Incidental Mutation 'R0723:Hoxd9'
ID 63589
Institutional Source Beutler Lab
Gene Symbol Hoxd9
Ensembl Gene ENSMUSG00000043342
Gene Name homeobox D9
Synonyms Hox-5.2, Hox-4.4
MMRRC Submission 038905-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0723 (G1)
Quality Score 81
Status Validated
Chromosome 2
Chromosomal Location 74528107-74530552 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 74529172 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Valine at position 258 (D258V)
Ref Sequence ENSEMBL: ENSMUSP00000058490 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000059272] [ENSMUST00000061745]
AlphaFold P28357
Predicted Effect probably damaging
Transcript: ENSMUST00000059272
AA Change: D258V

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000058490
Gene: ENSMUSG00000043342
AA Change: D258V

DomainStartEndE-ValueType
Pfam:Hox9_act 1 126 2e-47 PFAM
low complexity region 155 176 N/A INTRINSIC
low complexity region 208 225 N/A INTRINSIC
low complexity region 248 256 N/A INTRINSIC
HOX 272 334 6.25e-28 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000061745
SMART Domains Protein: ENSMUSP00000062412
Gene: ENSMUSG00000050368

DomainStartEndE-ValueType
low complexity region 24 43 N/A INTRINSIC
HOX 266 328 3.3e-27 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126966
SMART Domains Protein: ENSMUSP00000133930
Gene: ENSMUSG00000086077

DomainStartEndE-ValueType
low complexity region 23 42 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132326
Predicted Effect noncoding transcript
Transcript: ENSMUST00000136302
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152027
Predicted Effect noncoding transcript
Transcript: ENSMUST00000190845
Predicted Effect noncoding transcript
Transcript: ENSMUST00000198895
Meta Mutation Damage Score 0.7543 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.8%
  • 10x: 97.7%
  • 20x: 96.0%
Validation Efficiency 99% (69/70)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located at 2q31-2q37 chromosome regions. Deletions that removed the entire HOXD gene cluster or 5' end of this cluster have been associated with severe limb and genital abnormalities. The exact role of this gene has not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a targeted mutation exhibit anterior transformation of lumbar, sacral, and caudal vertebrae with abnormal humerus morphology. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930433I11Rik A T 7: 40,642,480 (GRCm39) T141S probably benign Het
Acbd5 T G 2: 22,959,608 (GRCm39) V54G probably damaging Het
Acin1 A T 14: 54,902,908 (GRCm39) S255T probably damaging Het
Adcy2 A G 13: 69,147,248 (GRCm39) L56P probably damaging Het
Akap6 G T 12: 53,188,685 (GRCm39) C2033F probably damaging Het
Ano5 A G 7: 51,237,506 (GRCm39) I777V probably benign Het
Arhgef28 A G 13: 98,075,987 (GRCm39) V1349A probably benign Het
Atosa G A 9: 74,916,733 (GRCm39) G444E probably damaging Het
Bank1 T C 3: 135,760,164 (GRCm39) probably null Het
C2cd5 T C 6: 142,987,281 (GRCm39) probably benign Het
Cadps2 A G 6: 23,287,697 (GRCm39) V1161A probably damaging Het
Car8 A T 4: 8,169,703 (GRCm39) D268E probably benign Het
Ciao3 G A 17: 26,000,795 (GRCm39) V406M probably damaging Het
Ckap5 T A 2: 91,385,676 (GRCm39) S175T probably damaging Het
Clk4 T A 11: 51,166,320 (GRCm39) Y67* probably null Het
Copg2 T C 6: 30,792,917 (GRCm39) I473V possibly damaging Het
Cstdc1 T C 2: 148,625,282 (GRCm39) I72T probably damaging Het
Cyp2s1 C T 7: 25,508,973 (GRCm39) V43I probably benign Het
Ddx54 A G 5: 120,761,703 (GRCm39) D493G probably benign Het
Efemp2 T C 19: 5,530,078 (GRCm39) S140P probably damaging Het
Fat1 C A 8: 45,479,786 (GRCm39) T2944K probably damaging Het
Fgfr1 T A 8: 26,047,784 (GRCm39) D43E probably damaging Het
Fry G A 5: 150,419,825 (GRCm39) A996T probably damaging Het
Fyb2 G A 4: 104,873,063 (GRCm39) V784I probably benign Het
Gm6507 T A 6: 89,162,144 (GRCm39) noncoding transcript Het
Gm7964 T C 7: 83,405,374 (GRCm39) noncoding transcript Het
Gucy2c T C 6: 136,704,799 (GRCm39) probably null Het
Hdac10 A T 15: 89,010,621 (GRCm39) L259Q probably damaging Het
Hs3st3b1 T C 11: 63,812,401 (GRCm39) T105A probably benign Het
Hsd17b7 A G 1: 169,783,595 (GRCm39) L271P probably damaging Het
Ifnlr1 T A 4: 135,428,524 (GRCm39) probably benign Het
Kif22 A T 7: 126,633,078 (GRCm39) M121K probably damaging Het
Kl G A 5: 150,876,566 (GRCm39) D129N probably damaging Het
Mettl13 A T 1: 162,361,999 (GRCm39) I648N probably damaging Het
Mlh1 C T 9: 111,100,540 (GRCm39) R18H probably damaging Het
Mtmr14 T C 6: 113,247,473 (GRCm39) probably benign Het
Myo15a C A 11: 60,369,803 (GRCm39) N854K possibly damaging Het
Myo1h T C 5: 114,457,741 (GRCm39) I84T probably benign Het
Myo9a A T 9: 59,778,383 (GRCm39) S1380C probably benign Het
Myof A G 19: 37,969,708 (GRCm39) V318A probably damaging Het
N4bp2l2 A G 5: 150,585,897 (GRCm39) S28P probably damaging Het
Nbr1 C T 11: 101,467,145 (GRCm39) Q570* probably null Het
Nhp2 C T 11: 51,510,750 (GRCm39) Q36* probably null Het
Or1e17 T G 11: 73,831,096 (GRCm39) V8G probably benign Het
Or8b37 G T 9: 37,959,123 (GRCm39) V202L probably benign Het
Poc1b T A 10: 98,965,457 (GRCm39) W129R probably damaging Het
Potegl T C 2: 23,146,936 (GRCm39) probably benign Het
Rapgef2 C T 3: 78,986,481 (GRCm39) E1018K probably benign Het
Rgs12 T C 5: 35,181,710 (GRCm39) probably benign Het
Rufy2 G A 10: 62,833,873 (GRCm39) V280I probably benign Het
Snx2 A G 18: 53,343,444 (GRCm39) I281V probably benign Het
Spag5 C A 11: 78,210,410 (GRCm39) probably benign Het
Spata31g1 T A 4: 42,971,691 (GRCm39) N341K probably damaging Het
Stxbp5 A T 10: 9,644,617 (GRCm39) I961N probably damaging Het
Tet2 T C 3: 133,173,045 (GRCm39) E1739G probably benign Het
Tmod2 A G 9: 75,502,337 (GRCm39) F50S possibly damaging Het
Tnfsf13b T G 8: 10,057,166 (GRCm39) probably null Het
Ttn T C 2: 76,616,679 (GRCm39) K16525E possibly damaging Het
Txnrd2 T C 16: 18,259,629 (GRCm39) probably benign Het
Ubr1 A T 2: 120,711,582 (GRCm39) Y1437* probably null Het
Vwf C A 6: 125,543,225 (GRCm39) D170E probably benign Het
Wdr95 C G 5: 149,497,513 (GRCm39) I230M probably damaging Het
Xirp2 C T 2: 67,342,559 (GRCm39) S1600F probably damaging Het
Zfp12 A G 5: 143,230,638 (GRCm39) K322E probably damaging Het
Other mutations in Hoxd9
AlleleSourceChrCoordTypePredicted EffectPPH Score
R3743:Hoxd9 UTSW 2 74,528,710 (GRCm39) missense probably damaging 0.99
R4155:Hoxd9 UTSW 2 74,529,667 (GRCm39) missense probably benign 0.15
R4261:Hoxd9 UTSW 2 74,526,031 (GRCm39) unclassified probably benign
R5794:Hoxd9 UTSW 2 74,529,617 (GRCm39) missense probably damaging 1.00
R6114:Hoxd9 UTSW 2 74,529,709 (GRCm39) missense probably damaging 1.00
R6197:Hoxd9 UTSW 2 74,529,166 (GRCm39) missense probably damaging 0.99
R6248:Hoxd9 UTSW 2 74,528,980 (GRCm39) missense probably benign 0.09
R6268:Hoxd9 UTSW 2 74,528,433 (GRCm39) missense probably damaging 1.00
R6717:Hoxd9 UTSW 2 74,528,733 (GRCm39) missense probably benign 0.01
R6809:Hoxd9 UTSW 2 74,529,590 (GRCm39) missense probably damaging 1.00
R7183:Hoxd9 UTSW 2 74,528,709 (GRCm39) missense possibly damaging 0.59
R7254:Hoxd9 UTSW 2 74,528,718 (GRCm39) missense probably damaging 1.00
R9160:Hoxd9 UTSW 2 74,529,761 (GRCm39) missense unknown
R9277:Hoxd9 UTSW 2 74,529,539 (GRCm39) missense possibly damaging 0.76
R9445:Hoxd9 UTSW 2 74,528,415 (GRCm39) missense probably damaging 0.99
Z1176:Hoxd9 UTSW 2 74,528,472 (GRCm39) missense probably damaging 0.99
Z1177:Hoxd9 UTSW 2 74,528,869 (GRCm39) missense probably benign 0.04
Predicted Primers PCR Primer
(F):5'- AGAATTCCCGTGCAACTCGTTCC -3'
(R):5'- AAAAGCCTTAATGCCCGCGCTC -3'

Sequencing Primer
(F):5'- TCCGAGCCCTCAGCTTG -3'
(R):5'- GCTCTGTTTACCGTACAAACCG -3'
Posted On 2013-07-30