Phenotypic Mutation 'Lowe' (pdf version)
AlleleLowe
Mutation Type missense
Chromosome7
Coordinate125,166,393 bp (GRCm39)
Base Change T ⇒ C (forward strand)
Gene Il4ra
Gene Name interleukin 4 receptor, alpha
Synonym(s) IL-4 receptor alpha chain, CD124, Il4r
Chromosomal Location 125,151,443-125,178,646 bp (+) (GRCm39)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the alpha chain of the interleukin-4 receptor, a type I transmembrane protein that can bind interleukin 4 and interleukin 13 to regulate IgE production. The encoded protein also can bind interleukin 4 to promote differentiation of Th2 cells. A soluble form of the encoded protein can be produced by proteolysis of the membrane-bound protein, and this soluble form can inhibit IL4-mediated cell proliferation and IL5 upregulation by T-cells. Allelic variations in this gene have been associated with atopy, a condition that can manifest itself as allergic rhinitis, sinusitus, asthma, or eczema. Polymorphisms in this gene are also associated with resistance to human immunodeficiency virus type-1 infection. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2012]
PHENOTYPE: Nullizygous mice exhibit reduced T helper 2 cell response to N. brasiliensis infection. Homozygotes for a null allele also display severe susceptibility to S. mansoni infection, enhanced carcinogen-induced intestinal tumour initiation, and altered control of chronic Leishmania major infection. [provided by MGI curators]
Accession Number

NCBI RefSeq: NM_001008700; MGI:105367

MappedYes 
Amino Acid Change Tryptophan changed to Arginine
Institutional SourceBeutler Lab
Gene Model predicted gene model for protein(s): [ENSMUSP00000033004] [ENSMUSP00000145725] [ENSMUSP00000146185] [ENSMUSP00000145824]
AlphaFold P16382
SMART Domains Protein: ENSMUSP00000033004
Gene: ENSMUSG00000030748
AA Change: W46R

DomainStartEndE-ValueType
Pfam:IL4Ra_N 28 122 9.9e-39 PFAM
FN3 124 211 3.14e0 SMART
low complexity region 369 385 N/A INTRINSIC
low complexity region 562 574 N/A INTRINSIC
low complexity region 617 630 N/A INTRINSIC
low complexity region 635 647 N/A INTRINSIC
low complexity region 674 683 N/A INTRINSIC
Predicted Effect probably damaging

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000033004)
Predicted Effect probably damaging

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000205985)
Predicted Effect probably benign
Predicted Effect probably damaging

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000206846)
Meta Mutation Damage Score 0.8771 question?
Is this an essential gene? Probably nonessential (E-score: 0.072) question?
Phenotypic Category Unknown
Candidate Explorer Status loading ...
Single pedigree
Linkage Analysis Data
Penetrance  
Alleles Listed at MGI

All Mutations and Alleles(11) : Targeted(11)

Lab Alleles
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00940:Il4ra APN 7 125168347 critical splice donor site probably null
IGL01067:Il4ra APN 7 125174333 missense probably benign 0.09
IGL01107:Il4ra APN 7 125175086 missense possibly damaging 0.88
IGL02224:Il4ra APN 7 125169271 splice site probably benign
IGL02249:Il4ra APN 7 125166396 missense probably benign 0.01
IGL02383:Il4ra APN 7 125170676 missense probably benign 0.06
IGL02614:Il4ra APN 7 125174962 nonsense probably null
IGL02879:Il4ra APN 7 125176069 missense possibly damaging 0.88
Haile UTSW 7 125173889 critical splice donor site probably null
BB006:Il4ra UTSW 7 125174348 missense probably benign 0.00
BB016:Il4ra UTSW 7 125174348 missense probably benign 0.00
IGL02991:Il4ra UTSW 7 125174833 missense possibly damaging 0.70
PIT4418001:Il4ra UTSW 7 125175510 missense probably benign 0.01
R0066:Il4ra UTSW 7 125175403 missense possibly damaging 0.80
R0127:Il4ra UTSW 7 125168242 missense probably damaging 1.00
R0148:Il4ra UTSW 7 125174709 missense probably damaging 1.00
R0238:Il4ra UTSW 7 125174371 splice site probably benign
R0239:Il4ra UTSW 7 125174371 splice site probably benign
R0884:Il4ra UTSW 7 125173835 missense probably damaging 1.00
R1102:Il4ra UTSW 7 125173889 critical splice donor site probably null
R1622:Il4ra UTSW 7 125169225 missense possibly damaging 0.87
R1773:Il4ra UTSW 7 125166354 missense possibly damaging 0.94
R4510:Il4ra UTSW 7 125175280 missense possibly damaging 0.63
R4511:Il4ra UTSW 7 125175280 missense possibly damaging 0.63
R4612:Il4ra UTSW 7 125175255 missense probably benign 0.14
R5865:Il4ra UTSW 7 125174348 missense probably benign 0.00
R5996:Il4ra UTSW 7 125166393 missense probably damaging 1.00
R6057:Il4ra UTSW 7 125170735 missense probably damaging 1.00
R6246:Il4ra UTSW 7 125175577 missense probably benign 0.00
R7218:Il4ra UTSW 7 125174950 missense probably benign 0.01
R7624:Il4ra UTSW 7 125168280 missense probably damaging 1.00
R7904:Il4ra UTSW 7 125164845 missense probably benign 0.05
R7929:Il4ra UTSW 7 125174348 missense probably benign 0.00
R8360:Il4ra UTSW 7 125169138 missense probably damaging 1.00
R9573:Il4ra UTSW 7 125169158 missense possibly damaging 0.95
Mode of Inheritance Unknown
Local Stock
Repository
Last Updated 2019-09-04 9:37 PM by Diantha La Vine
Record Created 2018-04-29 6:31 AM by Bruce Beutler
Record Posted 2018-11-16
Phenotypic Description

Figure 1. Lowe mice exhibited reduced circulating total IgE levels. IgE levels were determined by ELISA. Normalized data are shown. Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

The Lowe phenotype was identified among G3 mice of the pedigree R5996, some of which showed reduced total serum IgE levels (Figure 1).

Nature of Mutation

Figure 2. Linkage mapping of the reduced IgE levels using an additive model of inheritance. Manhattan plot shows -log10 P values (Y-axis) plotted against the chromosome positions of 71 mutations (X-axis) identified in the G1 male of pedigree R5996. Log data are shown for single locus linkage analysis without consideration of G2 dam identity. Horizontal pink and red lines represent thresholds of P = 0.05, and the threshold for P = 0.05 after applying Bonferroni correction, respectively.

Whole exome HiSeq sequencing of the G1 grandsire identified 71 mutations. The IgE phenotype was linked by continuous variable mapping to a mutation in Il4ra:  a T to C transition at base pair 125,567,221 (v38) on chromosome 7, or base pair 14,940 in the GenBank genomic region NC_000073. Linkage was found with an additive model of inheritance, wherein six variant homozygotes and 26 heterozygous mice departed phenotypically from 25 homozygous reference mice with a P value of 1.9 x 10-5 (Figure 3).  

The mutation corresponds to residue 377 in the mRNA sequence NM_001008700 within exon 4 of 11 total exons.

362 ACTTCCACGTGTGAGTGGTTCCTGGATAGCGCT
41  -T--S--T--C--E--W--F--L--D--S--A-

The mutated nucleotide is indicated in red. The mutation results in a tryptophan to arginine substitution at position 46 (W46R) in the IL-4Rα protein, and is strongly predicted by Polyphen-2 to be damaging (score = 1.000).

Illustration of Mutations in
Gene & Protein
Protein Prediction
Figure 3. Domain organization of IL-4Rα. The Lowe mutation results in a tryptophan to arginine substitution at position 46 of the protein. This image is interactive. Other mutations found in IL-4Rα are noted. Click on each mutation to view more information. Abbreviations: SP, signal peptide; FNIII, fibronectin type-III; TM, transmembrane; ITIM, immunoreceptor tyrosine-based inhibition motif

Il4ra encodes IL-4Rα, the alpha chain of the IL-4 receptor. IL-4Rα is a member of the type I cytokine receptor family. IL-4Rα is a single-pass transmembrane domain with an extracellular N-terminal tail and a cytoplasmic C-terminal tail (1). IL-4Rα has a fibronectin type-III (FNIII) domain as well as WSXWS, box 1, and ITIM (immunoreceptor tyrosine-based inhibition motif) motifs (Figure 3). The WSXWS motif is putatively necessary for proper protein folding and efficient intracellular transport as well as cell-surface receptor binding. The box 1 motif is required for JAK interaction and/or activation (see the Background section for more information about the relationship between JAK proteins and IL-4Rα). The phosphorylated ITIM motif can bind the SH2 domain of several phosphatases including SHP1 (see the record for spin) and SHP2, which negatively regulate IL-4R function (2).

A soluble form of IL-4R (sIL-4R) is detected in biological fluids. The sIL-4R contains only the extracellular portion of the IL-4R, and is produced by alternative splicing of IL4R (the human homolog of Il4ra) and/or proteolysis of the receptor (3;4). sIL-4R blocks B cell binding of IL-4, B cell proliferation, and IgE and IgG1 secretion in vitro (5). In anti-IgD-treated mice, sIL-4R inhibits IgE production by up to 85 percent as well as reduces airway inflammation (6). While sIL-4R blocks the effects of IL-4, it does not block the effects of IL-13, which binds a receptor comprised of IL-4Rα and IL-13Rα1 chains. Therefore, it is not an optimal therapy for treatments of IgE-mediated inflammatory diseases (e.g., asthma) (7).

The Lowe mutation results in a tryptophan to arginine substitution at position 46 (W46R) in the IL-4Rα protein; Trp46 is within an undefined region in the extracellular portion of the protein.

Expression/Localization

IL-4R is expressed in hematopoietic, endothelial, epithelial, muscle, fibroblast, hepatocyte, and brain tissues (8;9).

Background
Figure 4. IL-4R signaling. IL-4Rα is a component of both the type I (i.e., IL-4Rα and IL-4Rγ) and type II (i.e., IL-4Rα and IL-13Rα1)  receptor complexes. The type I receptor recognizes IL-4, while the type II receptor can recognize either IL-4 or IL-13. The IL-4Rs are associated with the normally dephosphorylated and inactive JAK tyrosine kinases. Latent STAT proteins exist in the cytoplasm as a monomer. Upon receptor stimulation, JAK proteins phosphorylate the receptor cytoplasmic domains. STAT proteins are recruited to the receptor, tyrosine phosphorylated by JAKs, and dimerize for translocation to the nucleus. Suppressors of cytokine signaling (SOCS) proteins can directly bind and suppress JAKs or can compete with STATs for receptor binding. The tyrosine phosphatases SHP1 and SHP2 inhibit signaling by dephosphorylating STAT proteins.

IL-4Rα is a component of both the type I (i.e., IL-4Rα and IL-4Rγ) and type II (i.e., IL-4Rα and IL-13Rα1) IL-4R receptor complexes (Figure 4) (10-12). The type I IL-4R recognizes IL-4 and signals to JAK1, JAK2, and JAK3 (see the record for mount_tai) and STAT3/6 (see the record for Stationary), while the type II IL-4R receptor complex recognizes IL-13 and IL-4 to signal to JAK1/JAK2/TYK2 and STAT1/3/6 (13). In canonical JAK-STAT signaling, the STAT proteins serve the dual functions of signal transduction and activation of transcription. The STAT proteins are transcription factors found latent in the cytoplasm until they are activated by extracellular signaling proteins such as cytokines, growth factors, and peptides. The JAK-STAT pathway, begins with the binding of one or more cytokines to their cognate cell-surface receptors. These receptors are associated with JAK tyrosine kinases, which are normally dephosphorylated and inactive. Receptor stimulation results in dimerization/oligomerization and subsequent apposition of JAK proteins, which are now capable of trans-phosphorylation as they are brought in close proximity. This activates JAKs to phosphorylate the receptor cytoplasmic domains, creating phosphotyrosine ligands for the SH2 domains of STAT proteins. Once recruited to the receptor, STAT proteins are also tyrosine phosphorylated by JAKs, a phosphorylation event which occurs on a single tyrosine residue that is found at around residue 700 of all STATs. Tyrosine phosphorylation of STATs may allow formation and/or conformational reorganization of the activated STAT dimer, involving reciprocal SH2 domain-phosphotyrosine interactions between STAT monomers. Phosphorylated, activated STATs enter the nucleus and accumulate there to promote transcription. Termination of STAT signaling requires ending both transcriptional activation and cytoplasmic STAT signaling.

Several other signaling pathways are activated by IL-4Rα-associated receptors [reviewed in (14)]. (i) The PI3-kinase (PI3K) pathway can be activated through an interaction with IRS1 (see the record for runt)/IRS2 (see the record for Dum_dum) molecules at the phosphorylated IL-4Rα intracellular tail. The PI3K-IRS1/2 interaction results in IRS1/2 phosphorylation by IL-4R-associated kinases, the interaction of the PI3K p85 subunit with IRS1/2, the production of phosphoinositides, and the activation of downstream effectors AKT and PKC. AKT and PKC (see the record Rigged for information about PKCd) activation result in cell growth and survival. (ii) Phosphorylated IL-4Rα can also act as a docking site for the adapter SHC (see the record shrine for information about SHC2) and subsequent activation of small GTPases (e.g., Ras) in a cell type-specific manner. Ras activation would regulate cell growth and differentiation. (iii) The adaptor Cbl is phosphorylated in response to IL-4 (15). Cbl recruitment to the receptor putatively links Grb2/Sos to the receptor complex and promotes activation of the Ras/MAPK pathway (15). The functional significance of IL-4R-associated Cbl phosphorylation is unknown.

Mutations in IL4R (alternatively, IL4RA) are linked to atopy susceptibility [OMIM: #147050; (16-19)]. Atopy is a broad term that describes the development of allergic disease, such as allergic rhinitis, asthma, hay fever, and atopic dermatitis (eczema). Mutations in IL4R are also associated with slow progression to AIDS after HIV infection [OMIM: #609423; (20)]. IL-4 initiates HIV co-receptor (i.e., CXCR4 and DC-SIGN) expression (21) as well as stimulates HIV execution to hasten disease pathogenesis (22).

Aberrant IL-4R-associated signaling is also linked to the progression of individual allergic and autoimmune diseases such as asthma (23;24) and rheumatoid arthritis (25). During the pathogenesis of asthma IL-4R-associated signaling promotes IgM to IgE antibody switching in B cells leading to activation of mast cells and the subsequent release of histamine, prostaglandins, and other cytokines. IL-4R-associated signaling also promotes eosinophil proliferation and recruitment to the airway passages, increased iNOS production by epithelial cells, increased proliferation, and activation of macrophages and dendritic cells [reviewed in (10)]. Increased IL-4 production, increased IL-4R expression, and aberrant IL-4R-associated signaling has been observed in several malignancies, including breast cancer, prostate cancer, non-small cell lung carcinoma, renal cell carcinoma, meningioma, and B-cell chronic lymphocytic leukemia [(26-31); reviewed in (10)].

Il4ra-deficient (Il4ra-/-) mice exhibited increased resistance to Leishmania major infection compared to BALB/c control mice (32). During further course of infection, the mice did develop progressive disease symptoms, whereas C57BL/6 mice and Il4-null BALB/c mice cleared the infection (32). The Il4ra-/- mice succumbed to Schistosoma infection in approximately 60 days; the Il4ra-/- mice showed reduced numbers of Th2 cells, liver inflammation, and impaired macrophage recruitment after infection (33). Macrophage/neutrophil-specific Il4ra-/-  mice showed protective immunity against Nippostrongylus brasiliensis, but susceptibility to Schistosoma mansoni infection (34).The Il4ra-/- mice showed reduced circulating levels of IgE and IgG1 (35). A second Il4ra-/- mouse model showed increased IgE levels and respiratory system inflammation (36). In an experimental model of renal fibrosis, Il4ra-/- mice showed aberrant bone marrow-derived fibroblast activation and subsequent extracellular matrix protein production and fibrosis development (37). Il4ra-/- mice showed susceptibility to oxazolone-induced colitis due to loss of IL-13-associated signaling (38).

Putative Mechanism

IL-4 is a cytokine produced by T cells that functions in IgE production as well as in the regulation of the proliferation and differentiation of Th2 cells and the growth and survival of B cells and mast cells (14). The phenotype observed in the Lowe mice indicates loss of IL-4Rα-associated function.

Primers PCR Primer
Lowe_pcr_F: CCTGTGCTTTAACGTGGTGC
Lowe_pcr_R: TCAGTAAGCTGCCACAAGC

Sequencing Primer
Lowe_seq_F: CTTCTGAGGGAGAGTGGCAC
Lowe_seq_R: GCATACAGCACAACATAGACTGG
Genotyping

PCR program

1) 94°C 2:00
2) 94°C 0:30
3) 55°C 0:30
4) 72°C 1:00
5) repeat steps (2-4) 40x
6) 72°C 10:00
7) 4°C hold


The following sequence of 407 nucleotides is amplified (chromosome 7, + strand):


1   cctgtgcttt aacgtggtgc ttctgaggga gagtggcacc taggtaggtg tgtgcgtgtg
61  caggcatgtg tgtcatgatc ctgatgcact agcctccctc tgaccttagt ggtgggagcc
121 cctgaccatg ccaccactga tctggccgtt ctgtctctgc agggagcatc aaggtcctgg
181 gtgagcccac ctgcttctct gactacatcc gcacttccac gtgtgagtgg ttcctggata
241 gcgctgtgga ctgcagttct cagctctgcc tacactacag gctgatgttc ttcgagttct
301 ctgagtaagt ggggtaggga ggcagcaccc caaggtctgt ccaggccttt gctattccag
361 gtgaacgcca gtctatgttg tgctgtatgc ttgtggcagc ttactga


Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red.

References
Science Writers Anne Murray
Illustrators Diantha La Vine
AuthorsTao Yue and Bruce Beutler