Incidental Mutation 'R6717:Hoxd9'
ID 543561
Institutional Source Beutler Lab
Gene Symbol Hoxd9
Ensembl Gene ENSMUSG00000043342
Gene Name homeobox D9
Synonyms Hox-5.2, Hox-4.4
MMRRC Submission 044835-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6717 (G1)
Quality Score 75.0075
Status Validated
Chromosome 2
Chromosomal Location 74528107-74530552 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 74528733 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Serine at position 112 (P112S)
Ref Sequence ENSEMBL: ENSMUSP00000058490 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000059272]
AlphaFold P28357
Predicted Effect probably benign
Transcript: ENSMUST00000059272
AA Change: P112S

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000058490
Gene: ENSMUSG00000043342
AA Change: P112S

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
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.7%
  • 20x: 96.5%
Validation Efficiency 98% (47/48)
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: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Akap9 C T 5: 4,114,086 (GRCm39) L3122F probably damaging Het
Atp6v1b1 A T 6: 83,730,632 (GRCm39) probably null Het
Ccdc178 A T 18: 22,153,946 (GRCm39) V621E probably damaging Het
Cfap126 T C 1: 170,941,671 (GRCm39) probably null Het
Cog2 T C 8: 125,252,488 (GRCm39) I64T probably damaging Het
Dhx9 A C 1: 153,349,210 (GRCm39) probably null Het
Efcab7 A G 4: 99,761,931 (GRCm39) D407G possibly damaging Het
Eif2b5 G T 16: 20,324,033 (GRCm39) G459C probably damaging Het
Eml5 T C 12: 98,793,765 (GRCm39) E1168G probably damaging Het
Flnc AGCTGTCAAGTATGCTG AGCTG 6: 29,450,901 (GRCm39) probably benign Het
Fry A G 5: 150,419,777 (GRCm39) T980A probably benign Het
Gabbr2 A G 4: 46,787,574 (GRCm39) V363A possibly damaging Het
Ggt6 T A 11: 72,328,346 (GRCm39) L244* probably null Het
Gprc6a T A 10: 51,491,233 (GRCm39) I768F probably damaging Het
Grk1 G A 8: 13,466,237 (GRCm39) M560I probably benign Het
Hapln4 G A 8: 70,537,740 (GRCm39) E145K probably damaging Het
Ly6g6f T A 17: 35,304,550 (GRCm39) M1L probably benign Het
Mast1 T C 8: 85,644,383 (GRCm39) T849A probably benign Het
Mob4 A T 1: 55,175,872 (GRCm39) M39L possibly damaging Het
Mrgpre A T 7: 143,335,260 (GRCm39) L81Q probably damaging Het
Mst1 T C 9: 107,957,774 (GRCm39) probably null Het
Muc5b A T 7: 141,411,559 (GRCm39) R1502* probably null Het
Or4b13 T A 2: 90,082,868 (GRCm39) I155L probably benign Het
Or5ap2 T A 2: 85,680,567 (GRCm39) I257N probably damaging Het
Or9e1 T C 11: 58,732,113 (GRCm39) Y58H probably damaging Het
Pdc A G 1: 150,208,769 (GRCm39) D84G probably damaging Het
Peak1 T C 9: 56,114,523 (GRCm39) N443D probably benign Het
Pkd1l3 T A 8: 110,341,401 (GRCm39) W85R unknown Het
Pramel31 G T 4: 144,089,227 (GRCm39) V182L probably benign Het
Rfc1 G A 5: 65,459,347 (GRCm39) Q190* probably null Het
Rfc1 A G 5: 65,470,304 (GRCm39) S68P probably damaging Het
Rnf145 T C 11: 44,452,317 (GRCm39) V432A probably benign Het
Ror2 A G 13: 53,273,018 (GRCm39) S204P probably damaging Het
Scn1a T C 2: 66,162,631 (GRCm39) E205G probably damaging Het
Slc2a8 A C 2: 32,866,189 (GRCm39) M277R probably damaging Het
Slc4a1 T C 11: 102,245,249 (GRCm39) Y566C probably damaging Het
Slc6a12 A G 6: 121,331,262 (GRCm39) N185S probably benign Het
Srcap GCTCCTCCTCCTCCTCCT GCTCCTCCTCCTCCT 7: 127,157,482 (GRCm39) probably benign Het
Stk33 T A 7: 108,926,823 (GRCm39) T279S possibly damaging Het
Taok3 A G 5: 117,379,015 (GRCm39) probably benign Het
Tlr11 A G 14: 50,599,561 (GRCm39) T516A probably benign Het
Tmem132c T A 5: 127,641,093 (GRCm39) L1088Q possibly damaging Het
Tmem132d T A 5: 127,861,485 (GRCm39) M879L probably benign Het
Tnk2 A G 16: 32,489,687 (GRCm39) E322G probably damaging Het
Ttc28 T C 5: 111,433,302 (GRCm39) V2081A probably benign Het
Ttn C T 2: 76,624,753 (GRCm39) probably null Het
Zfp105 T C 9: 122,759,373 (GRCm39) V348A possibly damaging Het
Zswim2 T C 2: 83,745,753 (GRCm39) R562G probably benign 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
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

Sequencing Primer
Posted On 2019-03-06