Phenotypic Mutation 'lochy'

• Allele: lochy
• Mutation Type: splice site
• Chromosome: 1
• Coordinate: 138,011,528 bp (GRCm39)
• Base Change: A ⇒ T (forward strand)
• Gene: Ptprc
• Gene Name: protein tyrosine phosphatase receptor type C
• Synonym(s): Ly-5, T200, CD45, B220, Lyt-4
• Chromosomal Location: 137,990,599-138,103,446 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 member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitosis, and oncogenic transformation. This PTP contains an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus is classified as a receptor type PTP. This PTP has been shown to be an essential regulator of T- and B-cell antigen receptor signaling. It functions through either direct interaction with components of the antigen receptor complexes, or by activating various Src family kinases required for the antigen receptor signaling. This PTP also suppresses JAK kinases, and thus functions as a regulator of cytokine receptor signaling. Alternatively spliced transcripts variants of this gene, which encode distinct isoforms, have been reported. [provided by RefSeq, Jun 2012] ; PHENOTYPE: Homozygous null mutants have defective T cell, B cell, and NK cell morphology and physiology. Mice carrying an engineered point mutation exhibit lymphoproliferation and autoimmunity that leads to premature death. [provided by MGI curators]
• Mapped: Yes
• Institutional Source: Australian Phenomics Network
• Gene Model: not available
• AlphaFold: P06800
• SMART Domains: Protein: ENSMUSP00000138800; Gene: ENSMUSG00000026395

Domain	Start	End	E-Value	Type
Pfam:PTP_N	7	32	4.2e-13	PFAM
low complexity region	33	66	N/A	INTRINSIC
Pfam:CD45	72	131	2.3e-24	PFAM
FN3	235	319	2.28e0	SMART
FN3	335	413	3.48e-1	SMART
transmembrane domain	428	449	N/A	INTRINSIC
PTPc	502	764	7.57e-127	SMART
PTPc	793	1079	1.39e-102	SMART

• Predicted Effect: probably benign
• SMART Domains: Protein: ENSMUSP00000138800; Gene: ENSMUSG00000026395

Domain	Start	End	E-Value	Type
Pfam:PTP_N	7	32	4.2e-13	PFAM
low complexity region	33	66	N/A	INTRINSIC
Pfam:CD45	72	131	2.3e-24	PFAM
FN3	235	319	2.28e0	SMART
FN3	335	413	3.48e-1	SMART
transmembrane domain	428	449	N/A	INTRINSIC
PTPc	502	764	7.57e-127	SMART
PTPc	793	1079	1.39e-102	SMART

• Predicted Effect: probably benign
• SMART Domains: Protein: ENSMUSP00000138275; Gene: ENSMUSG00000026395

Domain	Start	End	E-Value	Type
Pfam:PTP_N	7	34	5.5e-13	PFAM
Pfam:CD45	48	107	2.3e-24	PFAM
FN3	211	295	2.28e0	SMART
FN3	311	389	3.48e-1	SMART
transmembrane domain	404	425	N/A	INTRINSIC
PTPc	478	740	7.57e-127	SMART
PTPc	769	1055	1.39e-102	SMART

• Predicted Effect: probably benign
• SMART Domains: Protein: ENSMUSP00000138275; Gene: ENSMUSG00000026395

Domain	Start	End	E-Value	Type
Pfam:PTP_N	7	34	5.5e-13	PFAM
Pfam:CD45	48	107	2.3e-24	PFAM
FN3	211	295	2.28e0	SMART
FN3	311	389	3.48e-1	SMART
transmembrane domain	404	425	N/A	INTRINSIC
PTPc	478	740	7.57e-127	SMART
PTPc	769	1055	1.39e-102	SMART

• Predicted Effect: probably benign
• SMART Domains: Protein: ENSMUSP00000138350; Gene: ENSMUSG00000026395

Domain	Start	End	E-Value	Type
Pfam:PTP_N	7	33	2.7e-13	PFAM
low complexity region	111	128	N/A	INTRINSIC
low complexity region	170	205	N/A	INTRINSIC
Pfam:CD45	211	270	2.1e-24	PFAM
FN3	374	458	2.28e0	SMART
FN3	474	552	3.48e-1	SMART
transmembrane domain	567	588	N/A	INTRINSIC
PTPc	641	903	7.57e-127	SMART
PTPc	932	1218	1.39e-102	SMART

• Predicted Effect: probably benign
• SMART Domains: Protein: ENSMUSP00000138350; Gene: ENSMUSG00000026395

Domain	Start	End	E-Value	Type
Pfam:PTP_N	7	33	2.7e-13	PFAM
low complexity region	111	128	N/A	INTRINSIC
low complexity region	170	205	N/A	INTRINSIC
Pfam:CD45	211	270	2.1e-24	PFAM
FN3	374	458	2.28e0	SMART
FN3	474	552	3.48e-1	SMART
transmembrane domain	567	588	N/A	INTRINSIC
PTPc	641	903	7.57e-127	SMART
PTPc	932	1218	1.39e-102	SMART

• Predicted Effect: probably benign
• Meta Mutation Damage Score: Not available
• Is this an essential gene?: Non Essential (E-score: 0.000)
• Phenotypic Category: Autosomal Recessive
• Penetrance: 100%
• Mode of Inheritance: Autosomal Recessive
• Local Stock: None
• Last Updated: 2019-06-06 4:02 PM by Diantha La Vine
• Record Created: 2010-03-18 5:06 PM by Eva Marie Y. Moresco
• Record Posted: 2010-04-08
• Science Writers: Eva Marie Y. Moresco
• Illustrators: Katherine Timer
• Authors: Adele Yates, Aude M. Fahrer, Sylvie Lesage, Keats Nelms, Christopher C. Goodnow

Accession Number

NCBI RefSeq: NM_001111316 (isoform 1), NM_011210 (isoform 2); MGI: 97810

Alleles Listed at MGI

All alleles(8) : Targeted, knock-out(3) Targeted, other(3) Chemically induced(2)

Repository

Australian PhenomeBank: 157

Phenotypic Description

The lochy phenotype was identified among ENU-mutagenized G3 mice. Homozygous mice display reduced numbers of peripheral T cells, as well as a shift towards an activated/memory CD8⁺ T cell phenotype in which the proportion of naïve CD8⁺ T cells (CD8⁺CD44^lo) is reduced.  Co-receptor expression is 1.5-fold higher on lochy T cells versus wild type T cells. Single positive (SP) CD4⁺CD8^– and CD4^–CD8⁺ thymocytes are reduced 10-fold and 5-fold, respectively, in homozygous lochy relative to wild type mice.  DP thymocytes are reduced 3-fold and have 2.5-fold higher cell surface expression of CD4 and CD8 in lochy mice compared to wild type mice. The decrease in DP thymocytes is non-cell intrinsic, whereas the decrease in SP thymocytes is cell intrinsic. CD5 is downregulated on DP thymocytes in a cell-intrinsic manner; CD5 is upregulated on peripheral T cells of lochy mice. TCRβ is elevated on DP thymocytes and downregulated on mature T cells of lochy mice. Thymic selection is impaired in lochy mice, as indicated by reduced numbers of thymic TCRβ^hi and CD69⁺ T cells and a block in maturation from the DP to SP stage. No CD45 protein is visually detectable by immunoblot analysis of homozygous lochy thymocytes.

 

Homozygous lochy mice have normal numbers of B cells and bone marrow B220⁺CD19⁺ cells, but reduced numbers of bone marrow B220^loCD19⁺ cells. Numbers of IgM⁺IgD^–, IgM⁺IgD⁺ and IgD⁺CD21(CR2)⁺ B cells in lochy bone marrow are slightly diminished.  CD19⁺ B cells from homozygous lochy mice display reduced expression of CD45.

Nature of Mutation

The lochy mutation was mapped to Chromosome 1, and corresponds to a T to A transversion at position 91477 of the genomic DNA sequence of Ptprc (Genbank genomic region NC_000067), in intron 17. The mutation creates a splice acceptor site that is used preferentially over the normal splice acceptor site three nucleotides away, and thus results in the insertion of 5 bp (ATCAG) after nucleotide 1791 or 1374 of the mRNA for Ptprc isoform 1 (NM_001111316) or isoform 2 (NM_011210), respectively. The insertion causes a frame shift that introduces 26 aberrant amino acids before a premature stop (Figure 1).

           <--exon 17       intron 17        exon 18-->
86750 GCCAGCTACATTGAT gtaagta… gtgttttgatcag GGCTTCAAGGAA…TGACTTCTGGAGGATGA
      -A--S--Y--I--D-                  -I--R --A--S--R--N…M--T--S--G--G--*
         normal                                       aberrant

Figure 1. Domain structure of the CD45RABC isoform. The extracellular N-terminal A, B, and C regions are encoded by exons 4, 5, and 6, respectively, and are heavily O-glycosylated. The remainder of the extracelluar domain contains 15 sites for N-glycosylation. The catalytic cysteine (828) is indicated within the PTP D1 domain. The lochy mutation (shown in red) corresponds to a T to A transversion in intron 17. The mutation creates a splice acceptor site that is used preferentially over the normal splice acceptor site three nucleotides away, and thus results in the insertion of 5 bp (ATCAG). The insertion causes a frame shift that introduces 26 aberrant amino acids before a premature stop. FNIII=Type III fibronectin; TM=Transmembrane domain; PTP=Protein tyrosine phosphatase. This image is interactive. Other mutations found in CD45 are noted in red. Click on the mutations for more specific information. 

The mutated nucleotide is indicated within the Ptprc genomic sequence. The normal intron 17 splice donor site is in blue; the new splice donor site created by the mutation is highlighted in gray. Effect of the mutation at the protein level is shown.

 

Please see the record for belittle for information about CD45.

Putative Mechanism

Ptprc^-/- mice have profound defects in thymic development due to dysfunctional signaling through the preTCR and TCR, leading to a block in thymocyte development at β selection and at the DP stage (1-3). As a result, the absolute number of DP thymocytes is reduced twofold, and the number of single positive (SP) thymocytes is reduced five-fold. Peripheral B cell numbers are actually increased in CD45-deficient mice.  The similarity of phenotypes of Ptprc^lochy/lochy and Ptprc^-/- mice suggests that the lochy mutation abrogates CD45 expression, a hypothesis supported by absence of CD45 in immunoblot analysis of homozygous lochy thymocytes. However, lochy B cells display low levels of CD45 expression. It may be that the lochy mutation preferentially affects the shorter CD45 isoforms found on T cells over the full-length forms exclusively expressed on B cells. CD45 regulates TCR signaling; the shift towards an activated/memory CD8⁺ T cell phenotype suggests that TCR signaling is dysregulated in lochy mice.

Primers

Primers cannot be located by automatic search.

Genotyping

Genotyping protocols are from the Australian PhenomeBank.

Lochy

References

1. Mee, P. J., Turner, M., Basson, M. A., Costello, P. S., Zamoyska, R., and Tybulewicz, V. L. (1999) Greatly Reduced Efficiency of both Positive and Negative Selection of Thymocytes in CD45 Tyrosine Phosphatase-Deficient Mice. Eur. J. Immunol. 29, 2923-2933.

2. Byth, K. F., Conroy, L. A., Howlett, S., Smith, A. J., May, J., Alexander, D. R., and Holmes, N. (1996) CD45-Null Transgenic Mice Reveal a Positive Regulatory Role for CD45 in Early Thymocyte Development, in the Selection of CD4+CD8+ Thymocytes, and B Cell Maturation. J. Exp. Med. 183, 1707-1718.

3. Kishihara, K., Penninger, J., Wallace, V. A., Kundig, T. M., Kawai, K., Wakeham, A., Timms, E., Pfeffer, K., Ohashi, P. S., and Thomas, M. L. (1993) Normal B Lymphocyte Development but Impaired T Cell Maturation in CD45-exon6 Protein Tyrosine Phosphatase-Deficient Mice. Cell. 74, 143-156.