Incidental Mutation 'R4261:Hoxd9'
ID 322640
Institutional Source Beutler Lab
Gene Symbol Hoxd9
Ensembl Gene ENSMUSG00000043342
Gene Name homeobox D9
Synonyms Hox-5.2, Hox-4.4
MMRRC Submission 041074-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4261 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 74528107-74530552 bp(+) (GRCm39)
Type of Mutation unclassified
DNA Base Change (assembly) C to A at 74526031 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000062412 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000059272] [ENSMUST00000061745]
AlphaFold P28357
Predicted Effect probably benign
Transcript: ENSMUST00000059272
SMART Domains Protein: ENSMUSP00000058490
Gene: ENSMUSG00000043342

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
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.6%
Validation Efficiency 96% (53/55)
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: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700010I14Rik T C 17: 9,214,066 (GRCm39) S298P probably damaging Het
4930407I10Rik A G 15: 81,947,927 (GRCm39) D608G possibly damaging Het
Actr10 T C 12: 70,999,759 (GRCm39) V185A probably benign Het
Adam9 G A 8: 25,454,923 (GRCm39) Q733* probably null Het
Adamts4 C T 1: 171,086,673 (GRCm39) P822S probably benign Het
Arhgap9 G C 10: 127,164,334 (GRCm39) R537P probably damaging Het
Bsn T A 9: 107,987,883 (GRCm39) probably benign Het
Car5a A T 8: 122,671,488 (GRCm39) H15Q probably benign Het
Disp1 A T 1: 182,870,950 (GRCm39) I490N probably damaging Het
Dlgap5 T G 14: 47,651,245 (GRCm39) Y96S probably damaging Het
Dnah10 T A 5: 124,807,201 (GRCm39) V162D possibly damaging Het
Dock7 A T 4: 98,892,123 (GRCm39) M821K possibly damaging Het
Exoc3l T C 8: 106,017,599 (GRCm39) R528G probably damaging Het
Fam234b G A 6: 135,186,134 (GRCm39) G17E unknown Het
Grhl2 G A 15: 37,361,067 (GRCm39) G617D possibly damaging Het
Herc1 CTGAGGACTCTTTG CTG 9: 66,355,630 (GRCm39) probably null Het
Hspa9 A G 18: 35,072,476 (GRCm39) S550P probably damaging Het
Ide A C 19: 37,306,585 (GRCm39) S63A unknown Het
Kat6b T A 14: 21,719,737 (GRCm39) I1363N probably damaging Het
Ltbp1 T A 17: 75,598,362 (GRCm39) C614* probably null Het
Mphosph8 A G 14: 56,911,922 (GRCm39) D315G probably benign Het
Mthfr-ps1 A C 5: 78,622,330 (GRCm39) noncoding transcript Het
Mug1 A G 6: 121,850,693 (GRCm39) T730A probably benign Het
Myef2 T C 2: 124,957,399 (GRCm39) T119A possibly damaging Het
Pald1 A G 10: 61,179,471 (GRCm39) L466P probably damaging Het
Pcdh15 G A 10: 74,481,512 (GRCm39) V286M probably damaging Het
Pcdhgb2 A G 18: 37,824,950 (GRCm39) D647G probably damaging Het
Pdgfrb A C 18: 61,210,703 (GRCm39) T737P probably benign Het
Pgk2 T G 17: 40,518,274 (GRCm39) T385P probably benign Het
Pkp4 A G 2: 59,135,506 (GRCm39) Y126C probably damaging Het
Plppr1 A G 4: 49,300,993 (GRCm39) I109V probably benign Het
Ppcs A G 4: 119,279,106 (GRCm39) F149L probably damaging Het
Ppp2r5d G A 17: 46,998,007 (GRCm39) Q219* probably null Het
Raf1 C T 6: 115,600,015 (GRCm39) probably null Het
Rfx7 C T 9: 72,523,925 (GRCm39) R372W probably damaging Het
Robo4 C A 9: 37,316,877 (GRCm39) S397R probably benign Het
Sat1 T C X: 153,998,182 (GRCm39) probably benign Het
Serpina1c T C 12: 103,863,339 (GRCm39) K287R probably benign Het
Sgsm2 T A 11: 74,782,854 (GRCm39) H34L probably damaging Het
Slc38a4 A G 15: 96,896,374 (GRCm39) Y498H probably damaging Het
Ttn T A 2: 76,628,384 (GRCm39) Y14592F probably damaging Het
Ube3b T C 5: 114,536,489 (GRCm39) F245S possibly damaging Het
Ugt3a1 G A 15: 9,335,879 (GRCm39) probably null Het
Wdr91 T A 6: 34,881,457 (GRCm39) S297C possibly damaging Het
Zcwpw2 T C 9: 117,827,982 (GRCm39) noncoding transcript 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
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'- TTCAGTGAGCTCTTGGTGAC -3'
(R):5'- GTCACTTGCAACTGCTTTCAG -3'

Sequencing Primer
(F):5'- AGCTCTTGGTGACTTCTGGC -3'
(R):5'- CTGACAGCTCAGACACAGTGG -3'
Posted On 2015-06-20