Incidental Mutation 'R6809:Hoxd9'
ID 533688
Institutional Source Beutler Lab
Gene Symbol Hoxd9
Ensembl Gene ENSMUSG00000043342
Gene Name homeobox D9
Synonyms Hox-5.2, Hox-4.4
MMRRC Submission 044922-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6809 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 74528107-74530552 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 74529590 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 282 (Y282C)
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: Y282C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000058490
Gene: ENSMUSG00000043342
AA Change: Y282C

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
Meta Mutation Damage Score 0.6210 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.2%
  • 20x: 95.1%
Validation Efficiency 96% (51/53)
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: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A130010J15Rik T A 1: 192,857,089 (GRCm39) V147E possibly damaging Het
Abtb3 A G 10: 85,467,240 (GRCm39) T732A probably benign Het
Adgrv1 A T 13: 81,621,072 (GRCm39) M3893K probably benign Het
Aox3 T C 1: 58,157,840 (GRCm39) S66P probably damaging Het
Apeh G A 9: 107,969,878 (GRCm39) H186Y probably damaging Het
Bloc1s5 A G 13: 38,787,961 (GRCm39) V141A probably benign Het
Bltp1 A G 3: 36,928,431 (GRCm39) N61S probably damaging Het
Col28a1 T C 6: 7,999,468 (GRCm39) Y1083C probably damaging Het
Crb1 A G 1: 139,170,864 (GRCm39) V842A probably benign Het
Dapk1 A G 13: 60,899,103 (GRCm39) S858G probably benign Het
Dlgap2 G T 8: 14,229,619 (GRCm39) probably benign Het
Dpysl4 A G 7: 138,673,576 (GRCm39) D199G probably benign Het
Eml6 C T 11: 29,753,161 (GRCm39) V917I probably benign Het
Fut9 T A 4: 25,620,647 (GRCm39) T56S probably benign Het
Gtdc1 G C 2: 44,465,563 (GRCm39) S214* probably null Het
Gtdc1 A G 2: 44,715,396 (GRCm39) F49S probably damaging Het
Hrc A G 7: 44,985,803 (GRCm39) E318G probably benign Het
Ikzf2 T C 1: 69,609,661 (GRCm39) T195A probably damaging Het
Krt36 A T 11: 99,996,335 (GRCm39) S30T probably benign Het
Lrp1 A G 10: 127,390,925 (GRCm39) F2991L probably benign Het
Lrrc34 T A 3: 30,688,749 (GRCm39) Q184L possibly damaging Het
Mapk1 A T 16: 16,853,326 (GRCm39) M49L probably benign Het
Mroh2a G T 1: 88,162,938 (GRCm39) Q360H probably benign Het
Mrpl48 A G 7: 100,195,574 (GRCm39) probably benign Het
Ncln A G 10: 81,323,512 (GRCm39) probably null Het
Nol4 T A 18: 23,053,882 (GRCm39) Q96L probably damaging Het
Or2y1e G T 11: 49,218,687 (GRCm39) V150L probably benign Het
Or5g25 G A 2: 85,478,317 (GRCm39) A116V probably damaging Het
Padi2 A G 4: 140,674,077 (GRCm39) probably null Het
Pak5 T G 2: 135,939,501 (GRCm39) I545L possibly damaging Het
Paqr5 T A 9: 61,876,064 (GRCm39) R157W probably null Het
Pard3b G A 1: 62,200,340 (GRCm39) R293H probably damaging Het
Phf11d C A 14: 59,593,844 (GRCm39) C110F probably damaging Het
Pkn2 G A 3: 142,504,765 (GRCm39) P804S probably damaging Het
Pnpla6 G A 8: 3,584,611 (GRCm39) C743Y possibly damaging Het
Pramel14 A G 4: 143,719,651 (GRCm39) V238A probably benign Het
Pramel58 C A 5: 94,831,277 (GRCm39) Q95K probably benign Het
Psip1 A G 4: 83,386,879 (GRCm39) M164T probably benign Het
Rgs22 C G 15: 36,048,910 (GRCm39) S914T probably damaging Het
Rufy4 G A 1: 74,172,206 (GRCm39) V310I probably benign Het
Ryr2 G A 13: 11,741,816 (GRCm39) L2122F probably damaging Het
Sgcb T G 5: 73,798,036 (GRCm39) N142T probably benign Het
Slc27a6 A G 18: 58,738,126 (GRCm39) E394G probably benign Het
Slc29a2 T C 19: 5,079,271 (GRCm39) V298A probably damaging Het
Slf2 C A 19: 44,931,907 (GRCm39) T654N probably damaging Het
Spata4 A C 8: 55,055,368 (GRCm39) K123Q possibly damaging Het
Taar7b T C 10: 23,876,756 (GRCm39) V307A probably benign Het
Tenm4 G A 7: 96,202,703 (GRCm39) R106H probably benign Het
Ttn T C 2: 76,693,983 (GRCm39) E295G possibly damaging Het
Ubqln4 A T 3: 88,462,679 (GRCm39) Q48L possibly damaging Het
Ugt1a10 T A 1: 87,983,647 (GRCm39) D148E probably damaging Het
Vmn2r85 T A 10: 130,261,795 (GRCm39) N181Y probably benign Het
Wdfy3 C T 5: 102,071,813 (GRCm39) V1026I 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
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
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'- CCCAAGTTGTGAAAAGCGTC -3'
(R):5'- CTGCCTTTTGAGTGCTGCAG -3'

Sequencing Primer
(F):5'- AAAAGCGTCCATCCTTGGTG -3'
(R):5'- CACTGGGTCAGTCTCCTTTAGG -3'
Posted On 2018-09-12