Incidental Mutation 'R0727:Hoxa9'
ID 200636
Institutional Source Beutler Lab
Gene Symbol Hoxa9
Ensembl Gene ENSMUSG00000038227
Gene Name homeobox A9
Synonyms D6a9, Hox-1.7
MMRRC Submission 038909-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.884) question?
Stock # R0727 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 52200077-52203169 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 52201294 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 249 (V249A)
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: V249A

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000046939
Gene: ENSMUSG00000038227
AA Change: V249A

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 0.6157 question?
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.8%
  • 10x: 95.2%
  • 20x: 92.1%
Validation Efficiency 99% (70/71)
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
Actr3b T C 5: 26,016,937 (GRCm39) V83A possibly damaging Het
Adam2 A G 14: 66,267,180 (GRCm39) I693T probably damaging Het
Adamts1 T C 16: 85,595,536 (GRCm39) D214G possibly damaging Het
Atp6v1h T A 1: 5,154,781 (GRCm39) Y36* probably null Het
Cacna1d A G 14: 29,852,072 (GRCm39) probably null Het
Catsperb G T 12: 101,560,614 (GRCm39) probably null Het
Ccdc88b T C 19: 6,831,582 (GRCm39) M482V probably benign Het
Cemip T C 7: 83,610,786 (GRCm39) K723E probably benign Het
Cep112 G A 11: 108,397,380 (GRCm39) R375H probably damaging Het
Cpne7 T C 8: 123,853,025 (GRCm39) S211P probably damaging Het
Csde1 A G 3: 102,950,954 (GRCm39) T191A probably benign Het
Dapk3 A G 10: 81,026,096 (GRCm39) Y129C probably damaging Het
Dlc1 A G 8: 37,039,828 (GRCm39) V1027A probably damaging Het
Ergic2 T A 6: 148,100,898 (GRCm39) probably benign Het
Evpl T C 11: 116,123,311 (GRCm39) H307R probably damaging Het
Faah A G 4: 115,862,257 (GRCm39) I242T probably damaging Het
Farsa T A 8: 85,587,933 (GRCm39) probably null Het
Fat3 A C 9: 15,907,995 (GRCm39) L2669R probably damaging Het
Fgfr4 C A 13: 55,304,041 (GRCm39) probably null Het
Gnl3 A G 14: 30,739,034 (GRCm39) S55P probably damaging Het
Grhl3 T A 4: 135,273,565 (GRCm39) K562N possibly damaging Het
H2bl1 A G 13: 99,120,735 (GRCm39) V97A probably benign Het
Hyal1 T C 9: 107,455,601 (GRCm39) S304P possibly damaging Het
Igf1r T C 7: 67,861,906 (GRCm39) probably null Het
Kif3c A G 12: 3,416,776 (GRCm39) T266A probably benign Het
Lrp1b T C 2: 40,640,956 (GRCm39) D3496G probably benign Het
Man2b1 T G 8: 85,818,155 (GRCm39) V442G probably damaging Het
Mast1 T C 8: 85,648,044 (GRCm39) Y479C probably damaging Het
Mei1 A G 15: 81,954,350 (GRCm39) T52A probably benign Het
Micall1 A G 15: 79,004,978 (GRCm39) D150G probably benign Het
Muc4 A G 16: 32,590,221 (GRCm39) M2927V probably benign Het
Obi1 G C 14: 104,717,624 (GRCm39) L250V probably damaging Het
Or11h6 G T 14: 50,880,460 (GRCm39) V241L probably damaging Het
Or56b1b C T 7: 108,164,315 (GRCm39) R229H probably benign Het
Or5an10 T C 19: 12,276,458 (GRCm39) I13V probably benign Het
Or5w22 T A 2: 87,363,245 (GRCm39) Y289* probably null Het
Or8k27 T C 2: 86,276,282 (GRCm39) M15V probably benign Het
Or8k35 A T 2: 86,424,724 (GRCm39) Y149* probably null Het
Pabpc2 A C 18: 39,908,187 (GRCm39) Q484P probably benign Het
Pbld2 T A 10: 62,903,298 (GRCm39) V125D probably benign Het
Pkhd1l1 A G 15: 44,399,184 (GRCm39) T2083A possibly damaging Het
Pum2 A G 12: 8,794,465 (GRCm39) E785G probably damaging Het
Qser1 A G 2: 104,607,656 (GRCm39) probably benign Het
R3hcc1l A G 19: 42,564,514 (GRCm39) D29G probably damaging Het
Rabep1 T A 11: 70,791,318 (GRCm39) Y180* probably null Het
Rassf5 T C 1: 131,109,002 (GRCm39) S140G probably damaging Het
Rbpms2 ACTGCTGCTGCTGCTGC ACTGCTGCTGCTGCTGCTGC 9: 65,558,948 (GRCm39) probably benign Het
Resf1 A G 6: 149,227,320 (GRCm39) N122S possibly damaging Het
Rfpl4 T A 7: 5,118,292 (GRCm39) I93L probably benign Het
Ryr2 C T 13: 11,581,771 (GRCm39) G4798D probably damaging Het
Scaf11 G A 15: 96,317,324 (GRCm39) P747S probably damaging Het
Sgo2b T G 8: 64,380,816 (GRCm39) K672T probably damaging Het
Smg1 T C 7: 117,765,645 (GRCm39) probably benign Het
Sned1 G A 1: 93,209,376 (GRCm39) V830M possibly damaging Het
Ssh3 G T 19: 4,314,019 (GRCm39) H439Q probably damaging Het
Steap3 T A 1: 120,155,547 (GRCm39) T471S possibly damaging Het
Stk33 T A 7: 108,920,725 (GRCm39) I208L probably damaging Het
Sucnr1 A G 3: 59,994,081 (GRCm39) Y203C probably benign Het
Tlr11 T C 14: 50,598,926 (GRCm39) I304T possibly damaging Het
Top2a A T 11: 98,902,974 (GRCm39) C404* probably null Het
Trim43a G A 9: 88,464,199 (GRCm39) E37K probably benign Het
Zcwpw1 T C 5: 137,809,069 (GRCm39) probably benign Het
Zfhx4 A T 3: 5,466,133 (GRCm39) H2097L probably damaging Het
Zfp874b T C 13: 67,622,831 (GRCm39) K156E probably damaging Het
Zfyve16 T C 13: 92,630,386 (GRCm39) K1413E possibly damaging Het
Other mutations in Hoxa9
AlleleSourceChrCoordTypePredicted EffectPPH Score
R0370:Hoxa9 UTSW 6 52,202,684 (GRCm39) missense possibly damaging 0.48
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'- CAGAATGATCTGCCACACGAAGAGC -3'
(R):5'- TAACCAATTCAGCGGCATCCTGCAC -3'

Sequencing Primer
(F):5'- GATTTAGAGCCCCTTTGTGC -3'
(R):5'- GGGATGCTCCTTCTAAACCCAG -3'
Posted On 2014-05-23