Phenotypic Mutation 'lentil2' (pdf version)
Allelelentil2
Mutation Type missense
Chromosome2
Coordinate121,038,368 bp (GRCm39)
Base Change G ⇒ T (forward strand)
Gene Trp53bp1
Gene Name transformation related protein 53 binding protein 1
Synonym(s) 53BP1, p53BP1
Chromosomal Location 121,023,762-121,101,888 bp (-) (GRCm39)
MGI Phenotype PHENOTYPE: Homozygous mutations in this gene result in growth retardation, immunodeficiency, thymic hypoplasia, and increased incidence of thymic lymphomas. [provided by MGI curators]
Accession Number

NCBI RefSeq: NM_013735, NM_001290830; MGI:1351320

MappedYes 
Amino Acid Change Alanine changed to Aspartic acid
Institutional SourceBeutler Lab
Gene Model predicted gene model for protein(s): [ENSMUSP00000106277] [ENSMUSP00000106278] [ENSMUSP00000117548]
AlphaFold P70399
SMART Domains Protein: ENSMUSP00000106277
Gene: ENSMUSG00000043909
AA Change: A1440D

DomainStartEndE-ValueType
low complexity region 136 149 N/A INTRINSIC
low complexity region 158 169 N/A INTRINSIC
low complexity region 647 661 N/A INTRINSIC
low complexity region 1031 1042 N/A INTRINSIC
low complexity region 1099 1112 N/A INTRINSIC
low complexity region 1260 1272 N/A INTRINSIC
low complexity region 1290 1332 N/A INTRINSIC
Pfam:53-BP1_Tudor 1430 1551 2.5e-80 PFAM
low complexity region 1581 1601 N/A INTRINSIC
BRCT 1673 1785 7.13e-1 SMART
BRCT 1813 1901 1.03e-6 SMART
Predicted Effect probably damaging

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000110647)
SMART Domains Protein: ENSMUSP00000106278
Gene: ENSMUSG00000043909
AA Change: A1490D

DomainStartEndE-ValueType
low complexity region 136 149 N/A INTRINSIC
low complexity region 158 169 N/A INTRINSIC
low complexity region 647 661 N/A INTRINSIC
low complexity region 1031 1042 N/A INTRINSIC
low complexity region 1099 1112 N/A INTRINSIC
low complexity region 1260 1272 N/A INTRINSIC
low complexity region 1290 1332 N/A INTRINSIC
low complexity region 1389 1409 N/A INTRINSIC
Pfam:53-BP1_Tudor 1480 1601 1.5e-80 PFAM
low complexity region 1631 1651 N/A INTRINSIC
BRCT 1723 1835 7.13e-1 SMART
BRCT 1863 1951 1.03e-6 SMART
Predicted Effect probably damaging

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000110648)
Predicted Effect probably benign
Predicted Effect probably benign
SMART Domains Protein: ENSMUSP00000117548
Gene: ENSMUSG00000043909

DomainStartEndE-ValueType
Pfam:53-BP1_Tudor 1 70 2.5e-44 PFAM
low complexity region 100 120 N/A INTRINSIC
Predicted Effect probably benign
Meta Mutation Damage Score 0.9465 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(33) : Chemically induced (ENU) (2) Chemically induced (other)(1) Gene trapped(26) Radiation induced(1) Targeted(3

Lab Alleles
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00336:Trp53bp1 APN 2 121087060 missense possibly damaging 0.69
IGL00690:Trp53bp1 APN 2 121066476 missense probably damaging 1.00
IGL00922:Trp53bp1 APN 2 121038963 missense probably damaging 0.96
IGL01475:Trp53bp1 APN 2 121100800 splice site probably null
IGL01639:Trp53bp1 APN 2 121033173 missense possibly damaging 0.51
IGL01662:Trp53bp1 APN 2 121066506 missense probably damaging 1.00
IGL01757:Trp53bp1 APN 2 121041785 missense probably damaging 0.99
IGL01829:Trp53bp1 APN 2 121046377 missense probably benign 0.39
IGL02247:Trp53bp1 APN 2 121067070 missense probably damaging 1.00
IGL02349:Trp53bp1 APN 2 121029555 missense probably damaging 1.00
IGL02391:Trp53bp1 APN 2 121033191 missense possibly damaging 0.67
chives UTSW 2 121082349 missense probably null 0.13
concur UTSW 2 121100800 splice site probably null
confirmation UTSW 2 121035594 critical splice acceptor site probably null
Infra UTSW 2 121077980 critical splice donor site probably null
Legume UTSW 2 121029523 missense probably damaging 0.99
lentil UTSW 2 121082349 missense probably null 0.13
Profundus UTSW 2 121038284 missense probably damaging 1.00
split_pea UTSW 2 121059087 nonsense probably null
verily UTSW 2 121041794 missense probably damaging 1.00
PIT1430001:Trp53bp1 UTSW 2 121101756 missense probably damaging 1.00
R0045:Trp53bp1 UTSW 2 121034978 missense probably benign
R0060:Trp53bp1 UTSW 2 121035006 missense probably damaging 1.00
R0060:Trp53bp1 UTSW 2 121035006 missense probably damaging 1.00
R0103:Trp53bp1 UTSW 2 121067240 missense possibly damaging 0.92
R0103:Trp53bp1 UTSW 2 121067240 missense possibly damaging 0.92
R0281:Trp53bp1 UTSW 2 121100718 missense probably damaging 1.00
R0386:Trp53bp1 UTSW 2 121035424 missense probably damaging 1.00
R0427:Trp53bp1 UTSW 2 121066498 missense probably damaging 1.00
R0505:Trp53bp1 UTSW 2 121100450 missense probably damaging 0.99
R0522:Trp53bp1 UTSW 2 121082349 missense probably null 0.13
R0523:Trp53bp1 UTSW 2 121082349 missense probably null 0.13
R0525:Trp53bp1 UTSW 2 121082349 missense probably null 0.13
R0543:Trp53bp1 UTSW 2 121082349 missense probably null 0.13
R0559:Trp53bp1 UTSW 2 121058282 missense probably damaging 1.00
R0573:Trp53bp1 UTSW 2 121058653 splice site probably benign
R0593:Trp53bp1 UTSW 2 121101009 missense possibly damaging 0.95
R0648:Trp53bp1 UTSW 2 121066188 missense probably benign 0.20
R0680:Trp53bp1 UTSW 2 121082349 missense probably null 0.13
R0732:Trp53bp1 UTSW 2 121078745 missense probably null 0.96
R0905:Trp53bp1 UTSW 2 121034799 splice site probably benign
R1377:Trp53bp1 UTSW 2 121101123 missense probably damaging 1.00
R1415:Trp53bp1 UTSW 2 121066665 missense probably damaging 1.00
R1725:Trp53bp1 UTSW 2 121082481 missense possibly damaging 0.46
R1971:Trp53bp1 UTSW 2 121035517 missense probably damaging 1.00
R2045:Trp53bp1 UTSW 2 121034964 missense probably benign
R2143:Trp53bp1 UTSW 2 121046545 missense probably benign 0.00
R2282:Trp53bp1 UTSW 2 121100754 nonsense probably null
R2296:Trp53bp1 UTSW 2 121039728 missense possibly damaging 0.96
R3106:Trp53bp1 UTSW 2 121067133 missense probably damaging 1.00
R3792:Trp53bp1 UTSW 2 121030810 missense probably damaging 1.00
R3793:Trp53bp1 UTSW 2 121030810 missense probably damaging 1.00
R3946:Trp53bp1 UTSW 2 121059107 missense probably damaging 0.99
R4001:Trp53bp1 UTSW 2 121035566 missense probably damaging 1.00
R4327:Trp53bp1 UTSW 2 121087131 missense probably damaging 1.00
R4585:Trp53bp1 UTSW 2 121038432 missense probably damaging 1.00
R4630:Trp53bp1 UTSW 2 121038368 missense probably damaging 1.00
R4744:Trp53bp1 UTSW 2 121041794 missense probably damaging 1.00
R4751:Trp53bp1 UTSW 2 121058290 missense probably damaging 1.00
R4754:Trp53bp1 UTSW 2 121038360 missense probably damaging 1.00
R4755:Trp53bp1 UTSW 2 121059087 nonsense probably null
R4850:Trp53bp1 UTSW 2 121035594 critical splice acceptor site probably null
R4870:Trp53bp1 UTSW 2 121087122 missense probably damaging 1.00
R4879:Trp53bp1 UTSW 2 121033084 missense probably damaging 0.99
R4924:Trp53bp1 UTSW 2 121051701 nonsense probably null
R4962:Trp53bp1 UTSW 2 121101027 missense probably benign 0.12
R5019:Trp53bp1 UTSW 2 121100800 splice site probably null
R5111:Trp53bp1 UTSW 2 121041868 missense probably damaging 0.99
R5149:Trp53bp1 UTSW 2 121046598 missense probably benign 0.00
R5252:Trp53bp1 UTSW 2 121074464 missense probably benign 0.40
R5533:Trp53bp1 UTSW 2 121038227 missense probably damaging 1.00
R5642:Trp53bp1 UTSW 2 121067143 missense probably benign 0.00
R5773:Trp53bp1 UTSW 2 121074395 missense probably damaging 1.00
R5819:Trp53bp1 UTSW 2 121038873 nonsense probably null
R5886:Trp53bp1 UTSW 2 121035502 missense probably damaging 1.00
R5908:Trp53bp1 UTSW 2 121067304 missense probably benign 0.06
R6012:Trp53bp1 UTSW 2 121087083 missense probably benign 0.07
R6351:Trp53bp1 UTSW 2 121100426 missense probably damaging 1.00
R6406:Trp53bp1 UTSW 2 121101093 missense probably damaging 0.99
R6575:Trp53bp1 UTSW 2 121059084 missense probably damaging 1.00
R6619:Trp53bp1 UTSW 2 121077980 critical splice donor site probably null
R6626:Trp53bp1 UTSW 2 121038284 missense probably damaging 1.00
R6754:Trp53bp1 UTSW 2 121101057 missense possibly damaging 0.83
R6765:Trp53bp1 UTSW 2 121039790 missense probably damaging 1.00
R6806:Trp53bp1 UTSW 2 121059147 missense probably damaging 0.99
R6860:Trp53bp1 UTSW 2 121029594 missense probably damaging 1.00
R6991:Trp53bp1 UTSW 2 121038521 missense probably damaging 1.00
R7278:Trp53bp1 UTSW 2 121029516 missense probably damaging 1.00
R7339:Trp53bp1 UTSW 2 121066950 missense probably benign 0.00
R7357:Trp53bp1 UTSW 2 121041781 missense probably damaging 1.00
R7477:Trp53bp1 UTSW 2 121066827 missense probably benign 0.34
R7577:Trp53bp1 UTSW 2 121067119 missense possibly damaging 0.65
R7643:Trp53bp1 UTSW 2 121078295 splice site probably null
R7728:Trp53bp1 UTSW 2 121038380 missense probably damaging 1.00
R7806:Trp53bp1 UTSW 2 121035542 missense probably damaging 0.99
R7955:Trp53bp1 UTSW 2 121066225 missense possibly damaging 0.59
R8099:Trp53bp1 UTSW 2 121030230 missense probably damaging 1.00
R8200:Trp53bp1 UTSW 2 121066657 missense probably benign 0.00
R8282:Trp53bp1 UTSW 2 121029523 missense probably damaging 0.99
R9136:Trp53bp1 UTSW 2 121067092 missense possibly damaging 0.84
R9152:Trp53bp1 UTSW 2 121029056 missense probably damaging 0.99
R9292:Trp53bp1 UTSW 2 121046177 missense probably damaging 0.97
R9340:Trp53bp1 UTSW 2 121100460 missense probably benign 0.40
R9475:Trp53bp1 UTSW 2 121039761 missense probably benign 0.00
R9616:Trp53bp1 UTSW 2 121066657 missense probably benign 0.30
R9675:Trp53bp1 UTSW 2 121087089 missense probably benign 0.03
R9779:Trp53bp1 UTSW 2 121066469 missense probably damaging 1.00
RF046:Trp53bp1 UTSW 2 121046482 frame shift probably null
Z1088:Trp53bp1 UTSW 2 121084126 missense probably benign 0.04
Z1177:Trp53bp1 UTSW 2 121074541 missense probably benign 0.33
Mode of Inheritance Autosomal Recessive
Local Stock
Repository
Last Updated 2019-09-04 9:42 PM by Diantha La Vine
Record Created 2016-09-09 11:18 AM
Record Posted 2017-02-24
Phenotypic Description

Figure 1. Lentil2 mice exhibit reduced IgD expression on peripheral B cells. Flow cytometric analysis of peripheral blood was utilized to determine IgD mean fluourescence intensity. 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.

Figure 2. Lentil2 mice exhibit reduced percentages of IgD+ B cells. Flow cytometric analysis of peripheral blood was utilized to determine B cell frequency. 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.
Figure 3. Lentil2 mice exhibit reduced frequencies of naïve CD8 T cells in CD8 T cells. Flow cytometric analysis of peripheral blood was utilized to determine T cell frequency. 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.
Figure 4. Lentil2 mice exhibit increased expression of CD44 on CD8 T cells. Flow cytometric analysis of peripheral blood was utilized to determine CD44 MFI. 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.
Figure 5. Lentil2 mice exhibit increased frequencies of central memory CD8 T cells in CD8 T cells. Flow cytometric analysis of peripheral blood was utilized to determine T cell frequency. 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.
Figure 6. Homozygous lentil2 mice exhibit diminished T-dependent IgG responses to OVA/alum. IgG 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.

Figure 7. Homozygous lentil2 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. 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 lentil2 phenotype was identified among N-ethyl-N-nitrosourea (ENU)-mutagenized G3 mice of the pedigree R4630, some of which showed a decrease in IgD expression on B cells (Figure 1), a decreased percentage of IgD+ B cells (Figure 2), and a decrease in the frequency of naïve CD8 T cells in CD8 T cells (Figure 3) with a concomitant increase in CD44 expression on CD8 T cells (Figure 4) and an increased frequency of central memory CD8 T cells in CD8 T cells (Figure 5). The T-dependent antibody responses to ovalbumin administered with aluminum hydroxide (Figure 6) and to recombinant Semliki Forest virus (rSFV)-encoded β-galactosidase (rSFV-β-gal) (Figure 7) were also diminished
.

Nature of Mutation

Figure 8. Linkage mapping of the reduced T-dependent IgG response to rSFV-β-gal. Manhattan plot shows -log10 P values (Y-axis) plotted against the chromosome positions of 74 mutations (X-axis) identified in the G1 male of pedigree R4630. Normalized phenotype 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 74 mutations. All of the above anomalies were linked by continuous variable mapping to a mutation in Trp53bp1:  a C to A transversion at base pair 121,207,887 (v38) on chromosome 2, or base pair 82,439 in the GenBank genomic region NC_000068 encoding Trp53bp1.  The strongest association was found with a recessive model of linkage to the normalized T-dependent antibody response to rSFV-β-gal, wherein four variant homozygotes departed phenotypically from 10 homozygous reference mice and 14 heterozygous mice with a P value of 2.698 x 10-12 (Figure 8).  

The mutation corresponds to residue 4,448 in the mRNA sequence NM_001290830 within exon 20 of 27 total exons and residue 4,598 in the mRNA sequence NM_013735 within exon 21 of 28 total exons.

82423 GGTCTCCGTGTTGTAGCTAAGTGGTCATCCAAT

1435  -G--L--R--V--V--A--K--W--S--S--N- (isoform b; NP_001277759)

1485  -G--L--R--V--V--A--K--W--S--S--N- (isoform a; NP_038763)

Genomic numbering corresponds to NC_000068. The mutated nucleotide is indicated in red.  The mutation results in an alanine (A) to aspartic acid (D) substitution at position 1440 (A1440D) in the 53BP1 protein, and is strongly predicted by PolyPhen-2 to be damaging (score = 1.000).

Illustration of Mutations in
Gene & Protein
Protein Prediction
Figure 9. Domain structure of 53BP1. The lentil2 mutation (A1440D) is indicated in red. This image is interactive. Click on each allele for more information. See the text for more details on the domains of 53BP1. Abbreviations: KBD, kinetochore-binding domain; OLIGO, oligomerization domain; GAR, glycine/arginine-rich region; UDR, ubiquitin-dependent recruitment motif; NLS, nuclear localization signal; BRCT, BRCA1 C-terminus. The phosphoinositide 3-kinase-like kinase (PIKK) S/TQ phosphorylation sites are labeled (Ser6, Ser25, Ser29, Ser166, Ser176/Ser178, Thr302, Ser452, Ser831, and Ser1219) as well as the site of ubiquitination (Lys1523).

Trp53bp1 (transformation related protein 53 binding protein 1) encodes 53BP1. 53BP1 has two tandem Tudor domains at amino acids 1475-1575 (1) (alternatively, amino acids 1469-1574 (2) or amino acids 1480-1601, SMART) [Figure 9; (3;4)]. Amino acids 1220-1601 of 53BP1 comprise a kinetochore-binding domain (KBD) (1;5). A nuclear localization signal (NLS; amino acids 1645-1703) and the KBD are sufficient to target 53BP1 to IR-induced foci (IRIF) (2). Within the KBD, amino acids 1231–1270 are required for homo-oligomerization (6). 53BP1 has two tandem breast cancer 1 early-onset (BRCA1) C-terminus (BRCT) domains at amino acids 1708-1969 (alternatively, amino acids 1723-1951, SMART) (7). 53BP1 has a highly conserved glycine/arginine-rich region (GAR; RGRGRRGR; amino acids 1380-1386) (1;2). The lentil2 mutation results in an alanine (A) to aspartic acid (D) substitution at position 1440 (A1440D). Residue 1440 is within the KBD.

For more information about Trp53bp1, please see the record for lentil and (8).

Putative Mechanism

53BP1 has several functions including facilitating DNA damage signaling, telomere fusions, NHEJ of DNA double strand break (DSBs) in CSR, transducing ATM-dependent cell cycle checkpoints (intra-S and G2/M), accumulation of p53, phosphorylation of several ATM substrates (e.g., Chk2 and BRCA1) in response to IR, and tumor suppression (9-16).

Dysregulation of TRP53BP1 expression is associated with several human conditions. TRP53BP1 expression in BRCA1-associated breast cancers (17;18), lymphomas, and solid tumors is reduced (17;19-21). Low levels of TRP53BP1 are correlated with an aggressive form of the disease, correlating with increased metastases and decreased survival [reviewed in (22)]. 53BP1 deficiency and the deregulation of AID, leads to increased DSB formation, resulting in B cell lymphoma (23). Patients with RIDDLE syndrome (OMIM: #611943) lack the ability to recruit 53BP1 to the sites of DNA DSBs (24).

MEFs from both Trp53bp1-/- and m53BP1tr/tr embryos exhibited reduced proliferation compared to controls (25). Both models are viable, but exhibit growth retardation and increased cellular sensitivity to IR (25;26). The m53BP1tr/tr mice were fertile, but produced smaller litters than wild-type animals (26). After IR, Trp53bp1-/- cells arrested in G2 and exhibited a delayed exit from the G2/M phase; the percentage of mitotic cells 24 hours after IR was lower than wild-type cells (25). The Trp53bp1 mouse models exhibit immune deficiencies including defects in T cell maturation (25;26). The levels of CD4 T cells, γ–δ T cells, and B cells were all reduced in the Trp53bp1-/- mice with a concomitant increase in the percentage of CD4-CD8progenitors and apoptosis (25;27). In addition, the Trp53bp1-/- thymocytes exhibited an increased number of aberrant cells (either lost Cα (2 TCRVα, 1 TCRCα signal) or both Vα and Cα from one allele (1 TCRVα, 1 TCRCα)) (27). Bone marrow pro-B, pre-B, myeloid, and erthyroid progenitor populations were normal in the m53BP1tr/tr mice (16;26). However, the spleens from the m53BP1tr/tr mice were deficient in mature B cells (IgMloIgDhi(26). IgM levels in the Trp53bp1-/- mice were similar to those in wild-type mice, indicating that B cell activation to mediate IgM secretion is not affected upon loss of 53BP1, however, the levels of all IgG subclasses and IgA were decreased (16). CD4 and CD8 T cell populations were similar between m53BP1tr/tr and wild-type mice, but the progression out of the DNIII stage in development, when β-gene rearrangement occurs, was impaired in the m53BP1tr/tr mice (26). Thymus size in the m53BP1tr/tr mice was smaller and had fewer cells than wild-type mice; the lymphoid organ architecture was normal (26).  The phenotypes exhibited by the lentil2 mice indicate loss of 53BP1lentil2 function.

Primers PCR Primer
lentil2_pcr_F: CAGTCCATCTGTAGGGATCTGC
lentil2_pcr_R: AAGTCCTTCACCCGCATTATG

Sequencing Primer
lentil2_seq_F: GAAATATTCATCTTCTGAGAGGGCTG
lentil2_seq_R: GCATTATGCCTCGTGTGCCAG
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 401 nucleotides is amplified (chromosome 2, - strand):


1   aagtccttca cccgcattat gcctcgtgtg ccagattcta ccaaacggac ggatgccagt
61  tctagtactt tgcggcggag tgattctcca gagattcctt ttcaggctgc tactggttcc
121 tctgatggct tggattcctc atcttcagga aacagctttg tgggtctccg tgttgtagct
181 aagtggtcat ccaatggcta cttttactct gggaagatca cccgagatgt gggggctggg
241 aagtacaagc tgctctttga tgatgggtac gaatgtgacg tgctgggcaa agacattctc
301 ctgtgtgacc ccatccccct ggacactgaa gtgacagccc tctcagaaga tgaatatttc
361 agtgcaggta atgaaacaag cagatcccta cagatggact g


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, Ming Zeng, Xue Zhong, and Bruce Beutler