Incidental Mutation 'R1173:Hoxa9'
ID 99690
Institutional Source Beutler Lab
Gene Symbol Hoxa9
Ensembl Gene ENSMUSG00000038227
Gene Name homeobox A9
Synonyms D6a9, Hox-1.7
MMRRC Submission 039246-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.917) question?
Stock # R1173 (G1)
Quality Score 125
Status Validated
Chromosome 6
Chromosomal Location 52200077-52203169 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 52202693 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 131 (I131T)
Ref Sequence ENSEMBL: ENSMUSP00000046939 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000048680] [ENSMUST00000114425] [ENSMUST00000150041]
AlphaFold P09631
PDB Structure Crystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA [X-RAY DIFFRACTION]
Predicted Effect probably damaging
Transcript: ENSMUST00000048680
AA Change: I131T

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000046939
Gene: ENSMUSG00000038227
AA Change: I131T

DomainStartEndE-ValueType
Pfam:Hox9_act 1 192 3.8e-71 PFAM
HOX 205 267 3.3e-27 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000083509
Predicted Effect probably benign
Transcript: ENSMUST00000114425
SMART Domains Protein: ENSMUSP00000110068
Gene: ENSMUSG00000038227

DomainStartEndE-ValueType
Pfam:Hox9_act 1 105 5.9e-35 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000150041
SMART Domains Protein: ENSMUSP00000140519
Gene: ENSMUSG00000038236

DomainStartEndE-ValueType
low complexity region 19 34 N/A INTRINSIC
low complexity region 43 56 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154641
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156540
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174115
Meta Mutation Damage Score 0.3198 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.8%
  • 10x: 94.7%
  • 20x: 87.9%
Validation Efficiency 99% (72/73)
MGI Phenotype FUNCTION: This gene is located in a cluster of developmentally and temporally regulated genes on chromosome 6 encoding proteins involved in pattern formation. These proteins contain a characteristic DNA-binding motif called a homeodomain and function in transcriptional regulation. There are four distinct clusters of similar genes on chromosomes 2, 6, 11, and 15. The protein encoded by this gene is important for hematopoeisis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]
PHENOTYPE: Homozygotes for targeted null mutations exhibit homeotic transformations affecting lumbar vertebrae, reduced spleen and thymus weights, and defects in myeloid, erythroid, and lymphoid hematopoiesis. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Accsl A T 2: 93,696,589 (GRCm39) probably benign Het
Adam30 G A 3: 98,070,222 (GRCm39) S685N probably benign Het
Adamts12 T C 15: 11,071,843 (GRCm39) V129A probably benign Het
Agxt2 T C 15: 10,373,837 (GRCm39) F81S probably damaging Het
Ahnak2 A T 12: 112,749,409 (GRCm39) I186N probably damaging Het
Amz1 A T 5: 140,737,691 (GRCm39) probably null Het
Anapc5 G A 5: 122,926,481 (GRCm39) A619V possibly damaging Het
Aoc1l3 C A 6: 48,967,173 (GRCm39) P707H probably damaging Het
Bbox1 T C 2: 110,095,956 (GRCm39) D336G probably damaging Het
Bivm A G 1: 44,165,942 (GRCm39) T131A probably benign Het
Bpi A T 2: 158,109,660 (GRCm39) I203F probably benign Het
Cd151 A C 7: 141,050,569 (GRCm39) T241P probably damaging Het
Cdh20 G A 1: 109,988,862 (GRCm39) V255I probably benign Het
Cdh23 G A 10: 60,148,171 (GRCm39) probably benign Het
Cul9 C G 17: 46,833,101 (GRCm39) A1326P probably damaging Het
Dclre1b A C 3: 103,711,192 (GRCm39) S240A probably benign Het
Ddc A C 11: 11,796,634 (GRCm39) probably null Het
Dkk1 T C 19: 30,524,650 (GRCm39) R252G probably damaging Het
Dmrtc2 T A 7: 24,573,738 (GRCm39) M191K possibly damaging Het
Eml6 A G 11: 29,699,824 (GRCm39) S1771P possibly damaging Het
Emx1 T C 6: 85,165,353 (GRCm39) probably benign Het
Fah T C 7: 84,250,344 (GRCm39) M1V probably null Het
Fmo6 A T 1: 162,753,710 (GRCm39) M144K probably damaging Het
Frem1 A G 4: 82,868,589 (GRCm39) V1445A probably benign Het
Fsd2 T C 7: 81,209,518 (GRCm39) D108G probably benign Het
Gfm2 A G 13: 97,301,708 (GRCm39) probably null Het
Ghrhr T A 6: 55,365,254 (GRCm39) L416* probably null Het
Glipr1l2 C A 10: 111,919,371 (GRCm39) L31I possibly damaging Het
Gm19965 T A 1: 116,748,550 (GRCm39) probably benign Het
Gpr149 A G 3: 62,511,888 (GRCm39) L37P probably damaging Het
Htra4 T C 8: 25,520,635 (GRCm39) D342G possibly damaging Het
Idh1 G T 1: 65,200,319 (GRCm39) N348K probably benign Het
Impdh2 T C 9: 108,439,028 (GRCm39) F99S probably benign Het
Kank4 T C 4: 98,653,806 (GRCm39) Y874C probably damaging Het
Kazn A T 4: 141,886,349 (GRCm39) probably benign Het
Kcnq3 T A 15: 65,871,891 (GRCm39) T593S probably benign Het
Lamc1 T C 1: 153,122,977 (GRCm39) probably benign Het
Magi3 A G 3: 103,968,946 (GRCm39) probably null Het
Map3k19 A G 1: 127,751,617 (GRCm39) V578A probably benign Het
Meox2 T C 12: 37,159,151 (GRCm39) C108R possibly damaging Het
Nlrp9c C A 7: 26,079,860 (GRCm39) C722F probably damaging Het
Or2a5 T C 6: 42,874,285 (GRCm39) V300A probably benign Het
Pde10a C T 17: 9,139,378 (GRCm39) probably benign Het
Ppfia4 A G 1: 134,260,021 (GRCm39) probably benign Het
Psg18 T C 7: 18,088,742 (GRCm39) M1V probably null Het
Qtrt1 A G 9: 21,323,782 (GRCm39) T136A probably benign Het
Retsat T C 6: 72,580,634 (GRCm39) probably benign Het
Rxfp2 T C 5: 149,975,021 (GRCm39) V210A probably benign Het
Sfswap G A 5: 129,584,207 (GRCm39) probably null Het
Slc16a7 A T 10: 125,067,241 (GRCm39) L133I possibly damaging Het
Slc30a3 A T 5: 31,244,154 (GRCm39) M376K probably damaging Het
Spmip4 T A 6: 50,566,121 (GRCm39) K118M probably damaging Het
Srbd1 C T 17: 86,405,940 (GRCm39) C620Y probably null Het
Trip10 T A 17: 57,560,363 (GRCm39) L100Q probably damaging Het
Tyrp1 C T 4: 80,763,105 (GRCm39) Q331* probably null Het
Vangl2 G T 1: 171,832,353 (GRCm39) T501N probably damaging Het
Vdr A T 15: 97,767,214 (GRCm39) Y185N probably benign Het
Vmn1r123 C T 7: 20,896,257 (GRCm39) P50S probably damaging Het
Vmn1r158 T A 7: 22,489,870 (GRCm39) H113L probably benign Het
Vmn2r12 A T 5: 109,240,720 (GRCm39) I131N probably benign Het
Vmn2r72 T A 7: 85,401,152 (GRCm39) E89V probably damaging Het
Xrcc6 A G 15: 81,915,364 (GRCm39) D94G probably damaging Het
Zbtb32 T A 7: 30,290,692 (GRCm39) E201V possibly damaging Het
Zfp185 A T X: 72,042,929 (GRCm39) E138D possibly damaging Het
Zmynd11 T A 13: 9,739,585 (GRCm39) H437L probably damaging Het
Other mutations in Hoxa9
AlleleSourceChrCoordTypePredicted EffectPPH Score
R0370:Hoxa9 UTSW 6 52,202,684 (GRCm39) missense possibly damaging 0.48
R0727:Hoxa9 UTSW 6 52,201,294 (GRCm39) missense probably damaging 0.99
R1174:Hoxa9 UTSW 6 52,202,693 (GRCm39) missense probably damaging 0.99
R1175:Hoxa9 UTSW 6 52,202,693 (GRCm39) missense probably damaging 0.99
R4611:Hoxa9 UTSW 6 52,202,690 (GRCm39) missense probably damaging 1.00
R5857:Hoxa9 UTSW 6 52,201,277 (GRCm39) missense probably damaging 1.00
R7679:Hoxa9 UTSW 6 52,201,288 (GRCm39) missense probably damaging 0.99
R7756:Hoxa9 UTSW 6 52,202,542 (GRCm39) missense probably benign 0.17
R7758:Hoxa9 UTSW 6 52,202,542 (GRCm39) missense probably benign 0.17
R7922:Hoxa9 UTSW 6 52,201,289 (GRCm39) missense possibly damaging 0.92
R8398:Hoxa9 UTSW 6 52,201,403 (GRCm39) missense probably damaging 0.99
R8474:Hoxa9 UTSW 6 52,202,506 (GRCm39) critical splice donor site probably null
Predicted Primers
Posted On 2014-01-15