Incidental Mutation 'R1556:H2-Aa'
ID 170310
Institutional Source Beutler Lab
Gene Symbol H2-Aa
Ensembl Gene ENSMUSG00000036594
Gene Name histocompatibility 2, class II antigen A, alpha
Synonyms Ia1, I-Aalpha, H-2Aa, A alpha, Aalpha, Ia-1
MMRRC Submission 039595-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1556 (G1)
Quality Score 225
Status Not validated
Chromosome 17
Chromosomal Location 34501718-34506797 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 34503390 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Aspartic acid at position 69 (V69D)
Ref Sequence ENSEMBL: ENSMUSP00000046105 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000040655] [ENSMUST00000174751]
AlphaFold no structure available at present
PDB Structure CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IAb BOUND TO EALPHA3K PEPTIDE [X-RAY DIFFRACTION]
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 possibly damaging
Transcript: ENSMUST00000040655
AA Change: V69D

PolyPhen 2 Score 0.940 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000046105
Gene: ENSMUSG00000036594
AA Change: V69D

DomainStartEndE-ValueType
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 benign
Transcript: ENSMUST00000174751
SMART Domains Protein: ENSMUSP00000133399
Gene: ENSMUSG00000036594

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
IGc1 46 117 2.51e-27 SMART
low complexity region 141 158 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.1%
  • 10x: 95.4%
  • 20x: 89.3%
Validation Efficiency
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: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700030K09Rik T C 8: 73,203,477 (GRCm39) S302P probably damaging Het
Anapc1 T C 2: 128,466,819 (GRCm39) T1626A probably benign Het
Arhgef6 T C X: 56,383,922 (GRCm39) M5V probably benign Het
Arid5a T A 1: 36,359,245 (GRCm39) Y520* probably null Het
Aven G A 2: 112,461,230 (GRCm39) M215I probably damaging Het
Cabyr A G 18: 12,877,837 (GRCm39) D58G probably damaging Het
Ccdc146 A G 5: 21,535,551 (GRCm39) Y168H probably damaging Het
Ccnd2 A T 6: 127,107,363 (GRCm39) S269T probably benign Het
Cd68 T A 11: 69,556,676 (GRCm39) T44S probably damaging Het
Clstn2 A T 9: 97,338,558 (GRCm39) I867N probably benign Het
Cmss1 C T 16: 57,136,560 (GRCm39) R104H probably benign Het
Col6a6 A G 9: 105,586,672 (GRCm39) V1783A possibly damaging Het
Dach2 T C X: 112,208,214 (GRCm39) S31P probably benign Het
Dpp8 T A 9: 64,958,761 (GRCm39) W279R probably damaging Het
Fras1 A T 5: 96,890,921 (GRCm39) I2817F possibly damaging Het
Gabrr3 G A 16: 59,281,763 (GRCm39) D373N probably benign Het
Gdf7 T C 12: 8,351,698 (GRCm39) N79S unknown Het
Gpam A G 19: 55,064,763 (GRCm39) V647A possibly damaging Het
Gpatch1 T C 7: 34,994,776 (GRCm39) T497A probably benign Het
Grin2a A T 16: 9,525,579 (GRCm39) F337L probably benign Het
Gtf3c3 C T 1: 54,456,937 (GRCm39) A488T probably damaging Het
H2-M10.5 T C 17: 37,084,205 (GRCm39) Y56H probably damaging Het
Kcnu1 G A 8: 26,351,219 (GRCm39) probably null Het
Krt77 A G 15: 101,769,713 (GRCm39) S386P probably damaging Het
L3mbtl2 T A 15: 81,566,203 (GRCm39) M342K probably benign Het
Ldlrad1 A G 4: 107,075,010 (GRCm39) T186A probably benign Het
Lins1 C A 7: 66,360,385 (GRCm39) C168* probably null Het
Lrrtm3 G A 10: 63,923,928 (GRCm39) T413M probably damaging Het
Macf1 T C 4: 123,348,813 (GRCm39) D4038G probably damaging Het
Mark3 T G 12: 111,594,275 (GRCm39) N308K probably damaging Het
Mdga2 T A 12: 66,597,367 (GRCm39) Y709F possibly damaging Het
Mtus2 T A 5: 148,014,198 (GRCm39) S330R probably benign Het
Or1p1 T A 11: 74,179,762 (GRCm39) C97S probably damaging Het
Or4k15c G A 14: 50,321,916 (GRCm39) A74V possibly damaging Het
Or51a24 T A 7: 103,733,468 (GRCm39) H273L probably benign Het
Or6c76 T C 10: 129,612,242 (GRCm39) V168A probably benign Het
Ovgp1 A G 3: 105,894,068 (GRCm39) probably benign Het
P4ha2 A G 11: 54,015,836 (GRCm39) T408A probably damaging Het
Pcdh8 T G 14: 80,007,843 (GRCm39) D240A probably damaging Het
Pcyt2 T C 11: 120,502,911 (GRCm39) probably null Het
Pecr T A 1: 72,298,542 (GRCm39) I293L probably benign Het
Pogk A G 1: 166,226,402 (GRCm39) V583A possibly damaging Het
Prkg1 T C 19: 30,602,143 (GRCm39) K371R probably benign Het
Psmd2 T A 16: 20,474,335 (GRCm39) M297K possibly damaging Het
Rgs12 A G 5: 35,196,626 (GRCm39) R769G possibly damaging Het
Sgtb T A 13: 104,276,284 (GRCm39) N237K probably damaging Het
Sh3bgrl2 T C 9: 83,476,751 (GRCm39) V91A probably damaging Het
Slc4a1ap G A 5: 31,691,554 (GRCm39) probably null Het
Slc4a7 T C 14: 14,778,872 (GRCm38) V940A probably benign Het
Tep1 T C 14: 51,090,499 (GRCm39) T740A probably benign Het
Tnk2 G T 16: 32,489,737 (GRCm39) probably null Het
Trpv2 A G 11: 62,483,059 (GRCm39) Y450C probably damaging Het
Tut7 T C 13: 59,948,054 (GRCm39) T354A probably benign Het
Tvp23a A T 16: 10,264,862 (GRCm39) D16E probably damaging Het
Twnk T C 19: 44,997,850 (GRCm39) F460L possibly damaging Het
Unc80 C T 1: 66,560,740 (GRCm39) H823Y possibly damaging Het
Urb2 T C 8: 124,757,356 (GRCm39) L1021P probably damaging Het
Vps13c T C 9: 67,837,993 (GRCm39) Y1848H probably damaging Het
Vwa8 T G 14: 79,324,121 (GRCm39) N1141K probably benign Het
Yipf3 A G 17: 46,561,793 (GRCm39) Y200C probably damaging Het
Zbtb38 A G 9: 96,569,044 (GRCm39) V680A probably benign Het
Znrf3 T C 11: 5,231,347 (GRCm39) E722G probably benign Het
Zzef1 T A 11: 72,806,059 (GRCm39) L2665H probably damaging Het
Other mutations in H2-Aa
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00089:H2-Aa APN 17 34,503,504 (GRCm39) missense probably damaging 1.00
citation UTSW 17 34,506,651 (GRCm39) splice site probably null
reference UTSW 17 34,502,794 (GRCm39) missense probably damaging 1.00
G1citation:H2-Aa UTSW 17 34,506,651 (GRCm39) splice site probably null
R1901:H2-Aa UTSW 17 34,502,207 (GRCm39) missense possibly damaging 0.65
R2144:H2-Aa UTSW 17 34,502,801 (GRCm39) missense probably damaging 1.00
R4816:H2-Aa UTSW 17 34,502,794 (GRCm39) missense probably damaging 1.00
R5607:H2-Aa UTSW 17 34,502,816 (GRCm39) missense possibly damaging 0.89
R5608:H2-Aa UTSW 17 34,502,816 (GRCm39) missense possibly damaging 0.89
R6264:H2-Aa UTSW 17 34,502,172 (GRCm39) missense probably damaging 0.98
R6822:H2-Aa UTSW 17 34,506,651 (GRCm39) splice site probably null
R6917:H2-Aa UTSW 17 34,502,681 (GRCm39) missense probably damaging 1.00
R7052:H2-Aa UTSW 17 34,503,484 (GRCm39) missense possibly damaging 0.50
R7116:H2-Aa UTSW 17 34,502,601 (GRCm39) nonsense probably null
R8168:H2-Aa UTSW 17 34,506,695 (GRCm39) missense possibly damaging 0.83
R8257:H2-Aa UTSW 17 34,502,211 (GRCm39) missense probably damaging 0.97
R8264:H2-Aa UTSW 17 34,506,709 (GRCm39) missense probably benign 0.18
R8682:H2-Aa UTSW 17 34,502,734 (GRCm39) missense possibly damaging 0.75
R9667:H2-Aa UTSW 17 34,502,295 (GRCm39) missense probably benign
X0063:H2-Aa UTSW 17 34,506,785 (GRCm39) unclassified probably benign
Predicted Primers PCR Primer
(F):5'- TGCACACATGATGGTCACAGAGCC -3'
(R):5'- TTGTAATCCATACCAAGTGGGAGGGAG -3'

Sequencing Primer
(F):5'- TGGTCACAGAGCCCAATTGTC -3'
(R):5'- TGAGTGGTAGAAACAAACCCC -3'
Posted On 2014-04-13