Incidental Mutation 'R6268:Hoxd9'
ID 507135
Institutional Source Beutler Lab
Gene Symbol Hoxd9
Ensembl Gene ENSMUSG00000043342
Gene Name homeobox D9
Synonyms Hox-5.2, Hox-4.4
MMRRC Submission 044439-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6268 (G1)
Quality Score 80.0075
Status Validated
Chromosome 2
Chromosomal Location 74528107-74530552 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 74528433 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Leucine at position 12 (V12L)
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: V12L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000058490
Gene: ENSMUSG00000043342
AA Change: V12L

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: ENSMUST00000136302
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152027
Predicted Effect noncoding transcript
Transcript: ENSMUST00000190845
Predicted Effect noncoding transcript
Transcript: ENSMUST00000198895
Meta Mutation Damage Score 0.3476 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.3%
  • 20x: 95.5%
Validation Efficiency 99% (68/69)
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: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921504E06Rik A G 2: 19,545,219 (GRCm39) I78T probably benign Het
Afg3l1 A T 8: 124,219,665 (GRCm39) I398F probably damaging Het
Ahctf1 T C 1: 179,591,048 (GRCm39) H1244R probably benign Het
Ank1 A T 8: 23,599,687 (GRCm39) K797N probably damaging Het
Anxa6 G T 11: 54,877,903 (GRCm39) probably null Het
Aoc1l1 T A 6: 48,954,616 (GRCm39) Y585N probably benign Het
Ap1b1 T A 11: 4,969,493 (GRCm39) V310E probably damaging Het
C2cd2l T C 9: 44,228,963 (GRCm39) I123V probably damaging Het
Cars2 TCCCC TCCC 8: 11,579,599 (GRCm39) probably null Het
Cfap54 T A 10: 92,874,771 (GRCm39) I542F probably damaging Het
Cfap57 G T 4: 118,426,648 (GRCm39) Y1100* probably null Het
Coq9 A G 8: 95,576,862 (GRCm39) E158G probably benign Het
Cox15 A T 19: 43,728,365 (GRCm39) W303R possibly damaging Het
Cpa5 A G 6: 30,615,172 (GRCm39) Y103C probably damaging Het
Crygn A T 5: 24,961,189 (GRCm39) V39E probably damaging Het
Csf1 G T 3: 107,654,473 (GRCm39) S132R possibly damaging Het
Dapk1 G A 13: 60,909,580 (GRCm39) V1398M possibly damaging Het
Degs2 C A 12: 108,658,839 (GRCm39) V47L probably damaging Het
Dock5 C A 14: 68,027,724 (GRCm39) E1057* probably null Het
Dsg1b C A 18: 20,521,220 (GRCm39) Q26K probably benign Het
Elp1 T C 4: 56,762,305 (GRCm39) Y1098C probably damaging Het
Fam181a T C 12: 103,282,803 (GRCm39) V236A possibly damaging Het
Fam78b C A 1: 166,906,122 (GRCm39) P94T probably damaging Het
Fbxw25 T G 9: 109,483,718 (GRCm39) T165P probably damaging Het
Flg C A 3: 93,195,482 (GRCm39) probably benign Het
Frrs1 G T 3: 116,696,748 (GRCm39) V573F probably damaging Het
Gm7298 A G 6: 121,756,032 (GRCm39) T964A possibly damaging Het
Kcnt1 A G 2: 25,793,609 (GRCm39) probably null Het
Klhl3 G T 13: 58,161,656 (GRCm39) R480S probably damaging Het
Klhl36 A G 8: 120,597,406 (GRCm39) D369G probably damaging Het
Lama3 T A 18: 12,657,794 (GRCm39) N303K probably damaging Het
Lhcgr T C 17: 89,050,132 (GRCm39) T465A probably damaging Het
Llgl1 T C 11: 60,602,989 (GRCm39) V888A probably benign Het
Lrp1b T A 2: 40,711,729 (GRCm39) T3164S probably benign Het
Mmp3 T G 9: 7,447,622 (GRCm39) D202E possibly damaging Het
Mocs1 C A 17: 49,742,183 (GRCm39) T104K probably damaging Het
Mrpl42 A T 10: 95,332,569 (GRCm39) probably null Het
Mtch2 T C 2: 90,693,992 (GRCm39) C279R probably benign Het
Muc4 A T 16: 32,589,141 (GRCm39) D2836V probably damaging Het
Myh7 T C 14: 55,226,741 (GRCm39) E370G probably benign Het
Naa11 A G 5: 97,540,069 (GRCm39) Y30H probably damaging Het
Ntng1 T C 3: 109,842,351 (GRCm39) T141A probably damaging Het
Or5h26 A C 16: 58,987,656 (GRCm39) probably null Het
Or8c11 T C 9: 38,289,384 (GRCm39) I69T probably benign Het
Or9i14 A T 19: 13,792,671 (GRCm39) Y94* probably null Het
Pcdha12 G A 18: 37,155,477 (GRCm39) C732Y possibly damaging Het
Plekhm2 G A 4: 141,359,652 (GRCm39) Q392* probably null Het
Prr22 G A 17: 57,078,587 (GRCm39) V247M probably damaging Het
Rapgef6 T A 11: 54,540,073 (GRCm39) L716Q probably damaging Het
Rasgrp4 G A 7: 28,842,493 (GRCm39) V246I probably damaging Het
Rhbdd2 C T 5: 135,672,114 (GRCm39) T323I probably benign Het
Rsf1 CG CGACGGCGGTG 7: 97,229,115 (GRCm39) probably benign Homo
Scgb2b20 A T 7: 33,063,973 (GRCm39) I99K possibly damaging Het
Scyl3 C T 1: 163,773,786 (GRCm39) R324* probably null Het
Slc23a1 T C 18: 35,752,624 (GRCm39) Y551C probably damaging Het
Slc5a5 A T 8: 71,341,264 (GRCm39) S358R probably damaging Het
Sorcs3 T A 19: 48,778,605 (GRCm39) N1007K probably damaging Het
Stxbp4 T A 11: 90,431,027 (GRCm39) K428* probably null Het
Tmem63c T A 12: 87,128,727 (GRCm39) I584N probably damaging Het
Traf3ip3 C T 1: 192,880,344 (GRCm39) probably benign Het
Trgv2 G A 13: 19,521,001 (GRCm39) T31I probably benign Het
Ttll3 C T 6: 113,369,524 (GRCm39) R23C probably benign Het
Ugt2a3 A C 5: 87,477,472 (GRCm39) L309R probably damaging Het
Urb1 A G 16: 90,550,807 (GRCm39) M2015T probably benign Het
Vmn2r14 A C 5: 109,369,283 (GRCm39) S97A possibly damaging Het
Vps13c C A 9: 67,858,731 (GRCm39) T2727K probably benign Het
Xrn1 T A 9: 95,846,067 (GRCm39) I40K probably damaging Het
Zc3h11a A G 1: 133,552,295 (GRCm39) V604A probably benign Het
Zfp410 G A 12: 84,378,612 (GRCm39) R259H probably benign Het
Zfp748 A G 13: 67,690,705 (GRCm39) V185A possibly damaging Het
Other mutations in Hoxd9
AlleleSourceChrCoordTypePredicted EffectPPH Score
R0723:Hoxd9 UTSW 2 74,529,172 (GRCm39) missense probably damaging 1.00
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
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'- AAATATGATCACGTGGGCCGC -3'
(R):5'- AGGCTTAATCCCGTAGTGGC -3'

Sequencing Primer
(F):5'- CCGCGCGACCAATGGTG -3'
(R):5'- TCCATCCAGGAGCGTACGTAG -3'
Posted On 2018-03-15