Incidental Mutation 'R4816:H2-Aa'
ID 369855
Institutional Source Beutler Lab
Gene Symbol H2-Aa
Ensembl Gene ENSMUSG00000036594
Gene Name histocompatibility 2, class II antigen A, alpha
Synonyms H-2Aa, I-Aalpha, Ia-1, Aalpha, Ia1, A alpha
MMRRC Submission 042434-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4816 (G1)
Quality Score 165
Status Validated
Chromosome 17
Chromosomal Location 34282744-34287827 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to T at 34283820 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 124 (V124E)
Ref Sequence ENSEMBL: ENSMUSP00000046105 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000040655] [ENSMUST00000174751]
AlphaFold no structure available at present
Crystal structure of murine class II MHC I-Ab in complex with a human CLIP peptide [X-RAY DIFFRACTION]
Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR B3K506 [X-RAY DIFFRACTION]
Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR YAe62 [X-RAY DIFFRACTION]
Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR 2W20 [X-RAY DIFFRACTION]
Crystal Structure of 809.B5 TCR complexed with MHC Class II I-Ab/3k peptide [X-RAY DIFFRACTION]
J809.B5 TCR bound to IAb/3K [X-RAY DIFFRACTION]
J809.B5 Y31A TCR bound to IAb3K [X-RAY DIFFRACTION]
14.C6 TCR complexed with MHC class II I-Ab/3K peptide [X-RAY DIFFRACTION]
Predicted Effect probably damaging
Transcript: ENSMUST00000040655
AA Change: V124E

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000046105
Gene: ENSMUSG00000036594
AA Change: V124E

MHC_II_alpha 31 111 1.83e-45 SMART
IGc1 129 200 2.51e-27 SMART
Pfam:C1-set_C 203 255 2.1e-30 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000165139
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173944
Predicted Effect probably damaging
Transcript: ENSMUST00000174751
AA Change: V41E

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000133399
Gene: ENSMUSG00000036594
AA Change: V41E

signal peptide 1 23 N/A INTRINSIC
IGc1 46 117 2.51e-27 SMART
low complexity region 141 158 N/A INTRINSIC
Meta Mutation Damage Score 0.6059 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 93.0%
Validation Efficiency 97% (113/116)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] HLA-DQA1 belongs to the HLA class II alpha chain paralogues. The class II molecule is a heterodimer consisting of an alpha (DQA) and a beta chain (DQB), both anchored in the membrane. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen presenting cells (APC: B Lymphocytes, dendritic cells, macrophages). The alpha chain is approximately 33-35 kDa. It is encoded by 5 exons; exon 1 encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, and exon 4 encodes the transmembrane domain and the cytoplasmic tail. Within the DQ molecule both the alpha chain and the beta chain contain the polymorphisms specifying the peptide binding specificities, resulting in up to four different molecules. Typing for these polymorphisms is routinely done for bone marrow transplantation. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele lack cell surface expression of MHC class II molecules on macrophages and show decreased CD4-positive T cell number, increased CD8-positive T cell number, thymus hyperplasia, enlarged lymph nodes, and altered splenocyte response to staphylococcal enterotoxin B. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 107 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
0610010F05Rik A C 11: 23,615,243 (GRCm38) I248S possibly damaging Het
8030462N17Rik A T 18: 77,653,299 (GRCm38) probably null Het
Abcc8 C A 7: 46,104,707 (GRCm38) A1562S probably benign Het
Adam30 C A 3: 98,162,745 (GRCm38) D631E possibly damaging Het
Adgrv1 T C 13: 81,528,674 (GRCm38) T2013A probably damaging Het
Als2cr12 G A 1: 58,670,408 (GRCm38) A196V probably benign Het
Baiap3 T A 17: 25,247,295 (GRCm38) probably benign Het
Bicra T C 7: 15,988,906 (GRCm38) T229A possibly damaging Het
C1qbp A G 11: 70,982,364 (GRCm38) probably benign Het
C2cd3 C A 7: 100,391,019 (GRCm38) T265K probably benign Het
Cacna1s T A 1: 136,115,269 (GRCm38) I1331K possibly damaging Het
Cdadc1 AGACGGA AGA 14: 59,568,991 (GRCm38) probably null Het
Cdcp2 A G 4: 107,106,772 (GRCm38) Y273C probably damaging Het
Cdh23 A C 10: 60,409,077 (GRCm38) V1013G possibly damaging Het
Celf3 T A 3: 94,479,222 (GRCm38) I39N probably damaging Het
Cep152 A C 2: 125,563,754 (GRCm38) S1619R probably damaging Het
Cfap36 A G 11: 29,245,108 (GRCm38) I42T probably damaging Het
Cfap61 G T 2: 146,143,100 (GRCm38) V955L probably damaging Het
Cit G A 5: 115,908,691 (GRCm38) D388N probably damaging Het
Clca3a2 T C 3: 144,810,852 (GRCm38) M328V probably benign Het
Cntn4 A T 6: 106,550,497 (GRCm38) I447L probably benign Het
Csmd3 T C 15: 47,857,934 (GRCm38) T1538A possibly damaging Het
Cstf1 A G 2: 172,372,985 (GRCm38) K9E probably damaging Het
Dip2c T A 13: 9,575,150 (GRCm38) M560K probably benign Het
Dsg1a A T 18: 20,333,722 (GRCm38) T550S probably benign Het
Dtnb A G 12: 3,749,505 (GRCm38) E460G probably damaging Het
Dus1l GAGGTAAG GAG 11: 120,789,758 (GRCm38) probably benign Het
Efl1 T A 7: 82,671,719 (GRCm38) V120E probably damaging Het
Fbxl13 T C 5: 21,484,003 (GRCm38) Y769C probably benign Het
Fcho2 T C 13: 98,806,366 (GRCm38) Y22C probably damaging Het
Gbp3 T C 3: 142,567,574 (GRCm38) V294A probably damaging Het
Gls A G 1: 52,199,945 (GRCm38) probably benign Het
Gm15130 A T 2: 111,135,369 (GRCm38) probably benign Het
Gm6185 A T 1: 161,213,158 (GRCm38) noncoding transcript Het
Gpr171 T A 3: 59,098,096 (GRCm38) H86L probably damaging Het
Gpr179 T C 11: 97,339,248 (GRCm38) T694A probably damaging Het
H2-M5 A G 17: 36,989,417 (GRCm38) probably benign Het
Hist1h2bl A G 13: 21,715,965 (GRCm38) M60T probably benign Het
Igf2r A T 17: 12,684,097 (GRCm38) N2355K probably damaging Het
Il9r A C 11: 32,192,654 (GRCm38) S295A possibly damaging Het
Ipo9 T C 1: 135,406,550 (GRCm38) T313A probably benign Het
Kalrn C T 16: 34,514,019 (GRCm38) probably benign Het
Lama3 G A 18: 12,477,604 (GRCm38) V1175M possibly damaging Het
Lhpp T A 7: 132,670,375 (GRCm38) C242* probably null Het
Lipe A G 7: 25,380,143 (GRCm38) S1013P probably damaging Het
Lrrc25 C T 8: 70,618,076 (GRCm38) T169I probably benign Het
Lrrc39 T C 3: 116,568,866 (GRCm38) probably null Het
Lrrd1 T A 5: 3,851,126 (GRCm38) L477* probably null Het
Lrriq4 A G 3: 30,660,047 (GRCm38) I515V possibly damaging Het
Magel2 A G 7: 62,381,092 (GRCm38) Y1248C unknown Het
Maml1 G T 11: 50,258,335 (GRCm38) N859K possibly damaging Het
Mdm1 A T 10: 118,146,877 (GRCm38) H139L possibly damaging Het
Mef2d C T 3: 88,168,090 (GRCm38) P420S possibly damaging Het
Mgat4b A G 11: 50,211,021 (GRCm38) K38E probably benign Het
Mtmr4 T C 11: 87,604,097 (GRCm38) V405A probably damaging Het
Naip5 G A 13: 100,219,681 (GRCm38) S1142F probably benign Het
Naip5 G A 13: 100,219,687 (GRCm38) T1140M probably benign Het
Naip5 T C 13: 100,219,696 (GRCm38) Q1137R probably benign Het
Nfe2l3 T C 6: 51,456,624 (GRCm38) S239P probably damaging Het
Nlrp3 A G 11: 59,548,301 (GRCm38) I235V probably benign Het
Nyap2 T A 1: 81,241,313 (GRCm38) L318Q probably damaging Het
Nynrin G A 14: 55,872,001 (GRCm38) V1522M probably damaging Het
Olfr1016 A T 2: 85,800,047 (GRCm38) N74K probably benign Het
Olfr1461 A G 19: 13,165,124 (GRCm38) I37V probably benign Het
Olfr659 C T 7: 104,670,735 (GRCm38) P11L probably benign Het
Olfr810 T C 10: 129,791,439 (GRCm38) D50G probably damaging Het
Olfr875 T A 9: 37,773,430 (GRCm38) M257K possibly damaging Het
Oog3 A G 4: 144,159,161 (GRCm38) L289P probably damaging Het
Pax6 T C 2: 105,683,784 (GRCm38) probably benign Het
Pbrm1 G A 14: 31,110,448 (GRCm38) R1441K probably benign Het
Pcdha9 C T 18: 36,999,458 (GRCm38) R527W probably damaging Het
Pcdhb17 T C 18: 37,487,397 (GRCm38) S747P probably benign Het
Pcnx3 A C 19: 5,687,995 (GRCm38) probably null Het
Pds5a A T 5: 65,651,289 (GRCm38) V413E probably damaging Het
Phpt1 G T 2: 25,574,320 (GRCm38) probably benign Het
Phykpl A G 11: 51,592,953 (GRCm38) E220G probably benign Het
Pias2 T C 18: 77,105,891 (GRCm38) probably null Het
Pkhd1 T A 1: 20,199,415 (GRCm38) I3302L probably damaging Het
Poli A G 18: 70,522,751 (GRCm38) L241P probably damaging Het
Ppm1h T A 10: 122,679,379 (GRCm38) I65N possibly damaging Het
Ptpn14 T C 1: 189,856,800 (GRCm38) L954P probably damaging Het
Pxk T G 14: 8,136,893 (GRCm38) M138R probably damaging Het
Rasl11b G T 5: 74,198,397 (GRCm38) D188Y probably damaging Het
Rtraf A G 14: 19,822,576 (GRCm38) F59S probably benign Het
Serpinb5 G T 1: 106,872,339 (GRCm38) L86F probably damaging Het
Setdb2 G A 14: 59,413,646 (GRCm38) T412I probably benign Het
Shank2 C A 7: 144,052,306 (GRCm38) N75K probably damaging Het
Shank3 T A 15: 89,543,115 (GRCm38) I791N probably damaging Het
Slc25a13 T A 6: 6,114,274 (GRCm38) M213L possibly damaging Het
Slc25a21 T C 12: 56,713,838 (GRCm38) Y298C probably damaging Het
Slc34a2 A G 5: 53,069,020 (GRCm38) N495S probably damaging Het
Smc2 A G 4: 52,451,231 (GRCm38) T292A probably benign Het
Spag9 T C 11: 94,048,599 (GRCm38) probably benign Het
Tas2r113 C T 6: 132,893,782 (GRCm38) P258S probably benign Het
Tbkbp1 T C 11: 97,138,741 (GRCm38) S530G probably benign Het
Tenm2 A G 11: 36,027,290 (GRCm38) V1881A probably damaging Het
Tm9sf1 C T 14: 55,641,149 (GRCm38) R262Q possibly damaging Het
Tmcc3 G T 10: 94,578,784 (GRCm38) G147V possibly damaging Het
Trim38 A T 13: 23,788,281 (GRCm38) E195V probably damaging Het
Try5 T C 6: 41,313,415 (GRCm38) Y45C probably benign Het
Umad1 A C 6: 8,457,462 (GRCm38) probably benign Het
Vmn2r105 T C 17: 20,208,691 (GRCm38) I708V probably benign Het
Zc3h12d A T 10: 7,867,947 (GRCm38) S494C probably damaging Het
Zeb2 A G 2: 44,997,768 (GRCm38) S382P probably damaging Het
Zfc3h1 A G 10: 115,415,694 (GRCm38) S1304G probably benign Het
Zfp287 G T 11: 62,714,248 (GRCm38) T611K probably damaging Het
Zfp534 G A 4: 147,674,286 (GRCm38) T642I possibly damaging Het
Other mutations in H2-Aa
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00089:H2-Aa APN 17 34,284,530 (GRCm38) missense probably damaging 1.00
citation UTSW 17 34,287,677 (GRCm38) splice site probably null
reference UTSW 17 34,283,820 (GRCm38) missense probably damaging 1.00
G1citation:H2-Aa UTSW 17 34,287,677 (GRCm38) splice site probably null
R1556:H2-Aa UTSW 17 34,284,416 (GRCm38) missense possibly damaging 0.94
R1901:H2-Aa UTSW 17 34,283,233 (GRCm38) missense possibly damaging 0.65
R2144:H2-Aa UTSW 17 34,283,827 (GRCm38) missense probably damaging 1.00
R5607:H2-Aa UTSW 17 34,283,842 (GRCm38) missense possibly damaging 0.89
R5608:H2-Aa UTSW 17 34,283,842 (GRCm38) missense possibly damaging 0.89
R6264:H2-Aa UTSW 17 34,283,198 (GRCm38) missense probably damaging 0.98
R6822:H2-Aa UTSW 17 34,287,677 (GRCm38) splice site probably null
R6917:H2-Aa UTSW 17 34,283,707 (GRCm38) missense probably damaging 1.00
R7052:H2-Aa UTSW 17 34,284,510 (GRCm38) missense possibly damaging 0.50
R7116:H2-Aa UTSW 17 34,283,627 (GRCm38) nonsense probably null
R8168:H2-Aa UTSW 17 34,287,721 (GRCm38) missense possibly damaging 0.83
R8257:H2-Aa UTSW 17 34,283,237 (GRCm38) missense probably damaging 0.97
R8264:H2-Aa UTSW 17 34,287,735 (GRCm38) missense probably benign 0.18
R8682:H2-Aa UTSW 17 34,283,760 (GRCm38) missense possibly damaging 0.75
R9667:H2-Aa UTSW 17 34,283,321 (GRCm38) missense probably benign
X0063:H2-Aa UTSW 17 34,287,811 (GRCm38) unclassified probably benign
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2016-02-04