Phenotypic Mutation 'rain' (pdf version)
Allelerain
Mutation Type missense
Chromosome7
Coordinate30,576,959 bp (GRCm39)
Base Change A ⇒ G (forward strand)
Gene Cd22
Gene Name CD22 antigen
Synonym(s) Lyb8, Lyb-8
Chromosomal Location 30,564,829-30,579,767 bp (-) (GRCm39)
MGI Phenotype PHENOTYPE: Homozygous null mice have reduced mature B cell numbers with altered proliferation kinetics and reduced antibody production to T cell independent antigens. [provided by MGI curators]
Accession Number

NCBI RefSeq: NM_001043317 (variant 1), NM_009845 (variant 2); MGI:88322

MappedYes 
Limits of the Critical Region 30865402 - 30880342 bp
Amino Acid Change Isoleucine changed to Threonine
Institutional SourceBeutler Lab
Gene Model predicted gene model for protein(s): [ENSMUSP00000019248] [ENSMUSP00000103760] [ENSMUSP00000139685] [ENSMUSP00000140450] [ENSMUSP00000140521] [ENSMUSP00000139871] [ENSMUSP00000140528] [ENSMUSP00000150025] [ENSMUSP00000140014] [ENSMUSP00000141178]
AlphaFold no structure available at present
SMART Domains Protein: ENSMUSP00000019248
Gene: ENSMUSG00000030577
AA Change: I116T

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
IG 31 147 2.75e-1 SMART
IG_like 156 254 4.07e1 SMART
IGc2 269 337 2.68e-4 SMART
IGc2 365 424 4.52e-11 SMART
IG 448 523 1.21e-2 SMART
IGc2 541 599 6.75e-10 SMART
IGc2 628 687 2.68e-4 SMART
transmembrane domain 709 726 N/A INTRINSIC
Predicted Effect probably damaging

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000019248)
SMART Domains Protein: ENSMUSP00000103760
Gene: ENSMUSG00000030577
AA Change: I116T

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
IG 31 147 2.75e-1 SMART
IG_like 156 254 4.07e1 SMART
IGc2 269 337 2.68e-4 SMART
IGc2 365 424 4.52e-11 SMART
IG 448 523 1.21e-2 SMART
IGc2 541 599 6.75e-10 SMART
IGc2 628 687 2.68e-4 SMART
transmembrane domain 709 726 N/A INTRINSIC
Predicted Effect probably damaging

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000108125)
SMART Domains Protein: ENSMUSP00000139685
Gene: ENSMUSG00000030577
AA Change: I116T

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
IG 31 147 2.75e-1 SMART
IG_like 156 254 4.07e1 SMART
IGc2 269 337 2.68e-4 SMART
IGc2 365 424 4.52e-11 SMART
IG 448 523 1.21e-2 SMART
IGc2 541 599 6.75e-10 SMART
IGc2 628 687 2.68e-4 SMART
transmembrane domain 709 726 N/A INTRINSIC
Predicted Effect probably damaging

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000186154)
SMART Domains Protein: ENSMUSP00000140450
Gene: ENSMUSG00000030577
AA Change: I116T

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
IG 31 147 1.1e-3 SMART
Predicted Effect probably damaging

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000188157)
SMART Domains Protein: ENSMUSP00000140521
Gene: ENSMUSG00000030577
AA Change: I116T

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
IG 31 147 2.75e-1 SMART
IG_like 156 254 4.07e1 SMART
IGc2 269 337 2.68e-4 SMART
IGc2 365 424 4.52e-11 SMART
IG 448 523 1.21e-2 SMART
IGc2 541 599 6.75e-10 SMART
IGc2 628 687 2.68e-4 SMART
transmembrane domain 709 726 N/A INTRINSIC
Predicted Effect probably damaging

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000189718)
SMART Domains Protein: ENSMUSP00000139871
Gene: ENSMUSG00000030577
AA Change: I116T

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
IG 31 147 2.75e-1 SMART
IG_like 156 254 4.07e1 SMART
IGc2 269 337 2.68e-4 SMART
IGc2 365 424 4.52e-11 SMART
IG 448 523 1.21e-2 SMART
IGc2 541 599 6.75e-10 SMART
IGc2 628 687 2.68e-4 SMART
transmembrane domain 709 726 N/A INTRINSIC
Predicted Effect probably damaging

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000190617)
SMART Domains Protein: ENSMUSP00000140528
Gene: ENSMUSG00000030577
AA Change: I116T

DomainStartEndE-ValueType
signal peptide 1 18 N/A INTRINSIC
IG 31 147 1.1e-3 SMART
IG_like 166 245 1.6e-2 SMART
IGc2 269 337 1.1e-6 SMART
Predicted Effect probably damaging

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
(Using ENSMUST00000190646)
Predicted Effect unknown
Predicted Effect probably benign
Predicted Effect probably benign
Predicted Effect probably benign
Meta Mutation Damage Score 0.9292 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 mutations/alleles(19) : Chemically induced (ENU)(5) Targeted(13)

Lab Alleles
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00714:Cd22 APN 7 30575572 missense probably benign 0.01
IGL02236:Cd22 APN 7 30566893 missense possibly damaging 0.54
IGL02321:Cd22 APN 7 30569308 missense probably damaging 1.00
IGL02335:Cd22 APN 7 30575559 missense probably damaging 1.00
IGL02397:Cd22 APN 7 30577050 missense probably benign
IGL02402:Cd22 APN 7 30576955 missense possibly damaging 0.86
IGL02538:Cd22 APN 7 30576985 missense probably benign 0.40
IGL02736:Cd22 APN 7 30577470 splice site probably null
blitz UTSW 7 30569329 missense probably damaging 1.00
crullers UTSW 7 30569308 missense probably damaging 1.00
gansu UTSW 7 30569530 missense probably damaging 1.00
lacrima UTSW 7 30575578 missense probably damaging 1.00
Lluvia UTSW 7 30569912 missense possibly damaging 0.48
Mist UTSW 7 30566083 missense probably damaging 1.00
well UTSW 7 30577212 nonsense probably null
Yosemite UTSW 7 30568934 critical splice donor site probably null
FR4304:Cd22 UTSW 7 30577507 missense possibly damaging 0.95
FR4340:Cd22 UTSW 7 30577507 missense possibly damaging 0.95
FR4342:Cd22 UTSW 7 30577507 missense possibly damaging 0.95
FR4589:Cd22 UTSW 7 30577507 missense possibly damaging 0.95
LCD18:Cd22 UTSW 7 30577507 missense possibly damaging 0.95
PIT4142001:Cd22 UTSW 7 30577224 missense possibly damaging 0.92
R0123:Cd22 UTSW 7 30566533 splice site probably benign
R0130:Cd22 UTSW 7 30569389 missense possibly damaging 0.92
R0926:Cd22 UTSW 7 30568934 critical splice donor site probably null
R1245:Cd22 UTSW 7 30569308 missense probably damaging 1.00
R1332:Cd22 UTSW 7 30569912 missense possibly damaging 0.48
R1457:Cd22 UTSW 7 30572595 missense probably benign 0.07
R1716:Cd22 UTSW 7 30577103 missense probably damaging 1.00
R1980:Cd22 UTSW 7 30572658 missense probably damaging 1.00
R2017:Cd22 UTSW 7 30572205 missense probably damaging 0.99
R2061:Cd22 UTSW 7 30575581 missense probably benign 0.03
R2061:Cd22 UTSW 7 30569530 missense probably damaging 1.00
R2075:Cd22 UTSW 7 30569123 missense probably damaging 1.00
R2216:Cd22 UTSW 7 30566471 missense probably damaging 1.00
R3886:Cd22 UTSW 7 30569532 missense possibly damaging 0.57
R4599:Cd22 UTSW 7 30575325 missense probably damaging 0.98
R4701:Cd22 UTSW 7 30575578 missense probably damaging 1.00
R4796:Cd22 UTSW 7 30572381 splice site probably null
R5179:Cd22 UTSW 7 30575299 missense possibly damaging 0.81
R5233:Cd22 UTSW 7 30576959 missense probably damaging 1.00
R5456:Cd22 UTSW 7 30575464 missense probably benign 0.02
R5511:Cd22 UTSW 7 30569496 missense probably damaging 1.00
R5513:Cd22 UTSW 7 30566450 missense probably damaging 0.99
R5611:Cd22 UTSW 7 30577575 unclassified probably benign
R5656:Cd22 UTSW 7 30569198 missense probably damaging 1.00
R5966:Cd22 UTSW 7 30566083 missense probably damaging 1.00
R6329:Cd22 UTSW 7 30577193 missense probably damaging 0.99
R6356:Cd22 UTSW 7 30577127 missense probably damaging 1.00
R6455:Cd22 UTSW 7 30575578 missense probably damaging 1.00
R6550:Cd22 UTSW 7 30576977 missense probably benign 0.00
R6656:Cd22 UTSW 7 30577182 missense probably benign 0.11
R6688:Cd22 UTSW 7 30572389 missense possibly damaging 0.91
R6844:Cd22 UTSW 7 30572856 splice site probably null
R6957:Cd22 UTSW 7 30566999 missense possibly damaging 0.88
R7068:Cd22 UTSW 7 30577504 missense probably benign 0.03
R7083:Cd22 UTSW 7 30567473 missense probably damaging 0.99
R7225:Cd22 UTSW 7 30577059 missense not run
R7732:Cd22 UTSW 7 30569482 missense probably damaging 1.00
R8686:Cd22 UTSW 7 30569494 missense probably benign 0.03
R8851:Cd22 UTSW 7 30577084 missense probably benign 0.01
R8987:Cd22 UTSW 7 30577172 missense probably damaging 1.00
R9051:Cd22 UTSW 7 30575449 missense probably benign
R9098:Cd22 UTSW 7 30567391 missense probably benign 0.00
R9124:Cd22 UTSW 7 30572662 missense probably benign 0.01
R9167:Cd22 UTSW 7 30575430 missense probably benign 0.07
R9319:Cd22 UTSW 7 30569329 missense probably damaging 1.00
R9369:Cd22 UTSW 7 30576999 missense probably benign 0.09
X0025:Cd22 UTSW 7 30572844 splice site probably null
Z1176:Cd22 UTSW 7 30568955 missense probably damaging 1.00
Z1176:Cd22 UTSW 7 30567388 missense probably benign 0.03
Z1186:Cd22 UTSW 7 30566891 missense probably benign
Z1186:Cd22 UTSW 7 30566478 missense probably benign 0.01
Z1186:Cd22 UTSW 7 30575292 missense probably damaging 0.97
Mode of Inheritance Autosomal Recessive
Local Stock
Repository
Last Updated 2019-09-04 9:40 PM by Diantha La Vine
Record Created 2017-06-04 10:13 AM by Xue Zhong
Record Posted 2017-08-04
Phenotypic Description

Figure 1. Rain mice exhibit decreased B to T cell ratios. Flow cytometric analysis of peripheral blood was utilized to determine B and T cell frequencies. 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. Rain mice exhibit decreased frequencies of peripheral 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. Rain mice exhibit decreased frequencies of peripheral 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 4. Rain mice exhibit decreased frequencies of peripheral IgM+ 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 5. Rain mice exhibit increased frequencies of peripheral 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. Rain mice exhibit increased frequencies of peripheral CD4+ 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 7. Rain mice exhibit increased frequencies of peripheral 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 8. Rain mice exhibit decreased expression of IgD on peripheral B cells. Flow cytometric analysis of peripheral blood was utilized to determine IgD 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 9. Rain mice exhibit decreased expression of IgM on peripheral B cells. Flow cytometric analysis of peripheral blood was utilized to determine IgD 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.

The rain phenotype was identified among N-ethyl-N-nitrosourea (ENU)-mutagenized G3 mice of the pedigree R5233, some of which showed a reduced B to T cell ratio (Figure 1) due to reduced frequencies of B cells (Figure 2), IgD+ B cells (Figure 3), and IgM+ B cells (Figure 4) with concomitant increased frequencies of T cells (Figure 5), CD4+ T cells (Figure 6), and CD8+ T cells (Figure 7), all in the peripheral blood. The expression of IgD (Figure 8) and IgM (Figure 9) on peripheral B cells was reduced
.

Nature of Mutation

Figure 10. Linkage mapping of the reduced B cell frequency using a recessive model of inheritance. Manhattan plot shows -log10 P values (Y-axis) plotted against the chromosome positions of 56 mutations (X-axis) identified in the G1 male of pedigree R5233. 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 56 mutations. All of the above anomalies were linked by continuous variable mapping to a mutation in Cd22: an A to G transition at base pair 30,877,534 (v38) on chromosome 7, or base pair 2,808 in the GenBank genomic region NC_000073. The strongest association was found with a recessive model of linkage to the normalized frequency of B cells in the peripheral blood, wherein 12 variant homozygotes departed phenotypically from 29 homozygous reference mice and 41 heterozygous mice with a P value of 2.333 x 10-14 (Figure 10). A substantial semidominant effect was observed in several of the assays, but the mutation is preponderantly recessive, and in no assay was a purely dominant effect observed. 

The mutation corresponds to residue 709 in the mRNA sequence NM_001043317 (variant 1) within exon 5 of 16 total exons and to residue 584 in the mRNA sequence NM_009845 (variant 2) within exon 3 of 14 total exons.

2793 AATTGTACCCTGAAAATCCACCCGATACGTGCC

111  -N--C--T--L--K--I--H--P--I--R--A-

  

Genomic DNA numbering corresponds to NC_000073. The mutated nucleotide is indicated in red. The mutation results in an isoleucine to threonine substitution at position 116 (I116T) in both isoforms of the CD22 protein, and is strongly predicted by PolyPhen-2 to be damaging (score = 1.000).

Illustration of Mutations in
Gene & Protein
Protein Prediction
Figure 11. Domain structure of CD22. The rain mutation results in an isoleucine to threonine substitution at position 116 (I116T). Abbreviations: SP, signaling peptide; TM, transmembrane domain; ITIM, immunoreceptor tyrosine-based inhibitory motif. The image is interactive; click to view other mutations affecting CD22.

CD22 belongs to the Siglec (sialic acid-binding) family of adhesion molecules (1;2). Siglecs are members of the immunoglobulin (Ig) superfamily, which specifically recognize sialic acids attached to the terminal regions of cell-surface glycoconjugates. Siglec proteins are type 1 transmembrane proteins with a sialic acid-binding N-terminal Ig-like V-type domain, variable numbers of Ig-like C2-type domains, a transmembrane region, and a cytoplasmic tail. CD22 contains seven Ig-like C2-type domains in its extracellular region at amino acids 31-147, 156-254, 269-337, 365-424, 448-523, 541-599, and 628-687 (Figure 11(1). The rain mutation results in an isoleucine to threonine substitution at position 116 (I116T); residue 116 is within the Ig-like V-type domain.

See the record well for more information about Cd22.

Putative Mechanism

CD22 is one of two Siglecs expressed by B cells (the other being Siglec-G), and was originally identified as a B cell-associated adhesion protein that functions in the regulation of B cell activation [reviewed in (3;4)].  CD22 associates with a number of BCR signaling molecules including the BCR complex itself. Upon cross-linking of the BCR by antigen, associated CD22 is rapidly phosphorylated by Lyn (5-7).  The subsequent association of SHP1 with CD22 leads to the dephosphorylation of a number of BCR signaling components that dampens the BCR signal and Ca2+mobilization such as Vav-1, CD19, and BLNK (8-10). In response to BCR stimulation, CD22-deficient B cells predominantly undergo apoptosis (11). Although CD22 appears to be dispensable for the differentiation of B cells to mature follicular cells, CD22-deficient B cells express less surface IgM, which may be a consequence of a faster and more complete maturation process. In addition, CD22-deficient mice have severely reduced numbers of marginal zone B (MZB) cells, and increased numbers of B-1 peritoneal cells was observed in two of the four knockout strains (12-15). The loss of MZB cells and increased B-1 cell numbers in these mice may be due to altered BCR signaling during development as maturation into the three mature B cell subsets is driven in part by differences in BCR signal strength, and a strong BCR signal disrupts MZB development and promotes B-1 differentiation [reviewed by (16;17)]. Due to the lack of MZB cells, these animals display impaired immune responses to T-independent antigens (12;15;18), while T-dependent immune responses remain intact and subsequent germinal center formation occurs normally (11). Mice carrying the rain allele share several phenotypes with the Cd22 knockout mice including defects in peripheral B cell maturation that are likely caused by reduced MZB cell numbers. A defect in immune responses to T-dependent or T-independent antigens was not observed in the rain mice indicating that some residual CD22 function may occur in the rain mice.

Primers PCR Primer
rain_pcr_F: CAAAGCTTCCTATTTGGTGAGC
rain_pcr_R: AAGGCACGTCTGGACAACATC

Sequencing Primer
rain_seq_F: AGGAGCCAGCCATTCTTTG
rain_seq_R: GGACAACATCCTCCTTTTTCAGAAC
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 776 nucleotides is amplified (chromosome 7, - strand):


1   aaggcacgtc tggacaacat cctccttttt cagaactatg agtttgacaa ggccaccaag
61  aaattcacag gaactgtcct gtacaacgcc acaaagactg agaaggaccc agagtctgag
121 ctgtaccttt ctaagcaagg gagagtaaca tttctgggga acagaataga caattgtacc
181 ctgaaaatcc acccgatacg tgccaatgac agtgggaatc tggggttgag gatgaccgca
241 gggactgaac gatggatgga gcccattcac ctcaatgtct cgggtaaggc atggggagac
301 agccaactgt tctagcggca gcaaagaggg acctgctcaa accctggagc aaacagccaa
361 ggtgcctatt taacatatta aagagggcct ggcaccagat tctcccagca tccctcagtc
421 cctacctatt acaaagaatg gctggctcct ggcccccact ctctagccca tctccccagc
481 ccaagagccg ggctgcccct cccccaggct cttccctata taatccagcc atctgggtag
541 cccaccctct tttacctcta gcccatttcc ttggctgctg tacctggttc ccctctccca
601 cccttcctca cctggctcgg ggtcatatcc actctggact ctcccagatg tgcctgcctc
661 tggctatgtt ctccctttta tctacaatat aatttctctt ccaccacacc taggagcaat
721 catgttcttt cctttttatt tctccttttc atttgctcac caaataggaa gctttg


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

References
  1. Torres, R. M., Law, C. L., Santos-Argumedo, L., Kirkham, P. A., Grabstein, K., Parkhouse, R. M., and Clark, E. A. (1992) Identification and Characterization of the Murine Homologue of CD22, a B Lymphocyte-Restricted Adhesion Molecule. J Immunol. 149, 2641-2649.
Science Writers Anne Murray
AuthorsXue Zhong, Aijie Liu, Bruce Beutler