Incidental Mutation 'R5857:Hoxa9'
ID 454951
Institutional Source Beutler Lab
Gene Symbol Hoxa9
Ensembl Gene ENSMUSG00000038227
Gene Name homeobox A9
Synonyms D6a9, Hox-1.7
MMRRC Submission 044069-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.884) question?
Stock # R5857 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 52200077-52203169 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 52201277 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Tyrosine at position 255 (N255Y)
Ref Sequence ENSEMBL: ENSMUSP00000046939 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000048680] [ENSMUST00000114425] [ENSMUST00000150041] [ENSMUST00000153280]
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: N255Y

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000046939
Gene: ENSMUSG00000038227
AA Change: N255Y

DomainStartEndE-ValueType
Pfam:Hox9_act 1 192 3.8e-71 PFAM
HOX 205 267 3.3e-27 SMART
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 probably benign
Transcript: ENSMUST00000153280
SMART Domains Protein: ENSMUSP00000134641
Gene: ENSMUSG00000038236

DomainStartEndE-ValueType
HOX 8 70 1.72e-25 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154641
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156540
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174115
Meta Mutation Damage Score 0.9587 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 97.9%
  • 20x: 93.6%
Validation Efficiency 95% (55/58)
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: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700030K09Rik A G 8: 73,203,369 (GRCm39) I266V probably benign Het
Anks6 C T 4: 47,039,736 (GRCm39) A492T possibly damaging Het
Ano1 A T 7: 144,190,840 (GRCm39) C415S probably benign Het
Anxa3 T A 5: 96,976,651 (GRCm39) probably null Het
Apob T C 12: 8,065,397 (GRCm39) V4089A probably benign Het
Arhgap23 C T 11: 97,342,405 (GRCm39) A229V possibly damaging Het
Atad5 T C 11: 80,022,155 (GRCm39) F1447L probably benign Het
Btbd8 T A 5: 107,609,398 (GRCm39) D212E probably damaging Het
Ccdc38 G T 10: 93,398,695 (GRCm39) A58S possibly damaging Het
Cep112 T C 11: 108,422,297 (GRCm39) probably benign Het
Col4a2 G A 8: 11,475,442 (GRCm39) G622D probably damaging Het
Crhbp T A 13: 95,578,740 (GRCm39) Q134L probably benign Het
Ctnnbl1 T C 2: 157,631,018 (GRCm39) S145P probably damaging Het
Cyp4f16 T A 17: 32,755,998 (GRCm39) L9Q probably damaging Het
Dchs2 T G 3: 83,177,620 (GRCm39) I891S possibly damaging Het
Disp3 A T 4: 148,333,640 (GRCm39) V1066D probably benign Het
Dlgap1 A G 17: 71,122,388 (GRCm39) probably benign Het
Dnah3 TTCCTC TTC 7: 119,550,244 (GRCm39) probably benign Het
Efl1 T A 7: 82,412,397 (GRCm39) C929S probably benign Het
Gatb T C 3: 85,483,239 (GRCm39) F82S probably damaging Het
Gk5 C A 9: 96,001,508 (GRCm39) S2* probably null Het
Gpr135 G A 12: 72,117,614 (GRCm39) A51V probably benign Het
Igkv8-18 T C 6: 70,332,904 (GRCm39) V15A probably benign Het
Ism2 T C 12: 87,326,835 (GRCm39) D368G probably damaging Het
Krtap6-2 A T 16: 89,216,530 (GRCm39) S146T unknown Het
Lama1 T A 17: 68,114,838 (GRCm39) L2329H probably damaging Het
Llgl2 T A 11: 115,741,107 (GRCm39) I507N probably damaging Het
Lmna GCTGCCCACAC GC 3: 88,389,838 (GRCm39) probably benign Het
Lrfn3 A T 7: 30,058,863 (GRCm39) I454N possibly damaging Het
Mdn1 C A 4: 32,670,646 (GRCm39) T437K probably benign Het
Nat8f3 T C 6: 85,738,735 (GRCm39) Y9C probably damaging Het
Niban2 T A 2: 32,799,920 (GRCm39) N82K probably benign Het
Nlrp4d C A 7: 10,116,304 (GRCm39) G156V noncoding transcript Het
Npnt A T 3: 132,614,110 (GRCm39) C167S probably damaging Het
Nr3c2 A G 8: 77,635,496 (GRCm39) N199S possibly damaging Het
Or10x4 T G 1: 174,218,674 (GRCm39) I13R possibly damaging Het
Or8b12i C T 9: 20,082,535 (GRCm39) D111N probably damaging Het
Or8b37 T G 9: 37,959,049 (GRCm39) V177G probably benign Het
Pabpc1l T A 2: 163,886,175 (GRCm39) probably null Het
Pi4ka A G 16: 17,176,848 (GRCm39) I366T probably benign Het
Prl7a1 A T 13: 27,824,684 (GRCm39) D50E probably damaging Het
Rad52 T G 6: 119,887,968 (GRCm39) probably null Het
Rbm19 T A 5: 120,271,007 (GRCm39) L610Q probably damaging Het
Rnd2 C T 11: 101,359,825 (GRCm39) L57F probably damaging Het
Scube1 G T 15: 83,491,461 (GRCm39) probably benign Het
Sptbn4 G T 7: 27,118,138 (GRCm39) R314S possibly damaging Het
Togaram1 T A 12: 65,042,331 (GRCm39) I1130K possibly damaging Het
Tsc2 T C 17: 24,818,981 (GRCm39) E1352G probably damaging Het
Ube2d2a A G 18: 35,938,596 (GRCm39) T142A probably benign Het
Vps18 T C 2: 119,128,014 (GRCm39) Y946H 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
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
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'- TTTAGAGCCCCTTTGTGCG -3'
(R):5'- CCGGGATGCTCCTTCTAAAC -3'

Sequencing Primer
(F):5'- CCCCTTTGTGCGGGTGG -3'
(R):5'- GGGATGCTCCTTCTAAACCCAGTG -3'
Posted On 2017-02-10