Phenotypic Mutation 'bryce_canyon' (pdf version)
Allelebryce_canyon
Mutation Type critical splice donor site (2 bp from exon)
Chromosome18
Coordinate65,595,986 bp (GRCm39)
Base Change T ⇒ C (forward strand)
Gene Malt1
Gene Name MALT1 paracaspase
Synonym(s) D430033E09Rik, paracaspase, Pcasp1
Chromosomal Location 65,564,010-65,611,959 bp (+) (GRCm39)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene has been found to be recurrently rearranged in chromosomal translocation with two other genes - baculoviral IAP repeat-containing protein 3 (also known as apoptosis inhibitor 2) and immunoglobulin heavy chain locus - in mucosa-associated lymphoid tissue lymphomas. The protein encoded by this gene may play a role in NF-kappaB activation. Two alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous inactivation of this gene disrupts normal B cell development and leads to impaired cytokine production and T cell and B cell proliferative responses after antigen receptor engagement due to failure of NF-kappaB activation. [provided by MGI curators]
Accession Number

NCBI RefSeq: NM_172833; MGI:2445027

MappedYes 
Amino Acid Change
Institutional SourceBeutler Lab
Gene Model predicted gene model for protein(s): [ENSMUSP00000048376 ] [ENSMUSP00000153585 ]   † probably from a misspliced transcript
AlphaFold Q2TBA3
SMART Domains Protein: ENSMUSP00000048376
Gene: ENSMUSG00000032688

DomainStartEndE-ValueType
low complexity region 19 35 N/A INTRINSIC
low complexity region 38 51 N/A INTRINSIC
PDB:2G7R|B 52 132 3e-29 PDB
IGc2 145 203 8.19e-9 SMART
IGc2 248 306 2.88e-4 SMART
Pfam:Peptidase_C14 340 557 1.4e-19 PFAM
Predicted Effect probably null
Predicted Effect probably null
Meta Mutation Damage Score 0.9500 question?
Is this an essential gene? Possibly nonessential (E-score: 0.356) question?
Phenotypic Category Autosomal Recessive
Candidate Explorer Status loading ...
Single pedigree
Linkage Analysis Data
Penetrance  
Alleles Listed at MGI

All mutations/alleles(9) : Chemically induced (ENU)(1) Gene trapped(3) Targeted(5)

Lab Alleles
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00323:Malt1 APN 18 65582034 nonsense probably null
IGL01354:Malt1 APN 18 65608262 missense probably damaging 1.00
IGL01514:Malt1 APN 18 65609471 missense possibly damaging 0.74
IGL01968:Malt1 APN 18 65582087 missense probably benign 0.08
frappe UTSW 18 65606190 missense probably benign 0.01
mousebird UTSW 18 65608331 critical splice donor site probably null
yellowstone UTSW 18 65591271 missense probably damaging 1.00
H8930:Malt1 UTSW 18 65595886 nonsense probably null
R0319:Malt1 UTSW 18 65595986 critical splice donor site probably null
R0512:Malt1 UTSW 18 65591271 missense probably damaging 1.00
R0748:Malt1 UTSW 18 65608331 critical splice donor site probably null
R2085:Malt1 UTSW 18 65606218 missense probably damaging 1.00
R2962:Malt1 UTSW 18 65581406 missense probably benign 0.01
R4193:Malt1 UTSW 18 65580746 missense probably benign 0.00
R4359:Malt1 UTSW 18 65609300 missense probably benign 0.00
R4913:Malt1 UTSW 18 65609351 missense probably damaging 1.00
R5201:Malt1 UTSW 18 65609126 missense probably benign
R5925:Malt1 UTSW 18 65564439 missense possibly damaging 0.86
R6944:Malt1 UTSW 18 65570991 missense probably benign 0.08
R7108:Malt1 UTSW 18 65597122 missense probably damaging 1.00
R7184:Malt1 UTSW 18 65580764 missense probably benign
R7192:Malt1 UTSW 18 65570898 missense probably benign 0.07
R7307:Malt1 UTSW 18 65584640 missense possibly damaging 0.48
R7308:Malt1 UTSW 18 65582680 critical splice donor site probably null
R7490:Malt1 UTSW 18 65581282 missense probably benign 0.04
R7558:Malt1 UTSW 18 65595905 missense probably damaging 1.00
R7756:Malt1 UTSW 18 65606190 missense probably benign 0.01
R7758:Malt1 UTSW 18 65606190 missense probably benign 0.01
R7892:Malt1 UTSW 18 65597187 critical splice donor site probably null
R8112:Malt1 UTSW 18 65582680 critical splice donor site probably null
R8507:Malt1 UTSW 18 65603594 missense probably damaging 1.00
R9009:Malt1 UTSW 18 65577911 missense probably benign 0.15
R9760:Malt1 UTSW 18 65581283 missense probably benign 0.03
Z1177:Malt1 UTSW 18 65581355 missense probably damaging 1.00
Z1177:Malt1 UTSW 18 65564444 missense probably damaging 1.00
Mode of Inheritance Autosomal Recessive
Local Stock
MMRRC Submission 038221-MU
Last Updated 2019-09-04 9:44 PM by Anne Murray
Record Created 2015-09-15 2:27 PM
Record Posted 2015-09-24
Phenotypic Description
Figure 1. Homozygous bryce_canyon mice exhibit diminished T-dependent IgG responses to ovalbumin administered with aluminum hydroxide. IgG levels were determined by ELISA. Normalized data are shown from gene-based superpedigree analysis of three pedigrees R0512 (aqua), R0319 (gold), and R0748 (red). Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

Figure 2. Homozygous bryce_canyon mice exhibit diminished T-dependent IgG responses to recombinant Semliki Forest virus (rSFV)-encoded β-galactosidase (rSFV-β-gal). IgG levels were determined by ELISA. Normalized data are shown from gene-based superpedigree analysis of three pedigrees R0512 (aqua), R0319 (gold), and R0748 (red). Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

Figure 3. Homozygous bryce_canyon mice exhibit diminished T-independent IgM responses to 4-hydroxy-3-nitrophenylacetyl-Ficoll (NP-Ficoll). IgM levels were determined by ELISA. Normalized data are shown from gene-based superpedigree analysis of three pedigrees R0319 (gold) and R0748 (aqua). 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 bryce_canyon phenotype was identified by gene-based superpedigree analysis among N-ethyl-N-nitrosourea (ENU)-mutagenized G3 mice of the pedigree R0319, some of which showed diminished T-dependent antibody responses to ovalbumin administered with aluminum hydroxide (Figure 1) and recombinant Semliki Forest virus (rSFV)-encoded β-galactosidase (rSFV-β-gal) (Figure 2). The T-independent antibody response to 4-hydroxy-3-nitrophenylacetyl-Ficoll (NP-Ficoll) was also diminished (Figure 3). 

Nature of Mutation

Figure 4. Linkage mapping of the reduced T-dependent IgG responses to rSFV-β-gal using a recessive model of inheritance and gene-based superpedigree analysis. Manhattan plot shows -log10 P values (Y-axis) plotted against the chromosome positions of 177 mutations (X-axis) identified in the G1 males of pedigrees R0512 (contributing 92 mutations), R0319 (contributing 56 mutation), and R0748 (contributing 29 mutations) using gene-based superpedigree analysis.  Normalized phenotype data are shown for single locus linkage analysis with 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 in the R0319 pedigree identified 56 mutations. All of the above anomalies were linked by continuous variable mapping to a mutation in Malt1 by gene-based superpedigree analysis:  a T to C transition at base pair 65,462,915 (v38) on chromosome 18, or base pair 31,947 in the NC_000084 GenBank genomic region within the donor splice site of intron 10 (2 base pairs from exon 10).  The strongest association was found with a recessive model of linkage to the T-dependent antibody response to rSFV-β-gal, wherein five variant homozygotes from three pedigrees departed phenotypically from 29 homozygous reference mice and 45 heterozygous mice with a P value of 4.604 x 10-9 (Figure 4). A substantial semidominant effect was observed in most of the assays but the mutation is preponderantly recessive, and in no assay was a purely dominant effect observed. 

The effect of the mutation at the cDNA and protein level have not examined, but the mutation is predicted to result in skipping of the 178-base pair exon 10 (out of 16 total exons), resulting in a frame-shift and coding of 13 aberrant amino acids followed by a premature stop codon within exon 11 (after amino acid 418).

               <--exon 9       <--exon 10 intron 10-->          exon 11-->

27389 ……GACAAAGGAGTATATG ……ATGTGTCGGAAAAG gtaaaatgtctcatctctc…… AAATGACTACG……TGGACGCACTGA…… 33102

 
400   ……-D--K--G--V--Y-- ……-M--C--R--K--R                       E--M--T--S-……-W--T--H--*    418

            correct           deleted                                   aberrant

Genomic numbering corresponds to NC_000084. The donor splice site of intron 11, which is destroyed by the bryce_canyon mutation, is indicated in blue lettering and the mutated nucleotide is indicated in red. 

Illustration of Mutations in
Gene & Protein
Protein Prediction
Figure 5. Domain structure of MALT1. The location of the bryce_canyon mutation within intron 11 is indicated. Abbreviations: DD, death domain, Ig, immunoglobulin-like.

Malt1 encodes mucosa-associated lymphoid tissue translocation gene 1 (MALT1; alternatively paracaspase; Figure 5). MALT1 has several domains including a death domain (DD; amino acids 45-132), a paracaspase domain (amino acids 340-535), and three immunoglobulin (Ig)-like domains [amino acids 145-203 (Ig1), 248-306 (Ig2), and 581-715 (Ig3)] (1). The mutation in bryce_canyon is predicted to result in deletion of amino acids 406-464 as well as a frameshift after amino acid 405, coding of 13 aberrant amino acids followed by a premature stop codon.

For more information about Malt1, please see the record mousebird.

Putative Mechanism

Upon T cell activation by the TCR and costimulatory molecule engagement, CARMA1 associates with a complex containing Bcl10 and MALT1 and recruits these proteins to lipid rafts of the immunological synapse and to form a scaffold for the assembly of several signaling complexes including those that involve TNF receptor-associated factor 6 (TRAF6), TGF (transforming growth factor)-β-activated kinase 1 (TAK1), and NF-κB essential modulator (NEMO; see the record for panr2) to facilitate NF-κB activation and lymphocyte stimulation. In addition to T and B cells, MALT1 functions in mast cells, dendritic cells, macrophages and natural killer (NK) cells (2-4). Malt1-/- mice exhibit defective antigen receptor-induced lymphocyte activation (5;6). Malt1-/- mice exhibited reduced T-dependent antibody responses to keyhole limpet haemocyanin (KLH) in complete Freund's adjuvant (CFA) and 2,4-dinitrophenol–conjugated ovalbumin (DNP-OVA) as well as reduced T-independent antibody responses to tri-nitrophenol-(TNP)-Ficoll (5-7). The bryce_canyon mice also exhibit defects in both T-independent and T-dependent antibody responses indicating that the MALT1bryce_canyon protein, if expressed, exhibits loss-of-function.

Primers PCR Primer
bryce_canyon_pcr_F: AGGATTGTTATATTATGCAGGGCACGG
bryce_canyon_pcr_R: ACTGCTAGTCACATGGACATGGACTC

Sequencing Primer
bryce_canyon_seq_F: GGCACGGTTATGAAAACTTTGG
bryce_canyon_seq_R: TATAACTTGTACCTTTCACAGCAAAC
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 400 nucleotides is amplified (chromosome 18, + strand):


1   aggattgtta tattatgcag ggcacggtta tgaaaacttt ggaaacagtt tcatggtccc
61  tgttgatgct ccaaatccat ataggtctga aaattgccta tgcgtacaaa acatactgaa
121 attaatgcaa gaaaaggaga ctggcctgaa tgtgttcctg ttggatatgt gtcggaaaag
181 gtaaaatgtc tcatctctct atcaagtagc aaccttgaca aagtctatgt aaggcaattc
241 tgtacggtgg taagaacccc taggaactgt gaggttctgg aaacagactg gatatagata
301 tatttttagt atggatatct aattatttta actttctgtt tgctgtgaaa ggtacaagtt
361 atatactctc tctagagtcc atgtccatgt gactagcagt 


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

References
Science Writers Anne Murray
Illustrators Peter Jurek
AuthorsJin Huk Choi, Kuan-Wen Wang, and Bruce Beutler