014	protein coding gene	Chr2:117212311-117253677 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024168	protein coding gene	Chr2:113291076-113339589 (+)
CAST/EiJ	ENSTCUG00005016733	protein coding gene	Chr2:116484677-116526104 (+)
CBA/J	ENSMUSG00210007224	protein coding gene	Chr2:117394989-117439138 (+)
DBA/2J	ENSMUSG00185045144	protein coding gene	Chr2:117077949-117119369 (+)
FVB/NJ	ENSMUSG00205033514	protein coding gene	Chr2:116305684-116347163 (+)
JF1/MsJ	ENSUMUG00000030813	protein coding gene	Chr2:116960433-117001806 (+)
LP/J	ENSMUSG00230017854	protein coding gene	Chr2:118900519-118943147 (+)
NOD/ShiLtJ	ENSMUSG00190036585	protein coding gene	Chr2:117323216-117367365 (+)
NZO/HlLtJ	ENSMUSG00225002039	protein coding gene	Chr2:126836706-126847008 (+)
PWK/PhJ	ENSLUMG00010041111	protein coding gene	Chr2:116856192-116897432 (+)
SPRET/EiJ	ENSMSPG00010033126	protein coding gene	Chr2:119274042-119314778 (+)
WSB/EiJ	ENSIUOG00005023422	protein coding gene	Chr2:117054026-117095357 (+)

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Human Ortholog

CAPN3, calpain 3

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CAPN3, calpain 3
Synonyms

CANP3, CANPL3, LGMD2, LGMD2A, LGMDD4, LGMDR1, nCL-1, p94
Links

HGNC:1480

NCBI Gene ID: 825

UniProt: P20807
Chr Location

15q15.1; chr15:42359498-42412949 (+) GRCh38

MGI Vertebrate Homology

Capn3 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: CAPN3
Gene Tree

Capn3

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Diseases

1 with Capn3 mouse models; 3 with human CAPN3 associations

Human Disease

Mouse Models

Human and Mouse genes associated with disease

Human and Mouse genes associated with disease

autosomal recessive limb-girdle muscular dystrophy type 2A

IDs

View 3 models

Human gene associated with disease

autosomal dominant limb-girdle muscular dystrophy

IDs

muscular dystrophy

IDs

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

Mutations/Alleles

3 with disease annotations

References

4 with disease annotations

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Phenotype Summary

21 phenotypes from 12 alleles in 4 genetic backgrounds
4 phenotypes from multigenic genotypes
3 images
37 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

26
Chemically induced (other)

1
Endonuclease-mediated

7
Gene trapped

1
Radiation induced

1
Targeted

6
Transgenic

10
Genomic Mutations

2 involving Capn3
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

50 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous mutation of this gene results in muscle dystrophy. The psoas, soleus, and deltoid muscles are the most severely affected. The mutant allele appears to be preferentially transmitted resulting in ratio distortion.

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All GO Annotations

110
GO References

18

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

748
Tissues

46
cDNA Data

36
Literature Summary

12

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA CAPN3

Xenbase capn3

ZFIN capn3a

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All Sequences

87
RefSeq

6
UniProt

18
CCDS

CCDS16620.1, CCDS50679.1, CCDS50680.1

Ensembl

ENSMUSG00000079110 (Evidence)
NCBI Gene

12335

Representative Sequences				Length	Strain/Species	Flank
	genomic	12335	NCBI Gene Model \| MGI Sequence Detail	41327	C57BL/6J	± kb
	transcript	NM_007601	RefSeq \| MGI Sequence Detail	3167	ZRU/MplStud
	polypeptide	Q64691	UniProt \| EBI \| MGI Sequence Detail	821	Not Applicable

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UniProt

18 Sequences
Protein Ontology

PR:000005016 calpain-3

(term hierarchy)
EC

3.4.22.54
InterPro Domains

IPR054069 Calpain-3/13-like, C-terminal EF-hand

IPR029531 Calpain-3, penta-EF-hand

IPR032100 Calpain-3, unstructured region

IPR036213 Calpain large subunit, domain III superfamily

IPR033883 Calpain subdomain III

IPR000169 Cysteine peptidase, cysteine active site

IPR018247 EF-Hand 1, calcium-binding site

IPR002048 EF-hand domain

IPR011992 EF-hand domain pair

IPR038765 Papain-like cysteine peptidase superfamily

IPR001300 Peptidase C2, calpain, catalytic domain

IPR022683 Peptidase C2, calpain, domain III

IPR022684 Peptidase C2, calpain family

IPR022682 Peptidase C2, calpain, large subunit, domain III
GlyGen

Q64691 1 site

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All nucleic 82

Genomic 26

cDNA 38

Primer pair 8

Other 10

Antibodies 2

Microarray probesets 6

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MGD-MRK-1752, MGD-MRK-1756, MGD-MRK-35908, MGI:2138901, MGI:88265

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Summaries

All 112

Developmental Gene Expression 12

Diseases 4

Gene Ontology 18

Phenotypes 37
Earliest

J:109968 Roderick TH, et al., Nineteen paracentric chromosomal inversions in mice. Genetics. 1974 Jan;76(1):109-17
Latest

J:388222 Sudkamp N, et al., Evaluation of quantitative muscle MRI and an intelligent phenotyping housing system as advanced phenotyping methods in a mouse model of calpain 3-deficient muscular dystrophy. Animal Model Exp Med. 2026 Apr 6;

TSS for Capn3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr19693	Chr2:120294047-120294075 (+)	-13 bp
Tssr19694	Chr2:120307331-120307332 (+)	13,258 bp
Tssr19695	Chr2:120307382-120307385 (+)	13,310 bp
Tssr19696	Chr2:120307392-120307405 (+)	13,325 bp
Tssr619	Chr2:120310773-120310788 (+)	16,707 bp
Tssr19697	Chr2:120312430-120312456 (+)	18,369 bp
Tssr19698	Chr2:120314812-120314823 (+)	20,744 bp
Tssr19699	Chr2:120314824-120314836 (+)	20,756 bp
Tssr19700	Chr2:120314840-120314855 (+)	20,774 bp
Tssr19701	Chr2:120320564-120320594 (+)	26,505 bp
Tssr19702	Chr2:120330535-120330547 (+)	36,467 bp
Tssr19703	Chr2:120330938-120330949 (+)	36,870 bp
Tssr19704	Chr2:120331692-120331734 (+)	37,639 bp
Tssr620	Chr2:120331741-120331751 (+)	37,672 bp
Tssr19705	Chr2:120331788-120331816 (+)	37,728 bp
Tssr19706	Chr2:120332299-120332310 (+)	38,231 bp
Tssr19707	Chr2:120332800-120332813 (+)	38,733 bp
Tssr19708	Chr2:120332991-120333013 (+)	38,928 bp

Capn3 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Cdcs3	Chr2, 59.34 cM		J:109420	Microarray analysis was used to identify candidate genes for colitis susceptibility QTLs. Messenger RNA was analyzed for expression differences between colitis susceptible inbred strain C3H/HeJBir-Il10 and colitis resistant inbred strain C57BL/6J-Il10. Capn3 (67.2 cM) on mouse Chromosome 2 is upregulated 1.5- to 2-fold in C3H/HeJBir-Il10 animals. This candidate gene maps to the Cdcs3 (cytokine deficiency colitis susceptibility 3) interval centered near 65 cM. Gbp1 (67.4 cM) on mouse Chromosome 3 is upregulated over 15-fold in C3H/HeJBir-Il10 animals. This candidate gene is known to be polymorphic between C3H/HeJBir and C57BL/6J and exhibits expression differences in these parental wild type strains. Gbp1 maps to the Cdcs1 (cytokine deficiency colitis susceptibility 1) interval centered near 62 cM. Adh1 at 71.2 cM and Bglap2 at 42.6 cM also map to the same QTL interval. Adh1 is upregulated 1.5- to 2-fold, and Blgap2 is upregulated 2- to 5-fold, in C3H/HeJBir-Il10animals. Pla2g2a (68 cM) on mouse Chromosome 4 is upregulated over 15-fold in C3H/HeJBir-Il10 animals. This candidate gene is known to be polymorphic between C3H/HeJBir and C57BL/6J and exhibits expression differences in these parental wild typestrains. Pla2g2a maps to the Cdcs9 (cytokine deficiency colitis susceptibility 9) interval centered near 71 cM. Moreover, C57BL/6J animals are known to carry the frameshift mutation Pla2g2a resulting in multiple intestinal neoplasia. The human ortholog PLA2G2A maps near a irritable bowel disorder (IBD) susceptibility locus named IBD7. Gnb1 (79.4 cM) also maps to the Cdcs9 QTL interval and is upregulated 2- to 5-fold in C57BL/6J-Il10 animals. Errfi1 (formerly 1300002F13Rik) and Tceb3 also map to the Cdcs9 interval and are upregulated 1.5- to 2-fold in C57BL/6J-Il10 animals. Areg (51 cM) on mouse Chromosome 5 maps near the Cdcs10 QTL interval centered around 45 cM. This candidate gene is upregulated 1.5- to 2-fold in C57BL/6J-Il10 animals. Mtmr7 maps to mouse Chromosome 8 near the Cdcs4 interval centered around 21 cM. This candidate gene is upregulated over 15-fold in C57BL/6J-Il10 animals. Cd14 (31 cM) on mouse Chromosome 18 is upregulated 5- to 15-fold in C3H/HeJBir-Il10 animals. CD14 also exhibits expression differences in parental wild type strains C3H/HeJBir and C57BL/6J. This candidate gene maps to the Cdcs6 (cytokine deficiency colitis susceptibility 6) interval centered near 41 cM. The human ortholog CD14 maps near a human irritable bowel disorder (IBD) susceptibility locus named IBD5. Glo1 (16 cM) and Ly6g6c on mouse Chromosome 17 are upregulated 2- to 5-fold in C57BL/6J-Il10 animals. This candidate gene maps to the Cdcs5 (cytokine deficiency colitis susceptibility 5) interval centered near 19 cM. Hspa1a (18.9 cM) and Hspa1b (18.9 cM) also map to Cdcs5 and are upregulated 1.5- to 2-fold in C57BL/6J-Il10 animals.

*cM position of peak correlated region/marker

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