Incidental Mutation 'R1175:Hoxa9'
ID 99930
Institutional Source Beutler Lab
Gene Symbol Hoxa9
Ensembl Gene ENSMUSG00000038227
Gene Name homeobox A9
Synonyms D6a9, Hox-1.7
MMRRC Submission 039248-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.917) question?
Stock # R1175 (G1)
Quality Score 167
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: 88.0%
Validation Efficiency 100% (74/74)
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610318N02Rik T A 16: 16,935,446 (GRCm39) H214L probably benign Het
Abca17 T C 17: 24,508,325 (GRCm39) E1070G possibly damaging Het
Accsl A T 2: 93,696,589 (GRCm39) probably benign Het
Akp3 G A 1: 87,055,593 (GRCm39) G547R unknown Het
Anapc1 C A 2: 128,522,108 (GRCm39) C150F probably damaging Het
Aoc1l3 C A 6: 48,967,173 (GRCm39) P707H probably damaging Het
Arhgef18 T A 8: 3,439,023 (GRCm39) probably benign Het
Borcs5 T A 6: 134,687,096 (GRCm39) N150K probably damaging Het
C9orf72 C A 4: 35,218,630 (GRCm39) E76D probably damaging Het
Cdh20 G A 1: 109,988,862 (GRCm39) V255I probably benign Het
Cntnap5c C A 17: 58,671,241 (GRCm39) T1143K possibly damaging Het
Col7a1 A C 9: 108,784,402 (GRCm39) T137P unknown Het
Defb8 C T 8: 19,495,910 (GRCm39) G50E probably damaging Het
Dimt1 T A 13: 107,086,193 (GRCm39) probably benign Het
Dnajb11 T A 16: 22,689,423 (GRCm39) D281E probably damaging Het
Eci2 G T 13: 35,177,087 (GRCm39) N24K probably damaging Het
Fbn1 A T 2: 125,236,607 (GRCm39) C358S probably benign Het
Fbxl13 A T 5: 21,825,602 (GRCm39) probably benign Het
Fbxw11 T C 11: 32,661,922 (GRCm39) C121R probably damaging Het
Fsd2 T C 7: 81,209,518 (GRCm39) D108G probably benign Het
Gab1 C A 8: 81,511,471 (GRCm39) R458L 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
Gm19965 T A 1: 116,748,550 (GRCm39) probably benign Het
Gpr149 A G 3: 62,511,888 (GRCm39) L37P probably damaging Het
Itpkc T C 7: 26,927,195 (GRCm39) I240V probably benign Het
Jakmip3 A G 7: 138,629,515 (GRCm39) D552G probably damaging Het
Kank4 T C 4: 98,653,806 (GRCm39) Y874C probably damaging Het
Kdm3a T C 6: 71,577,011 (GRCm39) E768G possibly damaging Het
Klf6 A G 13: 5,911,711 (GRCm39) D25G probably benign Het
Lamc1 T C 1: 153,122,977 (GRCm39) probably benign Het
Laptm4a T C 12: 8,986,716 (GRCm39) V258A probably damaging Het
Map3k19 A G 1: 127,751,617 (GRCm39) V578A probably benign Het
Mast1 T C 8: 85,651,956 (GRCm39) E342G probably benign Het
Mgat5b T C 11: 116,868,622 (GRCm39) L515P probably damaging Het
Mink1 A G 11: 70,502,166 (GRCm39) D985G probably benign Het
Mphosph9 A G 5: 124,453,739 (GRCm39) V191A possibly damaging Het
Muc6 C T 7: 141,234,368 (GRCm39) G708S probably damaging Het
Pcnt A T 10: 76,228,878 (GRCm39) probably null Het
Psmd8 A T 7: 28,875,598 (GRCm39) Y174N probably damaging Het
Ptgdr2 C A 19: 10,918,292 (GRCm39) R270S possibly damaging Het
Rasal2 A G 1: 156,975,218 (GRCm39) M1172T probably damaging Het
Rif1 A G 2: 51,997,640 (GRCm39) probably benign Het
Rnf123 C T 9: 107,954,572 (GRCm39) R48H probably benign Het
Rsrc1 T C 3: 67,263,551 (GRCm39) probably benign 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
Sis A G 3: 72,865,437 (GRCm39) probably benign Het
Skint4 T C 4: 111,981,793 (GRCm39) M246T probably benign Het
Snrnp200 C A 2: 127,070,997 (GRCm39) R1093S probably damaging Het
Sp100 A G 1: 85,629,141 (GRCm39) N471D possibly damaging 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
Sufu T C 19: 46,389,703 (GRCm39) probably null Het
Synpo2l G A 14: 20,718,235 (GRCm39) T10I possibly damaging Het
Tdo2 A T 3: 81,881,683 (GRCm39) S40R probably damaging Het
Tent4b T A 8: 88,978,635 (GRCm39) F445L probably damaging Het
Terb1 G A 8: 105,210,938 (GRCm39) T363I probably benign Het
Timd4 C T 11: 46,708,498 (GRCm39) P175S probably damaging Het
Tlr3 C A 8: 45,850,171 (GRCm39) V833L probably damaging Het
Tpst2 T A 5: 112,455,911 (GRCm39) M150K probably damaging Het
Trim67 T A 8: 125,543,774 (GRCm39) V378E probably damaging Het
Tyrp1 C T 4: 80,763,105 (GRCm39) Q331* probably null Het
Ubap2l A T 3: 89,930,807 (GRCm39) S413T probably benign Het
Uimc1 G A 13: 55,176,415 (GRCm39) T701I possibly damaging Het
Vangl2 G T 1: 171,832,353 (GRCm39) T501N probably damaging Het
Vmn1r60 A G 7: 5,547,621 (GRCm39) S160P probably benign Het
Vmn2r66 G T 7: 84,654,799 (GRCm39) D503E probably benign Het
Vmn2r72 T A 7: 85,401,152 (GRCm39) E89V probably damaging Het
Zfp457 G A 13: 67,441,748 (GRCm39) P180S 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
R1173:Hoxa9 UTSW 6 52,202,693 (GRCm39) missense probably damaging 0.99
R1174: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