Incidental Mutation 'R0370:Hoxa9'
ID 30421
Institutional Source Beutler Lab
Gene Symbol Hoxa9
Ensembl Gene ENSMUSG00000038227
Gene Name homeobox A9
Synonyms D6a9, Hox-1.7
MMRRC Submission 038576-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.917) question?
Stock # R0370 (G1)
Quality Score 225
Status Not validated
Chromosome 6
Chromosomal Location 52200077-52203169 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 52202684 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 134 (E134G)
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 possibly damaging
Transcript: ENSMUST00000048680
AA Change: E134G

PolyPhen 2 Score 0.484 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000046939
Gene: ENSMUSG00000038227
AA Change: E134G

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
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 96.0%
  • 20x: 91.7%
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: 41 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Afg3l1 T C 8: 124,228,293 (GRCm39) S666P probably damaging Het
B3gntl1 A T 11: 121,514,980 (GRCm39) W263R probably damaging Het
Carmil3 A G 14: 55,732,899 (GRCm39) N270S possibly damaging Het
Ctdp1 T C 18: 80,492,569 (GRCm39) E642G probably damaging Het
Cyp2b9 A T 7: 25,909,531 (GRCm39) K433M probably damaging Het
Dcc A G 18: 71,721,056 (GRCm39) V435A possibly damaging Het
Defa26 A T 8: 22,108,875 (GRCm39) M87L probably benign Het
Dnah11 T A 12: 117,958,962 (GRCm39) I2974L probably benign Het
Dnah3 T C 7: 119,685,943 (GRCm39) D131G possibly damaging Het
Dock6 A T 9: 21,725,861 (GRCm39) S1447R probably benign Het
Dtl G T 1: 191,307,462 (GRCm39) N17K probably benign Het
Grid2 A G 6: 64,322,718 (GRCm39) I573V possibly damaging Het
Kcnn3 A T 3: 89,574,399 (GRCm39) N637I probably damaging Het
Ktn1 T C 14: 47,901,532 (GRCm39) F97L probably benign Het
Lmbrd2 T C 15: 9,165,939 (GRCm39) I271T probably damaging Het
Lrp6 A C 6: 134,456,729 (GRCm39) I845S probably damaging Het
Med13l T A 5: 118,879,891 (GRCm39) N994K probably benign Het
Mrrf A T 2: 36,067,125 (GRCm39) probably null Het
Mtmr1 G A X: 70,431,837 (GRCm39) V125I probably damaging Het
Nol8 C T 13: 49,815,923 (GRCm39) A677V possibly damaging Het
Or13g1 T A 7: 85,956,057 (GRCm39) N88I probably benign Het
Or51k1 T G 7: 103,661,266 (GRCm39) L214F probably damaging Het
Or8k3 A T 2: 86,059,057 (GRCm39) V86D probably damaging Het
Paxip1 C A 5: 27,965,084 (GRCm39) V659F probably damaging Het
Pclo T C 5: 14,571,104 (GRCm39) V163A probably damaging Het
Pkn3 T A 2: 29,977,184 (GRCm39) H641Q probably damaging Het
Plekhg6 G A 6: 125,347,623 (GRCm39) R444C probably damaging Het
Rfx2 T C 17: 57,106,308 (GRCm39) E175G probably benign Het
Samd9l A C 6: 3,377,264 (GRCm39) probably benign Het
Sec14l5 A T 16: 4,998,570 (GRCm39) T537S probably damaging Het
Serpinb9d A G 13: 33,379,949 (GRCm39) E96G probably damaging Het
Setd4 T C 16: 93,388,006 (GRCm39) E160G probably damaging Het
Sf3b2 C T 19: 5,324,852 (GRCm39) D845N probably damaging Het
Slc16a4 A G 3: 107,208,413 (GRCm39) I308V possibly damaging Het
Slco2b1 T A 7: 99,339,644 (GRCm39) N100Y probably damaging Het
Sptbn1 A T 11: 30,071,545 (GRCm39) S1475R probably benign Het
Tecta T C 9: 42,278,100 (GRCm39) D1136G probably benign Het
Tmem94 G C 11: 115,679,543 (GRCm39) R273S probably damaging Het
Tns3 A G 11: 8,395,730 (GRCm39) S1225P possibly damaging Het
Ugt2b36 A G 5: 87,239,834 (GRCm39) Y184H probably benign Het
Vmn2r59 A T 7: 41,662,150 (GRCm39) M555K probably benign Het
Other mutations in Hoxa9
AlleleSourceChrCoordTypePredicted EffectPPH Score
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
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 PCR Primer
(F):5'- AACCGCCCAAAGTCTGTCTGTC -3'
(R):5'- GACTTCAGTCCTTGCAGCTTCCAG -3'

Sequencing Primer
(F):5'- TTCTCGGACCCTAGATCCAGAG -3'
(R):5'- TTGCAGCTTCCAGTCCAAGG -3'
Posted On 2013-04-24