Incidental Mutation 'R1174:Hoxa9'
ID 99805
Institutional Source Beutler Lab
Gene Symbol Hoxa9
Ensembl Gene ENSMUSG00000038227
Gene Name homeobox A9
Synonyms D6a9, Hox-1.7
MMRRC Submission 039247-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.917) question?
Stock # R1174 (G1)
Quality Score 225
Status Not 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: 99.0%
  • 3x: 98.1%
  • 10x: 95.4%
  • 20x: 89.3%
Validation Efficiency
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: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610318N02Rik T A 16: 16,935,446 (GRCm39) H214L probably benign Het
Actn3 A G 19: 4,914,784 (GRCm39) L477P probably damaging 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
Alpk1 T A 3: 127,474,459 (GRCm39) S515C probably damaging Het
Aoc1l3 C A 6: 48,967,173 (GRCm39) P707H probably damaging Het
Bivm A G 1: 44,165,942 (GRCm39) T131A probably benign Het
Borcs5 T A 6: 134,687,096 (GRCm39) N150K probably damaging Het
Cdh20 G A 1: 109,988,862 (GRCm39) V255I probably benign Het
Cox4i1 C A 8: 121,400,789 (GRCm39) N151K probably benign Het
Cpeb4 T C 11: 31,870,472 (GRCm39) L432P probably damaging Het
Dnajb11 T A 16: 22,689,423 (GRCm39) D281E probably damaging Het
Eml6 A G 11: 29,699,824 (GRCm39) S1771P possibly damaging Het
Fes A T 7: 80,027,699 (GRCm39) I815N probably damaging 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
Gm1818 A G 12: 48,602,982 (GRCm39) noncoding transcript Het
Gpr149 A G 3: 62,511,888 (GRCm39) L37P probably damaging Het
Hdac1-ps A T 17: 78,799,507 (GRCm39) Y166F probably benign Het
Idh1 G T 1: 65,200,319 (GRCm39) N348K probably benign Het
Klf6 A G 13: 5,911,711 (GRCm39) D25G probably benign Het
Laptm4a T C 12: 8,986,716 (GRCm39) V258A probably damaging Het
Lypd6b C T 2: 49,833,609 (GRCm39) A83V possibly damaging Het
Map3k19 A G 1: 127,751,617 (GRCm39) V578A probably benign Het
Mfsd13a T A 19: 46,363,125 (GRCm39) I511N probably benign Het
Mrm3 T C 11: 76,140,850 (GRCm39) V286A probably damaging Het
Muc6 C T 7: 141,234,368 (GRCm39) G708S probably damaging Het
Neurl4 T C 11: 69,794,547 (GRCm39) probably null Het
Pclo T C 5: 14,727,660 (GRCm39) probably benign Het
Pcnt A T 10: 76,228,878 (GRCm39) probably null Het
Pik3r4 G T 9: 105,540,373 (GRCm39) G754C probably damaging Het
Qtrt1 A G 9: 21,323,782 (GRCm39) T136A probably benign Het
Rgs12 T A 5: 35,123,809 (GRCm39) C531S probably benign Het
Rin1 C A 19: 5,105,231 (GRCm39) Q764K probably benign Het
Robo4 C T 9: 37,324,348 (GRCm39) R959W probably damaging Het
Rxfp2 T C 5: 149,975,021 (GRCm39) V210A probably benign Het
Serpinb9d C T 13: 33,384,608 (GRCm39) P195L probably benign Het
Sos1 A C 17: 80,753,037 (GRCm39) Y323* probably null Het
Spmip4 T A 6: 50,566,121 (GRCm39) K118M probably damaging Het
Ssxb8 T G X: 8,556,062 (GRCm39) H88P probably damaging Het
Tas2r140 T C 6: 133,031,834 (GRCm39) E308G probably benign Het
Tdo2 A T 3: 81,881,683 (GRCm39) S40R probably damaging Het
Tle4 C T 19: 14,445,626 (GRCm39) V207I probably benign Het
Txlnb A G 10: 17,718,504 (GRCm39) N445S probably benign Het
Ubap2l A T 3: 89,930,807 (GRCm39) S413T probably benign Het
Vangl2 G T 1: 171,832,353 (GRCm39) T501N probably damaging Het
Vmn2r12 A T 5: 109,240,720 (GRCm39) I131N probably benign Het
Vwa1 C T 4: 155,857,723 (GRCm39) G25D probably damaging Het
Zfp185 A T X: 72,042,929 (GRCm39) E138D possibly 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
R1173: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