Incidental Mutation 'R6114:Hoxd9'
ID 484993
Institutional Source Beutler Lab
Gene Symbol Hoxd9
Ensembl Gene ENSMUSG00000043342
Gene Name homeobox D9
Synonyms Hox-5.2, Hox-4.4
MMRRC Submission 044263-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6114 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 74697727-74700208 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to G at 74699365 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Asparagine to Aspartic acid at position 322 (N322D)
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: N322D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000058490
Gene: ENSMUSG00000043342
AA Change: N322D

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: ENSMUST00000152027
Predicted Effect noncoding transcript
Transcript: ENSMUST00000190845
Predicted Effect noncoding transcript
Transcript: ENSMUST00000198895
Meta Mutation Damage Score 0.9671 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.0%
  • 20x: 94.0%
Validation Efficiency 94% (60/64)
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: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamdec1 C A 14: 68,571,803 (GRCm38) V237L probably benign Het
Aff1 T C 5: 103,842,297 (GRCm38) S878P probably damaging Het
Ahcy A C 2: 155,062,159 (GRCm38) L386R probably damaging Het
Ank2 T C 3: 127,011,051 (GRCm38) N607D probably damaging Het
Arid5b T C 10: 68,097,744 (GRCm38) D776G possibly damaging Het
Art4 T A 6: 136,857,213 (GRCm38) T11S unknown Het
Blm T C 7: 80,513,487 (GRCm38) T39A probably damaging Het
Cabin1 T A 10: 75,747,971 (GRCm38) M221L probably benign Het
Cacna1c T C 6: 118,596,140 (GRCm38) T1675A probably benign Het
Cacnb2 A T 2: 14,975,201 (GRCm38) H285L possibly damaging Het
Cchcr1 A G 17: 35,525,330 (GRCm38) E339G probably damaging Het
Cd14 A G 18: 36,725,953 (GRCm38) W150R probably damaging Het
Cep162 A G 9: 87,203,710 (GRCm38) I1187T probably benign Het
Cntnap4 A G 8: 112,841,753 (GRCm38) H807R probably damaging Het
Copb1 T A 7: 114,246,801 (GRCm38) H178L probably benign Het
Cpxm2 A G 7: 132,154,306 (GRCm38) V103A probably benign Het
Egfr A G 11: 16,904,374 (GRCm38) T849A possibly damaging Het
Endou T A 15: 97,713,876 (GRCm38) K294* probably null Het
Hsph1 C A 5: 149,627,387 (GRCm38) V416L possibly damaging Het
Igkv4-78 T A 6: 69,059,759 (GRCm38) T97S possibly damaging Het
Itga10 G T 3: 96,649,035 (GRCm38) C162F probably damaging Het
Lmod2 A G 6: 24,603,692 (GRCm38) E222G probably damaging Het
Lpar5 A G 6: 125,081,676 (GRCm38) N120S probably damaging Het
Lrrc37 T A 11: 103,617,791 (GRCm38) probably benign Het
Lrrk2 A G 15: 91,747,826 (GRCm38) I1318V probably benign Het
Lst1 T C 17: 35,188,360 (GRCm38) T11A possibly damaging Het
Mfn1 C A 3: 32,563,836 (GRCm38) A106D probably damaging Het
Ms4a12 G T 19: 11,215,290 (GRCm38) N227K probably benign Het
Nr1h4 T A 10: 89,478,816 (GRCm38) N273Y possibly damaging Het
Nrdc A T 4: 109,044,585 (GRCm38) K617M probably damaging Het
Or10a3b A T 7: 108,845,386 (GRCm38) M208K possibly damaging Het
Or1l8 A T 2: 36,927,689 (GRCm38) C142S possibly damaging Het
Or6c202 T A 10: 129,160,333 (GRCm38) H217L probably benign Het
Pcdhgc3 C G 18: 37,807,872 (GRCm38) T442R probably benign Het
Pcnx2 T C 8: 125,773,947 (GRCm38) N1468S probably damaging Het
Pde2a A T 7: 101,511,112 (GRCm38) probably null Het
Pitx2 C G 3: 129,204,413 (GRCm38) probably null Het
Reck T A 4: 43,922,895 (GRCm38) I390N probably damaging Het
Rora A G 9: 69,371,323 (GRCm38) N254S probably benign Het
Samd4b A G 7: 28,522,792 (GRCm38) probably null Het
Scn8a A G 15: 101,040,596 (GRCm38) T1949A probably damaging Het
Slc22a15 A T 3: 101,860,852 (GRCm38) Y346* probably null Het
Slc24a5 A G 2: 125,083,092 (GRCm38) T218A probably benign Het
Slc38a10 G A 11: 120,129,312 (GRCm38) Q305* probably null Het
Slc45a4 G A 15: 73,605,604 (GRCm38) P28S probably damaging Het
Smyd5 A T 6: 85,440,262 (GRCm38) probably benign Het
Sox8 T C 17: 25,567,520 (GRCm38) D403G probably damaging Het
Stx7 A G 10: 24,184,985 (GRCm38) probably null Het
Svil T C 18: 5,108,639 (GRCm38) S1522P probably damaging Het
Sycp2 G C 2: 178,348,245 (GRCm38) R1403G probably benign Het
Tasor2 G A 13: 3,590,081 (GRCm38) T352M probably damaging Het
Tcf25 A T 8: 123,384,375 (GRCm38) K192M probably damaging Het
Tecpr1 C T 5: 144,204,640 (GRCm38) G804S possibly damaging Het
Teddm1a C G 1: 153,891,868 (GRCm38) S26C probably damaging Het
Usp13 C T 3: 32,854,669 (GRCm38) P155S probably damaging Het
Usp17lb T A 7: 104,840,364 (GRCm38) D451V possibly damaging Het
Vmn1r173 A G 7: 23,702,829 (GRCm38) N163S possibly damaging Het
Vmn2r103 G T 17: 19,812,325 (GRCm38) C787F probably damaging Het
Vmn2r106 G A 17: 20,268,376 (GRCm38) P587L probably benign Het
Wdr24 C T 17: 25,824,605 (GRCm38) H134Y probably benign Het
Zbtb40 T A 4: 136,988,691 (GRCm38) I988F probably damaging Het
Zbtb47 T A 9: 121,765,595 (GRCm38) F540Y probably damaging Het
Zfp536 A T 7: 37,479,736 (GRCm38) I84N probably damaging Het
Other mutations in Hoxd9
AlleleSourceChrCoordTypePredicted EffectPPH Score
R0723:Hoxd9 UTSW 2 74,698,828 (GRCm38) missense probably damaging 1.00
R3743:Hoxd9 UTSW 2 74,698,366 (GRCm38) missense probably damaging 0.99
R4155:Hoxd9 UTSW 2 74,699,323 (GRCm38) missense probably benign 0.15
R4261:Hoxd9 UTSW 2 74,695,687 (GRCm38) unclassified probably benign
R5794:Hoxd9 UTSW 2 74,699,273 (GRCm38) missense probably damaging 1.00
R6197:Hoxd9 UTSW 2 74,698,822 (GRCm38) missense probably damaging 0.99
R6248:Hoxd9 UTSW 2 74,698,636 (GRCm38) missense probably benign 0.09
R6268:Hoxd9 UTSW 2 74,698,089 (GRCm38) missense probably damaging 1.00
R6717:Hoxd9 UTSW 2 74,698,389 (GRCm38) missense probably benign 0.01
R6809:Hoxd9 UTSW 2 74,699,246 (GRCm38) missense probably damaging 1.00
R7183:Hoxd9 UTSW 2 74,698,365 (GRCm38) missense possibly damaging 0.59
R7254:Hoxd9 UTSW 2 74,698,374 (GRCm38) missense probably damaging 1.00
R9160:Hoxd9 UTSW 2 74,699,417 (GRCm38) missense unknown
R9277:Hoxd9 UTSW 2 74,699,195 (GRCm38) missense possibly damaging 0.76
R9445:Hoxd9 UTSW 2 74,698,071 (GRCm38) missense probably damaging 0.99
Z1176:Hoxd9 UTSW 2 74,698,128 (GRCm38) missense probably damaging 0.99
Z1177:Hoxd9 UTSW 2 74,698,525 (GRCm38) missense probably benign 0.04
Predicted Primers PCR Primer
(F):5'- TTCCTAGACAACCCTGCAGC -3'
(R):5'- GCGAGCAAATACAGTGTCCC -3'

Sequencing Primer
(F):5'- TGCAGCGAACTGGATCCAC -3'
(R):5'- TCCGAGTCGCTGCAGAGTTTC -3'
Posted On 2017-08-16