Ctla4 MGI Mouse Gene Detail - MGI:88556 - cytotoxic T-lymphocyte-associated protein 4

Symbol

Ctla4
Name

cytotoxic T-lymphocyte-associated protein 4
Synonyms

Cd152, Ctla-4, Ly-56

Feature Type

protein coding gene
IDs

MGI:88556
NCBI Gene: 12477
Alliance

genome feature page
Transcription Start Sites

12 TSS
Candidate for QTL

2 QTL

Sequence Map

Chr1:60948184-60954991 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 30.58 cM, cytoband C
Mapping Data

47 experiments

SNPs within 2kb

73 from dbSNP Build 142
Strain Annotations

18
PCR

1
RFLP

5

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_88556	protein coding gene	Chr1:60926159-60954991 (+)
129S1/SvImJ	ENSMUSG00200018201	protein coding gene	Chr1:58448107-58454910 (+)
A/J	ENSMUSG00195027122	protein coding gene	Chr1:57987436-57994242 (+)
AKR/J	no annotation
BALB/cJ	ENSMUSG00180013570	protein coding gene	Chr1:58241954-58248743 (+)
C3H/HeJ	ENSMUSG00175000983	protein coding gene	Chr1:58364757-58371560 (+)
C57BL/6NJ	ENSMUSG00215030092	protein coding gene	Chr1:58296673-58303481 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014192	protein coding gene	Chr1:55010456-55039392 (+)
CAST/EiJ	ENSTCUG00005012584	protein coding gene	Chr1:58129924-58136726 (+)
CBA/J	ENSMUSG00210033645	protein coding gene	Chr1:58050451-58057255 (+)
DBA/2J	ENSMUSG00185038648	protein coding gene	Chr1:59169509-59176312 (+)
FVB/NJ	ENSMUSG00205011655	protein coding gene	Chr1:58002297-58009100 (+)
JF1/MsJ	ENSUMUG00000035273	protein coding gene	Chr1:58129807-58136565 (+)
LP/J	ENSMUSG00230025136	protein coding gene	Chr1:59169967-59176770 (+)
NOD/ShiLtJ	ENSMUSG00190028578	protein coding gene	Chr1:58234942-58241729 (+)
NZO/HlLtJ	ENSMUSG00225000638	protein coding gene	Chr1:62394052-62400840 (+)
PWK/PhJ	ENSLUMG00010024779	protein coding gene	Chr1:57656945-57663745 (+)
SPRET/EiJ	ENSMSPG00010023315	protein coding gene	Chr1:59594086-59599821 (+)
WSB/EiJ	ENSIUOG00005019777	protein coding gene	Chr1:57832179-57838978 (+)

Human Ortholog

CTLA4, cytotoxic T-lymphocyte associated protein 4

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CTLA4, cytotoxic T-lymphocyte associated protein 4
Synonyms

ALPS5, CD, CD152, CELIAC3, CTLA-4, GRD4, GSE, IDDM12
Links

HGNC:2505

NCBI Gene ID: 1493

UniProt: P16410
Chr Location

2q33.2; chr2:203853888-203873965 (+) GRCh38

MGI Vertebrate Homology

Ctla4 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: CTLA4
Gene Tree

Ctla4

Diseases

42 with human CTLA4 associations

				Human Disease	Mouse Models
				acute myeloid leukemia IDs acute myeloid leukemia DOID:9119 DOID:9118 DOID:9171 ICD10CM:C92.0 ICD9CM:205.0 KEGG:05221 MESH:D015470 NCI:C3171 OMIM:601626 UMLS_CUI:C0023467
				alcohol-associated liver disease IDs alcohol-associated liver disease DOID:0070658 ICD10CM:K70 ICD9CM:571.3 MESH:D008108 NCI:C34783 UMLS_CUI:C0023896
				alopecia areata IDs alopecia areata DOID:986 EFO:0004192 ICD10CM:L63 ICD9CM:704.01 MESH:D000506 OMIM:104000 OMIM:610753 UMLS_CUI:C0002171
				anti-basement membrane glomerulonephritis IDs anti-basement membrane glomerulonephritis DOID:4780 NCI:C35798 UMLS_CUI:C1332309
				asthma IDs asthma DOID:2841 DOID:12703 DOID:13829 DOID:13830 DOID:2840 DOID:5783 ICD10CM:J45 ICD9CM:493 ICD9CM:493.9 KEGG:05310 MESH:D001249 NCI:C28397 OMIM:600807 UMLS_CUI:C0004096
				atopic dermatitis IDs atopic dermatitis DOID:3310 EFO:0000274 ICD10CM:L20 MESH:D003876 NCI:C211594 OMIM:603165 OMIM:PS603165 UMLS_CUI:C0011615
				autoimmune hemolytic anemia IDs autoimmune hemolytic anemia DOID:718 ICD9CM:283.0 MESH:D000744 NCI:C34378 OMIM:205700 UMLS_CUI:C0002880
				autoimmune hepatitis IDs autoimmune hepatitis DOID:2048 DOID:4745 ICD9CM:571.42 MESH:D019693 NCI:C27778 UMLS_CUI:C0241910 UMLS_CUI:C1332355
				autoimmune thyroiditis IDs autoimmune thyroiditis DOID:7188 DOID:0050435 ICD10CM:E06.3 MESH:D013967 NCI:C38766 UMLS_CUI:C0920350
				basal cell carcinoma IDs basal cell carcinoma DOID:2513 DOID:4275 DOID:4276 EFO:0004193 KEGG:05217 MESH:D018295 NCI:C156767 NCI:C3784 UMLS_CUI:C0007117 UMLS_CUI:C0206710 UMLS_CUI:C1368295
				Behcet's disease IDs Behcet's disease DOID:13241 EFO:0003780 ICD10CM:M35.2 ICD9CM:136.1 ICD9CM_2006:136.1 MESH:D001528 NCI:C34416 OMIM:109650 UMLS_CUI:C0004943
				breast cancer IDs breast cancer DOID:1612 DOID:1648 DOID:4241 ICD10CM:C50 ICD9CM:174.8 MESH:D001943 NCI:C9335 OMIM:114480 UMLS_CUI:C0006142
				celiac disease IDs celiac disease DOID:10608 EFO:0001060 ICD10CM:K90.0 ICD9CM:579.0 MESH:D002446 NCI:C26714 OMIM:607202 OMIM:609754 OMIM:611598 OMIM:612005 OMIM:612006 OMIM:612007 OMIM:612008 OMIM:612009 OMIM:612011 ORDO:555 UMLS_CUI:C0007570
				chronic obstructive pulmonary disease IDs chronic obstructive pulmonary disease DOID:3083 DOID:11500 DOID:6144 EFO:0000341 ICD10CM:J44.9 MESH:D029424 NCI:C3199 OMIM:606963 UMLS_CUI:C0024117
				end stage renal disease IDs end stage renal disease DOID:783
				graft-versus-host disease IDs graft-versus-host disease DOID:0081267 MESH:D006086 OMIM:614395 ORDO:39812
				granulomatosis with polyangiitis IDs granulomatosis with polyangiitis DOID:12132 ICD10CM:M31.3 ICD9CM:446.4 MESH:D014890 NCI:C3444 OMIM:608710 UMLS_CUI:C3495801
				Graves ophthalmopathy IDs Graves ophthalmopathy DOID:0081120 MESH:D049970
				Graves' disease IDs Graves' disease DOID:12361 EFO:0004237 ICD10CM:E05.0 MESH:D006111 NCI:C3071 OMIM:275000 UMLS_CUI:C0018213
				hepatitis B IDs hepatitis B DOID:2043 DOID:12591 DOID:12592 DOID:2042 EFO:0004197 MESH:D006509 NCI:C3097 UMLS_CUI:C0019163
				hepatocellular carcinoma IDs hepatocellular carcinoma DOID:684 DOID:5005 EFO:0000182 ICD10CM:C22.0 MESH:D006528 NCI:C3099 OMIM:114550 ORDO:88673 UMLS_CUI:C2239176
				immunoglobulin alpha deficiency IDs immunoglobulin alpha deficiency DOID:0060025 MESH:D017098 OMIM:137100 OMIM:269650 OMIM:609529 ORDO:69127 UMLS_CUI:C0162538
				iridocyclitis IDs iridocyclitis DOID:9383 DOID:9376 DOID:9380 ICD10CM:H20.01 ICD9CM:364.01 ICD9CM:364.2 UMLS_CUI:C0007832 UMLS_CUI:C0154909
				kidney disease IDs kidney disease DOID:557 EFO:0003086 ICD10CM:N08 ICD9CM:588.8 ICD9CM:588.89 MESH:D007674 NCI:C3149 UMLS_CUI:C0022658
				latent autoimmune diabetes in adults IDs latent autoimmune diabetes in adults DOID:0080846 MESH:D000071698
				lupus nephritis IDs lupus nephritis DOID:0080162 MESH:D008181
				melanoma IDs melanoma DOID:1909 EFO:0000756 KEGG:05218 MESH:D008545 NCI:C3224 UMLS_CUI:C0025202
				monoclonal gammopathy of uncertain significance IDs monoclonal gammopathy of uncertain significance DOID:7442
				multiple myeloma IDs multiple myeloma DOID:9538 EFO:0001378 ICD10CM:C90.0 ICD9CM:203.0 MESH:D009101 NCI:C3242 OMIM:254500 ORDO:29073 UMLS_CUI:C0026764
				multiple sclerosis IDs multiple sclerosis DOID:2377 ICD10CM:G35 ICD9CM:340 MESH:D009103 NCI:C3243 OMIM:612594 OMIM:612595 OMIM:612596 UMLS_CUI:C0026769
				myocardial infarction IDs myocardial infarction DOID:5844 EFO:0000612 ICD10CM:I21 MESH:D009203 NCI:C27996 OMIM:608557 UMLS_CUI:C0027051
				non-Hodgkin lymphoma IDs non-Hodgkin lymphoma DOID:0060060 ICD10CM:C85.9 MESH:D008228 NCI:C3211 OMIM:605027 ORDO:547 UMLS_CUI:C0024305
				primary biliary cholangitis IDs primary biliary cholangitis DOID:12236 DOID:1851 EFO:0004267 ICD10CM:K74.3 ICD10CM:K74.5 ICD9CM:571.6 MESH:D008105 NCI:C27167 NCI:C51225 OMIM:PS109720 ORDO:186 UMLS_CUI:C0008312 UMLS_CUI:C0023892
				psoriasis IDs psoriasis DOID:8893 EFO:0000676 ICD10CM:L40 MESH:D011565 NCI:C3346 OMIM:PS177900 UMLS_CUI:C0033860
				renal cell carcinoma IDs renal cell carcinoma DOID:4450 EFO:0000681 MESH:D002292 NCI:C9385 OMIM:300854 ORDO:217071 UMLS_CUI:C0007134
				sarcoidosis IDs sarcoidosis DOID:11335 ICD10CM:D86 ICD9CM:135 MESH:D012507 NCI:C34995 ORDO:797 UMLS_CUI:C0036202
				Sjogren's syndrome IDs Sjogren's syndrome DOID:12894 DOID:416 ICD10CM:M35.0 ICD9CM:710.2 MESH:D012859 NCI:C26883 NCI:C70647 OMIM:270150 UMLS_CUI:C0086981 UMLS_CUI:C1527336
				squamous cell carcinoma IDs squamous cell carcinoma DOID:1749 DOID:5512 EFO:0000707 MESH:D002294 MESH:D018307 NCI:C2929 UMLS_CUI:C0007137 UMLS_CUI:C0751688
				systemic lupus erythematosus IDs systemic lupus erythematosus DOID:9074 ICD10CM:M32.9 ICD9CM:710.0 KEGG:05322 MESH:D008180 NCI:C3201 OMIM:152700 OMIM:300809 OMIM:605480 OMIM:608437 OMIM:609903 OMIM:609939 OMIM:610065 OMIM:610066 OMIM:612254 OMIM:612378 OMIM:613145 OMIM:614420 ORDO:536 UMLS_CUI:C0024141
				type 1 diabetes mellitus IDs type 1 diabetes mellitus DOID:9744 ICD10CM:E10 KEGG:04940 MESH:D003922 NCI:C2986 OMIM:222100 UMLS_CUI:C0011854
				urinary schistosomiasis IDs urinary schistosomiasis DOID:1394 ICD9CM:120.0 ICD9CM_2006:120.0 MESH:D012553 NCI:C39294 UMLS_CUI:C0276926
				vitiligo IDs vitiligo DOID:12306 EFO:0004208 ICD10CM:L80 ICD9CM:709.01 MESH:D014820 NCI:C26915 OMIM:193200 UMLS_CUI:C0042900

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

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Phenotype Summary

45 phenotypes from 6 alleles in 10 genetic backgrounds
29 phenotypes from multigenic genotypes
140 phenotype references

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

31
Chemically induced (ENU)

1
Chemically induced (other)

1
Endonuclease-mediated

13
Radiation induced

1
Targeted

14
Transgenic

1
Genomic Mutations

2 involving Ctla4
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

31 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit lethality at 3 to 4 weeks of age, decreased T cell numbers, abnormal T cell physiology, inflammation in mutliple organs, abnormal thymus morphology, and lymph node hypoplasia.

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All GO Annotations

28
GO References

9

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

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

597
cDNA Data

18

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

47
RefSeq

6
UniProt

7
CCDS

CCDS14993.1, CCDS69893.1

Ensembl

ENSMUSG00000026011 (Evidence)
NCBI Gene

12477

			Length	Strain/Species	Flank
genomic	12477	NCBI Gene Model \| MGI Sequence Detail	6808	C57BL/6J	± kb
transcript	NM_009843	RefSeq \| MGI Sequence Detail	1933	ZRU/MplStud
polypeptide	P09793	UniProt \| EBI \| MGI Sequence Detail	223	Not Applicable

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UniProt

7 Sequences
Protein Ontology

PR:000001852 cytotoxic T-lymphocyte protein 4

(term hierarchy)
PDB

1DQT, 5E56, 5E5M, 9DQ4, 9DQ5
InterPro Domains

IPR008096 Cytotoxic T-lymphocyte antigen 4

IPR040216 Cytotoxic T-lymphocyte protein 4/CD28

IPR003599 Immunoglobulin domain subtype

IPR007110 Immunoglobulin-like domain

IPR036179 Immunoglobulin-like domain superfamily

IPR013783 Immunoglobulin-like fold

IPR013106 Immunoglobulin V-set domain
GlyGen

P09793 3 sites, 1 N-linked glycan (1 site)

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All nucleic 22

Genomic 2

cDNA 19

Primer pair 1

Microarray probesets 3

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MGD-MRK-2224, MGD-MRK-2234

Summaries

All 496

Gene Ontology 9

Phenotypes 140
Earliest

J:134667 Roderick TH, et al., Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci U S A. 1970 Oct;67(2):961-7
Latest

J:378405 Ge X, et al., Targeting LRBA triggers CTLA4 degradation and antitumor immunity for cancer immunotherapy. Nat Commun. 2025 Dec 14;17(1):623

TSS for Ctla4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr6954	Chr1:60948152-60948192 (+)	-12 bp
Tssr6955	Chr1:60948244-60948261 (+)	69 bp
Tssr6956	Chr1:60948307-60948318 (+)	129 bp
Tssr6957	Chr1:60948382-60948425 (+)	220 bp
Tssr6958	Chr1:60948509-60948515 (+)	328 bp
Tssr6959	Chr1:60950226-60950231 (+)	2,045 bp
Tssr6960	Chr1:60950240-60950253 (+)	2,063 bp
Tssr6961	Chr1:60950271-60950281 (+)	2,092 bp
Tssr6962	Chr1:60951084-60951091 (+)	2,904 bp
Tssr6963	Chr1:60952825-60952831 (+)	4,644 bp
Tssr6964	Chr1:60953079-60953093 (+)	4,902 bp
Tssr6965	Chr1:60953783-60953819 (+)	5,617 bp

Ctla4 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Idd5	Chr1, syntenic		J:71276	The authors mention the following genes mapping near Idd5 as possible candidates: Bcl2, Casp8, and Ctla4.
Idd5.1	Chr1, syntenic	Chr1:57728276-62946882	J:83656	Ctla4 is a previously identified candidate gene for the diabetes susceptibility QTL Idd5a. A silent polymorphism was previously identified in exon2 of Ctla4. In this study a splice variant of Ctla4 was identified that is generated by the skipping of exon2. This isoform encodes a transmembrane protein lacking the CD80/CD86 binding domain and is expressed four-fold greater in activated and resting spleen cells of diabetes resistant strains C57BL/10J and C57BL/6J. It is believed that an exon 2 SNP at nucleotide 77 is responsible forthe difference in mRNA expression. Resistant strains C57BL/10J and C57BL/6J carry an A allele at nucleotide 77 whereas susceptible strain NOD carries the mutant G allele.

*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)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 09/01/2026 MGI 6.24