Phenotypic Mutation 'Surface' (pdf version)
AlleleSurface
Mutation Type missense
Chromosome12
Coordinate113,379,819 bp (GRCm39)
Base Change T ⇒ C (forward strand)
Gene Ighd
Gene Name immunoglobulin heavy constant delta
Synonym(s) IgD
Chromosomal Location 113,371,155-113,379,944 bp (-) (GRCm39)
MGI Phenotype PHENOTYPE: Homozygotes for a null allele show delayed antibody affinity maturation and reduced IgE levels. Homozygotes for another null allele show 30-50% less B cells in spleen and lymph nodes, reduced IgG2b levels, and increased IgA levels. Homozygotes for an ENU-induced allele show shifted IgD expression. [provided by MGI curators]
Accession Number

MGI:96447

MappedYes 
Limits of the Critical Region 113406604 - 113416324 bp
Amino Acid Change Lysine changed to Glutamic Acid
Institutional SourceBeutler Lab
Gene Model predicted gene model for protein(s):
AlphaFold no structure available at present
Meta Mutation Damage Score 0.0898 question?
Is this an essential gene? Probably nonessential (E-score: 0.095) question?
Phenotypic Category Autosomal Semidominant
Candidate Explorer Status loading ...
Single pedigree
Linkage Analysis Data
Penetrance  
Alleles Listed at MGI

All Mutations and Alleles(5) : Chemically induced (ENU)(1) Targeted(2) Transgenic (2)

Lab Alleles
AlleleSourceChrCoordTypePredicted EffectPPH Score
surface2 UTSW 12 113379661 critical splice donor site probably benign
R4703:Ighd UTSW 12 113379661 critical splice donor site probably benign
R4792:Ighd UTSW 12 113379819 missense probably benign 0.01
R5087:Ighd UTSW 12 113378047 unclassified probably benign
R5821:Ighd UTSW 12 113373253 missense probably benign 0.02
R8020:Ighd UTSW 12 113378168 missense probably benign 0.01
R8073:Ighd UTSW 12 113379789 missense probably benign 0.01
R8732:Ighd UTSW 12 113378183 missense
R9168:Ighd UTSW 12 113379203 missense
R9707:Ighd UTSW 12 113378108 missense
R9802:Ighd UTSW 12 113371455 missense
Mode of Inheritance Autosomal Semidominant
Local Stock
Repository
Last Updated 2017-01-31 12:06 PM by Anne Murray
Record Created 2016-10-22 10:01 AM by Jin Huk Choi
Record Posted 2017-01-31
Phenotypic Description

Figure 1. Surface mice exhibit reduced expression of IgD on B cells. Flow cytometric analysis of peripheral blood was utilized to determine IgD mean fluorescence 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. Surface mice exhibit a decreased percentage 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.

The Surface phenotype was identified among N-ethyl-N-nitrosourea (ENU)-mutagenized G3 mice of the pedigree R4792, some of which showed reduced expression of IgD on B cells (Figure 1) with a concomitant reduction in the percentage of IgD+ B cells (Figure 2) in the peripheral blood.

Nature of Mutation

Figure 3. Linkage mapping of the reduced percentage of IgD+ B cells using an additive model of inheritance. Manhattan plot shows -log10 P values (Y-axis) plotted against the chromosome positions of 91 mutations (X-axis) identified in the G1 male of pedigree R4792. 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 91 mutations. Both of the above anomalies were linked by continuous variable mapping to a mutation in Ighd:  an A to G transition at base pair 113,416,199 (v38) on chromosome 12, or base pair 126 in the GenBank genomic region NC_000078 encoding Ighd.  The strongest association was found with an additive model of linkage to the normalized percentage of IgD+ B cells, wherein two variant homozygotes and 11 heterozygous mice departed phenotypically from four homozygous reference mice with a P value of 3.993 x 10-12 (Figure 3).  

The mutation corresponds to residue 126 in the cDNA sequence ENSMUST00000194162.5 within exon 1 of 5 total exons.

 
111 AGCTGGGAGCCAAAGAAGTCAAGTATAGTTGAA
37  -S--W--E--P--K--K--S--S--I--V--E-

 

Genomic numbering corresponds to NC_000078. The mutated nucleotide is indicated in red. The mutation results in a lysine (K) to glutamic acid (E) substitution at position 42 (K42E) in the IgD protein, and is strongly predicted by PolyPhen-2 to be benign (score = 0.015).

Illustration of Mutations in
Gene & Protein
Protein Prediction
Figure 4. Crystal structure of human Immunoglobulin M. UCSF Chimera model is based on PDB 2RCJ, Perkins et al. J.Mol.Biol. 221, 1345-1366 (1991). Click on the 3D structure to view it rotate.
Figure 5. Domain structure of Cδ. Mouse IgD heavy chain has two Ig-like domains (CH1 and CH2). The two CH domains are connected through a flexible hinge region. The transmembrane domain is indicated. The Surface mutation results in a lysine (K) to glutamic acid (E) substitution at position 42. This image is interactive; click to view other mutations and click the mutations to view more information.

The B cell receptor (BCR) consist of two functional components: an antigen binding component and a signaling component [reviewed in (1)]. The antigen binding component is a membrane bound form of immunoglobulin (mIg), which is a heterotetramer of two identical transmembrane spanning heavy chains (alpha, delta, epsilon, gamma, or mu) and two associated identical light chains (Figure 4). Ighd encodes immunoglobulin heavy chain constant delta (Cδ). A heterodimer of Igα (see the record for crab) and Igβ constitutes the signaling component of the BCR (2-4). The Igα/Igβ heterodimer associates noncovalently with all mIg isotypes (IgM, IgD, IgG, IgA, and IgE) (5), and is found in each BCR complex in a 1:1 stoichiometry with mIg (6).

Immunoglobulin heavy chain genes have a variable domain and a constant region. The variable domain is jointly contributed by the Ig heavy chain variable (V), diversity (D), and joining (J) genes. The IgD heavy chain has a high degree of structural plasticity and low conservation among vertebrates (7;8). Mouse IgD heavy chain has two Ig-like domains (CH1 and CH2, respectively) at the N-terminus and a transmembrane domain (Figure 5). The two CH domains are connected through a flexible hinge region. The number of Ig-like domains varies among vertebrates. Human Cδ has three CH domains and a long hinge region. The intracellular tail of membrane-bound IgD consists of three amino acids: Lys-Val-Lys (KVK). Because the cytoplasmic portion of mIg heavy chains is very short (three amino acids for IgM and IgD), BCR signaling depends on the interactions of the cytoplasmic domains of Igα and Igβ with downstream signaling molecules.

The human IgD heavy chain constant region is N-linked glycosylated at three sites (Asn354, Asn445, and Asn496) (9;10). N-linked glycosylation of Asn354 is essential for secretion. IgD molecules that lack that glycan were able to assemble only to the heavy/light chain half-molecule stage, but the heavy chains were retained in the endoplasmic reticulum (9). N-linked glycosylation of Asn445 and Asn496 were not required for IgD assembly and secretion.  

The Surface mutation results in a lysine (K) to glutamic acid (E) substitution at position 42. Amino acid 42 is within the first Ig-like domain.

Expression/Localization

Immature B cells in the bone marrow or fetal liver express IgM, but not IgD, on their surface. Most mature peripheral B cells in the adult express both IgM and IgD on their cell surface (11-13). IgD is the dominant antigen receptor on the surface of mature B2 cells.  Soluble IgD is expressed at lower levels than IgG, IgA, and IgM, but at higher levels than IgE.

After B cell activation by antigens, IgD is downregulated and the B cells enter the pathways of plasma cell or memory cell generation (14;15). Upon IgD downregulation, IgM expression is upregulated (16). ZFP318 (see the record for Wonton) functions as a transcription factor to regulate the expression of Ighm and Ighd during B cell maturation (17;18). B cell expression of IgD occurs developmentally through alternative splicing of the VDJH exon to the Ighm and Ighd exons (19-21). ZFP318 is required for balancing IgD and IgM output from Igh, but is not necessary for B cell maturation (17).

Background
Figure 6. BCR Signaling. In resting B cells (inset), BCRs are dispersed as monomers with one Igα/β heterodimer in a “closed” position. Upon stimulation, receptors translocate into lipid rafts and aggregate to form caps. The tails of Igα and Igβ become phosphorylated by Src family kinases (typically Lyn), causing them to take an open conformation and serve as docking sites for the adapter protein BLNK and the SH2 domains of SYK. SYK phosphorylates a number of downstream targets including BLNK, PLC-γ2 and protein kinase C β (PKCβ). BCR stimulation also activates phosphatidylinositol 3 kinase (PI3K) resulting in the generation of 3′-phosphorylated phosphoinositides. One of these lipids, phosphatidylinositol-3,4,5-triphosphate (PIP3), binds selectively to the pleckstrin homology (PH) domain of Btk, facilitating membrane recruitment of the kinase. Phosphorylated BLNK also provides docking sites for Btk, as well as PLC-γ2, which results in the additional phosphorylation and activation of PLC-γ2 by Btk leading to the hydrolysis of phosphatidylinositol-4,5-diphosphate (PIP2) to inositol-1,4,5-trisphosphate (IP3) and diacylglycerol (DAG). Soluble IP3 and membrane-bound DAG initiate downstream signal transduction pathways involving calcium (Ca2+) mobilization and PKC, respectively. The recruitment of Vav, Nck and Ras by BLNK to the BCR activates MAP kinase cascades such as JNK, p38 and extracellular signal regulated kinase (ERK). Together, these signals allow the activation of multiple transcription factors, including nuclear factor of activated T cells (NF-AT), nuclear factor (NF)-κB and AP-1, which subsequently regulate biological responses including cell proliferation, differentiation and apoptosis, as well as the secretion of antigen-specific antibodies. Other molecules that play important roles in BCR signaling include Bcl10, mucosa-associated lymphoid tissue translocation gene 1 (MALT1), and caspase recruitment domain family, member 11 (CARMA1 or CARD11), which are involved in NF-κB activation along with PKCβ. This image is interactive. Click on the image to view mutations found within the pathway (red) and the genes affected by these mutations (black). Click on the mutations for more specific information.

During B cell differentiation from immature to mature follicular or marginal zone cells, antibody isotypes serve as cell surface markers of B cell maturation, as distinct receptors for B cell activation, and as secreted mediators of antibody effector functions (22). During B cell maturation, immature B cells in the bone marrow only express the IgM isotype on their cell surface (23). The IgM isotype is comprised of heavy (H) chains with an N-terminal variable domain, C-terminal constant region domains, a transmembrane segment, and a cytoplasmic tail. Upon maturation into circulating follicular B cells, the B cells coexpress a second isotype, IgD. Mature follicular B cells display cell surface B cell receptors comprised of the same variable domain joined to either IgD or IgM constant regions (11;19). Upon B cell activation by antigens and helper T cells, the B cells undergo isotype switching and lose IgM and IgD, switching to express the same variable domain linked to IgG, IgA, or IgE constant region domains. Isotype switching involves DNA recombination of the Ig heavy chain locus, Igh, and subsequent deletion of Ighm and Ighd constant region exons and the reorganization of the IghgIghe, or Igha constant region exons immediately 3’ to the VDJH variable exon. The VDJH exon is then spliced to IgG, IgE, or IgA constant region exons in the mRNA (24;25).

B cells induce numerous responses to microbial infections, including antigen internalization, proliferation, T cell-independent antibody production, and the T cell-dependent antibody response.  These responses are initiated upon antigen binding by the BCR, which rapidly recruits a signaling complex through interactions with Src family kinases (SFK) and the tyrosine kinase Syk (Figure 6).  These kinases recruit and activate other molecules, notably BLNK (see busy) and Pik3ap1 (also called BCAP) (see sothe) followed by PI-3K and Btk, that lead to activation of PLC-γ2 (see queen), which hydrolyzes phosphatidylinositol-4,5-bisphosphate (PIP2) to diacylglycerol (DAG) and inositol-1,4,5-triphosphate (IP3).  Ultimately, through activation of IP3 receptors on the endoplasmic reticulum, IP3 triggers a large influx of Ca2+ to the cytoplasm. Sustained elevation of cytosolic Ca2+ regulates the activity of transcription factors including NF-AT and NF-κB (see xander and Finlay).  BCR engagement also activates pathways regulated by PKCβ (see Untied), PI-3K, and Ras/MAPK, which further modulate B cell responses [see (26;27for reviews of B cell antigen receptor signaling]. For more information about BCR-associated signaling, please see the record for crab. IgD is a potent inducer of TNF, IL1B, and IL1RN. IgD also induces release of IL6, IL10, and LIF from peripheral blood mononuclear cells. The function of soluble IgD is not known.

IgD-deficient mice have normal frequencies of B cells in the lymph node and spleen (28). A second study found that IgD-deficient mice exhibited 30 to 50% less B cells in the spleen and lymph nodes, but had a normal pre-B cell compartment (16). The loss of IgD expression resulted in an increase in IgM expression and comparable amounts of surface Ig expressed on B cells (16;28). T cell frequency and the ratio of CD4 to CD8 T cells in the IgD-deficient mice were normal (28). The IgD-deficient mice respond efficiently to both T-dependent and T-independent antigens (16;28). Affinity maturation of serum antibodies was delayed in the IgD-deficient mice (28).

Putative Mechanism

The phenotypes observed in the Surface mice indicate loss of IgD expression and/or function.

Primers PCR Primer
Surface_pcr_F: TTCTGAGGTGTGGATGTCAAGTG
Surface_pcr_R: TGTCTTGCAGGTAATGAAAAGGG

Sequencing Primer
Surface_seq_F: GTGTTGTGTTGATGAAGCAG
Surface_seq_R: GACCTGACATGTTCCTCCTC
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 485 nucleotides is amplified (chromosome 12, - strand):


1   tgtcttgcag gtaatgaaaa gggacctgac atgttcctcc tctcagagtg caaagcccca
61  gaggaaaatg aaaagataaa cctgggctgt ttagtaattg gaagtcagcc actgaaaatc
121 agctgggagc caaagaagtc aagtatagtt gaacatgtct tcccctctga aatgagaaat
181 ggcaattata caatggtcct ccaggtcact gtgctggcct cagaactgaa cctcaaccac
241 acttgcacca taaataaacc caaaaggaaa gaaaaacctt tcaagtttcc tggtgagtat
301 ccctggacca tgcagaaggg ccttgtggga cttctcatac ccacactcag ctaatcccca
361 aagattgact gaagcaagac atccccccaa ctttgatccc tccccttcct tgctcttccc
421 ccattcattc cctccctttt ctcagctgct tcatcaacac aacacttgac atccacacct
481 cagaa


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

Science Writers Anne Murray
Illustrators Diantha La Vine, Katherine Timer
AuthorsMing Zeng, Xue Zhong, Jin Huk Choi, and Bruce Beutler