Phenotypic Mutation 'shook' (pdf version)
Alleleshook
Mutation Type nonsense
Chromosome16
Coordinate91,296,425 bp (GRCm39)
Base Change C ⇒ T (forward strand)
Gene Ifnar1
Gene Name interferon (alpha and beta) receptor 1
Synonym(s) Ifar, Ifrc, IFN-alpha/betaR
Chromosomal Location 91,282,126-91,304,329 bp (+) (GRCm39)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a type I membrane protein that forms one of the two chains of a receptor for interferons alpha and beta. Binding and activation of the receptor stimulates Janus protein kinases, which in turn phosphorylate several proteins, including STAT1 and STAT2. The encoded protein also functions as an antiviral factor. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations exhibit increased susceptibility to viral infection, elevated levels of myeloid lineage cells in the peripheral blood and bone marrow, and reduced immune response to immunostimulatory DNA. [provided by MGI curators]
Accession Number

NCBI RefSeq: NM_010508.2; MGI: 107658

MappedYes 
Amino Acid Change Glutamine changed to Stop codon
Institutional SourceBeutler Lab
Gene Model predicted gene model for protein(s): [ENSMUSP00000023689] [ENSMUSP00000112670] [ENSMUSP00000119160 ] [ENSMUSP00000120945] [ENSMUSP00000156101]   † probably from a misspliced transcript
AlphaFold P33896
PDB Structure Murine Ifnar1 in complex with interferon-beta [X-RAY DIFFRACTION]
SMART Domains Protein: ENSMUSP00000023689
Gene: ENSMUSG00000022967
AA Change: Q309*

DomainStartEndE-ValueType
low complexity region 2 16 N/A INTRINSIC
FN3 29 110 6.97e0 SMART
FN3 128 213 7.02e1 SMART
low complexity region 267 275 N/A INTRINSIC
FN3 332 409 3.23e0 SMART
PDB:4PO6|B 469 499 3e-7 PDB
low complexity region 550 562 N/A INTRINSIC
Predicted Effect probably null
SMART Domains Protein: ENSMUSP00000112670
Gene: ENSMUSG00000022967
AA Change: Q309*

DomainStartEndE-ValueType
low complexity region 2 16 N/A INTRINSIC
FN3 29 110 6.97e0 SMART
FN3 128 213 7.02e1 SMART
low complexity region 267 275 N/A INTRINSIC
FN3 332 409 3.23e0 SMART
PDB:4PO6|B 469 499 3e-7 PDB
low complexity region 550 562 N/A INTRINSIC
Predicted Effect probably null
SMART Domains Protein: ENSMUSP00000119160
Gene: ENSMUSG00000022967

DomainStartEndE-ValueType
low complexity region 2 16 N/A INTRINSIC
FN3 29 110 6.97e0 SMART
FN3 128 213 7.02e1 SMART
low complexity region 267 275 N/A INTRINSIC
FN3 332 409 3.23e0 SMART
PDB:4PO6|B 469 499 3e-7 PDB
low complexity region 550 562 N/A INTRINSIC
Predicted Effect probably benign
SMART Domains Protein: ENSMUSP00000120945
Gene: ENSMUSG00000022967

DomainStartEndE-ValueType
low complexity region 2 16 N/A INTRINSIC
FN3 29 110 6.97e0 SMART
Predicted Effect probably benign
Predicted Effect probably benign
Meta Mutation Damage Score 0.9755 question?
Is this an essential gene? Non Essential (E-score: 0.000) question?
Phenotypic Category Autosomal Recessive
Candidate Explorer Status loading ...
Single pedigree
Linkage Analysis Data
Penetrance  
Alleles Listed at MGI

All alleles(10) : Targeted(5) Gene trapped(4) Chemically induced(1)

Lab Alleles
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00229:Ifnar1 APN 16 91286670 missense probably damaging 0.99
IGL02183:Ifnar1 APN 16 91302034 missense possibly damaging 0.94
IGL02828:Ifnar1 APN 16 91302304 critical splice donor site probably null
macro-1 UTSW 16 91296773 missense probably damaging 0.98
sneffels UTSW 16 91298508 critical splice acceptor site probably null
R0124:Ifnar1 UTSW 16 91296425 nonsense probably null
R0502:Ifnar1 UTSW 16 91298639 missense probably damaging 1.00
R0617:Ifnar1 UTSW 16 91298570 missense probably damaging 1.00
R1509:Ifnar1 UTSW 16 91300384 missense probably damaging 1.00
R4111:Ifnar1 UTSW 16 91293046 missense probably damaging 1.00
R4473:Ifnar1 UTSW 16 91292058 missense probably damaging 0.98
R4964:Ifnar1 UTSW 16 91301974 missense probably benign 0.08
R5497:Ifnar1 UTSW 16 91302252 missense probably benign 0.01
R6135:Ifnar1 UTSW 16 91298508 critical splice acceptor site probably null
R6398:Ifnar1 UTSW 16 91302303 critical splice donor site probably null
R6505:Ifnar1 UTSW 16 91296425 nonsense probably null
R6620:Ifnar1 UTSW 16 91293155 splice site probably null
R7229:Ifnar1 UTSW 16 91296444 missense probably benign 0.00
R7664:Ifnar1 UTSW 16 91292082 missense probably damaging 1.00
R8337:Ifnar1 UTSW 16 91302224 missense possibly damaging 0.70
R8348:Ifnar1 UTSW 16 91292187 missense probably benign 0.00
R8531:Ifnar1 UTSW 16 91292344 nonsense probably null
R8683:Ifnar1 UTSW 16 91296332 missense probably damaging 1.00
R9031:Ifnar1 UTSW 16 91302079 missense probably benign 0.13
R9110:Ifnar1 UTSW 16 91302150 missense probably benign 0.04
R9278:Ifnar1 UTSW 16 91302013 missense probably damaging 1.00
R9356:Ifnar1 UTSW 16 91292367 missense probably benign 0.06
R9359:Ifnar1 UTSW 16 91292367 missense probably benign 0.06
R9388:Ifnar1 UTSW 16 91292367 missense probably benign 0.06
R9443:Ifnar1 UTSW 16 91292367 missense probably benign 0.06
R9444:Ifnar1 UTSW 16 91292367 missense probably benign 0.06
R9445:Ifnar1 UTSW 16 91292367 missense probably benign 0.06
X0057:Ifnar1 UTSW 16 91302171 missense possibly damaging 0.92
X0057:Ifnar1 UTSW 16 91292312 missense probably damaging 0.98
Mode of Inheritance Autosomal Recessive
Local Stock Live Mice
MMRRC Submission 036965-MU
Last Updated 2018-11-06 7:54 PM by Diantha La Vine
Record Created 2013-02-08 12:08 AM by Hexin Shi
Record Posted 2013-07-18
Phenotypic Description
Figure 1. Shook peritoneal macrophages were defective in producing type I interferon (IFN) in response to dsDNA (red dots).

Shook was initially identified among N-ethyl-N-nitrosourea (ENU)-induced G3 animals in the Double-stranded DNA Macrophage ScreenShook peritoneal macrophages were defective in producing type I interferon (IFN) in response to dsDNA (Figure 1, red dots).

Nature of Mutation

Whole exome HiSeq sequencing of the G1 grandsire identified 59 mutations. Four G3 mice with the shook phenotype were genotyped at all 59 mutation sites and two mutations on chromosome 16 were homozygous in all four of the shook mice. Subsequent analysis of five additional affected mice and 21 unaffected mice supported a causal relationship between the mutation and the phenotype (LOD =5.49).  Sequencing of the mutated gene identified a C to T transition at base pair 91499537 (v38) on Chromosome 16 in the GenBank genomic region NC_000082 encoding Ifnar1. The mutation corresponds to residue 1054 in the mRNA sequence (NM_010508.2) within exon 7 of 11 total exons.

 
1039 TTCTTTCTCCATGTACAAGCCTCAGAGGGAAAT

304  -F--F--L--H--V--Q--A--S--E--G--N-

The mutated nucleotide is indicated in red.  The mutation results in a glutamine (Q) to premature stop codon (*) substitution at residue 309. 

Illustration of Mutations in
Gene & Protein
Protein Prediction

Figure 2. Domain structure of IFNAR1. IFNAR1 belongs to the class II helical cytokine receptor (hCR) family. The extracellular ligand-binding region of IFNAR1 contains four fibronectin type III subdomains known as SD1-4. The shook mutation results in a conversion of glutamine to a premature stop codon at residue 309 within the SD3 domain. Image is interactive. Other mutaions found in IFNAR1 are noted in red. Click on each mutataion for more information.

The shook mutation (Q309*) is within the fibronectin type-III subdomain 3 (SD3) of the IFNAR1 protein (Figure 2). It is unknown whether this protein is expressed and localized normally.

Please see the record macro-1 for information about Ifnar1.

Putative Mechanism

Shook mice produce significantly reduced amounts of type I IFN in response to dsDNA stimulation of macrophages ex vivo.  This finding suggests that the shook mutation impairs signaling through the IFNAR receptor, thus preventing activation of the positive feedback loop for type I IFN production. 

Primers PCR Primer
shook_pcr_F: GGTCCACAGTGCTTACTACAGTGTC
shook_pcr_R: CGCCCTACATGAGGAATTACACTCC

Genotyping

Shook genotyping is performed by amplifying the region containing the mutation using PCR, followed by sequencing of the amplified region to detect the single nucleotide transition. The same primers are used for PCR amplification and for sequencing.

PCR Primers

Shook(F): 5’- GGTCCACAGTGCTTACTACAGTGTC-3’

Shook(R): 5’- CGCCCTACATGAGGAATTACACTCC-3’

 
Sequencing Primer

Shook_seq(F): 5’- TGTCTTAGGTATTATAGAGCCTCAG-3’
 

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               ∞

The following sequence of 496 nucleotides (from Genbank genomic region NC_000082 for linear DNA sequence of Ifnar1) is amplified:

14085                                                 ggtcca cagtgcttac    

14101 tacagtgtct taggtattat agagcctcag tacatagtga attaattcat gattggattg    

14161 gattttgttt ttgctttctg ttttcaaagt ggctattcaa aaagcagttc tggaagccgt    

14221 tcagataaat ggaaaccaat accaacctgt gcaaatgtcc agactacgca ctgtgtcttt    

14281 tctcaagata ctgtctacac aggaacgttc tttctccatg tacaagcctc agagggaaat    

14341 cacacatcct tttggtctga agagaagttt attgattctc aaaaacacag taagccgagt    

14401 tttctttgag acagtctgac actgtagccc aggctggcct ggaactcacg gtgtagccca    

14461 gggtagcttc aaacttatgg cagtcctcct gcctgagctc ctgagagctg aggttgtggg    

14521 tgtggtccat gcctgctgta tagcaagcgc tttctggagt gtaattcctc atgtagggcg

Primer binding sites are underlined and the sequencing primer is highlighted; the mutated C is shown in red text.

Science Writers Anne Murray
Illustrators Peter Jurek
AuthorsHexin Shi, Ying Wang, Bruce Beutler