Incidental Mutation 'R4824:Hoxc9'
ID 374266
Institutional Source Beutler Lab
Gene Symbol Hoxc9
Ensembl Gene ENSMUSG00000036139
Gene Name homeobox C9
Synonyms Hox-3.2
MMRRC Submission 042440-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4824 (G1)
Quality Score 225
Status Validated
Chromosome 15
Chromosomal Location 102885467-102893324 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) T to A at 102890225 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Stop codon at position 47 (C47*)
Ref Sequence ENSEMBL: ENSMUSP00000001706 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001706] [ENSMUST00000173306]
AlphaFold P09633
Predicted Effect probably null
Transcript: ENSMUST00000001706
AA Change: C47*
SMART Domains Protein: ENSMUSP00000001706
Gene: ENSMUSG00000036139
AA Change: C47*

DomainStartEndE-ValueType
Pfam:Hox9_act 1 179 2e-63 PFAM
HOX 192 254 8.84e-28 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000173306
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174869
Meta Mutation Damage Score 0.9754 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 94.0%
Validation Efficiency 98% (123/126)
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, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXC genes located in a cluster on chromosome 12. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for disruptions in this gene grow more slowly than normal and develop hunched backs. Forward transformations seen in vertebrae from L1 and forward to around T10. Abnormalities in the sternum and ribs attachments to the sternum are also seen. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 107 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik A G 3: 137,771,437 (GRCm39) T209A probably benign Het
1700086D15Rik T C 11: 65,043,441 (GRCm39) probably benign Het
A130010J15Rik G A 1: 192,856,965 (GRCm39) V106I probably benign Het
Abca16 C A 7: 120,074,702 (GRCm39) N580K possibly damaging Het
Actrt2 A T 4: 154,751,344 (GRCm39) F264Y probably damaging Het
Adh4 G A 3: 138,134,807 (GRCm39) S327N possibly damaging Het
Alkbh5 T C 11: 60,444,697 (GRCm39) probably null Het
Anapc1 T A 2: 128,470,610 (GRCm39) T1507S possibly damaging Het
Anapc2 A G 2: 25,167,764 (GRCm39) R444G probably damaging Het
Apoh G T 11: 108,305,087 (GRCm39) W335L probably benign Het
B4galt7 A T 13: 55,752,162 (GRCm39) H71L possibly damaging Het
Bicd2 A G 13: 49,532,488 (GRCm39) E358G probably damaging Het
Bmper T A 9: 23,134,956 (GRCm39) V7D possibly damaging Het
Brca2 T C 5: 150,463,200 (GRCm39) F988S probably damaging Het
Brix1 A G 15: 10,485,828 (GRCm39) V49A possibly damaging Het
Brpf3 T C 17: 29,025,460 (GRCm39) S178P probably benign Het
Btaf1 A G 19: 36,958,448 (GRCm39) Y655C possibly damaging Het
C1rl C G 6: 124,486,040 (GRCm39) Y470* probably null Het
Cacnb4 A G 2: 52,565,822 (GRCm39) V21A probably benign Het
Caskin1 C A 17: 24,720,103 (GRCm39) P437T probably benign Het
Casz1 C A 4: 149,029,028 (GRCm39) P1158T probably damaging Het
Ccdc141 T A 2: 76,954,680 (GRCm39) Q189L probably damaging Het
Ccr3 T C 9: 123,828,809 (GRCm39) V48A probably damaging Het
Cebpd G A 16: 15,705,978 (GRCm39) G264S probably benign Het
Cert1 C T 13: 96,752,995 (GRCm39) P350S probably benign Het
Cfap20dc A T 14: 8,665,997 (GRCm38) M1K probably null Het
Chd1 C A 17: 15,953,386 (GRCm39) S440R probably damaging Het
Clip1 T A 5: 123,769,086 (GRCm39) E504D probably damaging Het
Cmya5 T C 13: 93,230,082 (GRCm39) R1669G probably benign Het
Col11a2 T A 17: 34,269,937 (GRCm39) F456I probably damaging Het
Ctnna2 A T 6: 76,957,764 (GRCm39) M130K probably damaging Het
Elmo2 A T 2: 165,133,922 (GRCm39) probably benign Het
F11 T C 8: 45,708,379 (GRCm39) D27G probably damaging Het
Faap100 A T 11: 120,266,412 (GRCm39) probably null Het
Fat1 A G 8: 45,442,151 (GRCm39) E1151G probably damaging Het
Fbll1 T A 11: 35,688,652 (GRCm39) I204F probably damaging Het
Gle1 T A 2: 29,830,215 (GRCm39) V257D possibly damaging Het
Hsd17b6 A G 10: 127,829,524 (GRCm39) V226A probably benign Het
Hsd17b7 C T 1: 169,788,764 (GRCm39) R151Q probably benign Het
Hsh2d G A 8: 72,954,304 (GRCm39) D229N probably benign Het
Ido2 A G 8: 25,023,875 (GRCm39) I321T probably benign Het
Irf2bp2 T C 8: 127,318,172 (GRCm39) T465A probably benign Het
Kdm2a A G 19: 4,412,815 (GRCm39) M34T probably damaging Het
Klhl6 C T 16: 19,775,778 (GRCm39) R260H probably damaging Het
Kntc1 T A 5: 123,928,196 (GRCm39) L1231* probably null Het
Lca5l A C 16: 95,963,229 (GRCm39) Y412* probably null Het
Lipt1 T C 1: 37,914,513 (GRCm39) S190P possibly damaging Het
Ly6f T A 15: 75,143,569 (GRCm39) V92D probably damaging Het
Matn4 T A 2: 164,235,151 (GRCm39) M433L probably benign Het
Mbtd1 C A 11: 93,816,528 (GRCm39) P370T probably benign Het
Mcph1 T A 8: 18,682,703 (GRCm39) probably null Het
Muc5b T A 7: 141,417,922 (GRCm39) C3623S probably damaging Het
Myt1l C A 12: 29,899,399 (GRCm39) H134N probably benign Het
Nav2 A T 7: 49,058,749 (GRCm39) probably benign Het
Ndufaf8 T C 11: 119,989,992 (GRCm39) C35R probably damaging Het
Neb G A 2: 52,094,891 (GRCm39) T5130I possibly damaging Het
Nlrp9c T C 7: 26,079,989 (GRCm39) N624S possibly damaging Het
Nr0b2 C A 4: 133,283,334 (GRCm39) H190Q probably damaging Het
Nrg4 A G 9: 55,156,405 (GRCm39) probably benign Het
Nup88 A T 11: 70,852,450 (GRCm39) V215E probably benign Het
Oas2 T G 5: 120,876,411 (GRCm39) T511P probably benign Het
Or1e25 A G 11: 73,493,426 (GRCm39) T7A possibly damaging Het
Or2t6 A G 14: 14,175,885 (GRCm38) S66P probably damaging Het
Or5d14 A C 2: 87,880,432 (GRCm39) F179V probably damaging Het
Or5w8 T C 2: 87,687,621 (GRCm39) V34A probably benign Het
Or8g26 A G 9: 39,095,501 (GRCm39) N9S probably benign Het
Or9q1 A C 19: 13,805,718 (GRCm39) L14R probably damaging Het
Pcdhgb2 T A 18: 37,823,502 (GRCm39) N164K probably damaging Het
Pde4d C G 13: 109,253,400 (GRCm39) P76A probably benign Het
Phlda1 T C 10: 111,343,516 (GRCm39) probably benign Het
Plekhh1 A G 12: 79,101,577 (GRCm39) T216A probably benign Het
Plppr3 T A 10: 79,701,507 (GRCm39) E445V possibly damaging Het
Prom1 A G 5: 44,191,732 (GRCm39) V337A probably damaging Het
Prr14l T C 5: 33,001,743 (GRCm39) probably benign Het
Psmd1 A G 1: 86,064,820 (GRCm39) I951V probably benign Het
Rab35 T G 5: 115,781,454 (GRCm39) I85M possibly damaging Het
Rad9a A T 19: 4,250,536 (GRCm39) S93T probably benign Het
Ric1 G A 19: 29,563,242 (GRCm39) C555Y probably damaging Het
Rnd2 C T 11: 101,359,825 (GRCm39) L57F probably damaging Het
Ror2 T A 13: 53,264,719 (GRCm39) Q791L probably benign Het
Rps8 G C 4: 117,012,352 (GRCm39) probably benign Het
Sdr16c5 C T 4: 4,016,216 (GRCm39) W70* probably null Het
Senp3 A G 11: 69,568,821 (GRCm39) V408A probably benign Het
Sh2d4b C A 14: 40,562,301 (GRCm39) W288L probably benign Het
Slc38a9 A T 13: 112,859,832 (GRCm39) D422V probably damaging Het
Slc4a2 T C 5: 24,645,141 (GRCm39) F1104L probably damaging Het
Slc4a3 A G 1: 75,527,267 (GRCm39) K113E possibly damaging Het
Spata3 G A 1: 85,952,048 (GRCm39) probably null Het
Spata31d1d A T 13: 59,877,055 (GRCm39) V160E possibly damaging Het
Sprr2f A G 3: 92,273,203 (GRCm39) M1V probably null Het
Sptbn1 A G 11: 30,068,295 (GRCm39) V1733A possibly damaging Het
Syce1 C A 7: 140,359,809 (GRCm39) L83F probably damaging Het
Tardbp A G 4: 148,702,050 (GRCm39) I295T probably benign Het
Tmem212 A G 3: 27,939,157 (GRCm39) S110P probably damaging Het
Tnc G A 4: 63,935,857 (GRCm39) Q360* probably null Het
Tnrc6c C A 11: 117,613,731 (GRCm39) Q630K probably damaging Het
Ttc19 G A 11: 62,199,922 (GRCm39) R235H probably benign Het
Ube3b T A 5: 114,553,787 (GRCm39) probably null Het
Vmn2r31 C T 7: 7,390,062 (GRCm39) probably null Het
Vmn2r92 T A 17: 18,372,183 (GRCm39) probably benign Het
Washc5 A T 15: 59,205,485 (GRCm39) Y685* probably null Het
Wdr93 T A 7: 79,399,817 (GRCm39) Y135* probably null Het
Wdr95 T A 5: 149,518,797 (GRCm39) I546K probably damaging Het
Zbtb38 T A 9: 96,570,254 (GRCm39) T277S probably benign Het
Zfp13 T C 17: 23,795,797 (GRCm39) D258G possibly damaging Het
Zfp397 T A 18: 24,093,249 (GRCm39) S245T probably benign Het
Zfp646 T C 7: 127,482,907 (GRCm39) Y1695H probably benign Het
Other mutations in Hoxc9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01413:Hoxc9 APN 15 102,892,432 (GRCm39) missense probably damaging 1.00
IGL01418:Hoxc9 APN 15 102,892,432 (GRCm39) missense probably damaging 1.00
IGL03031:Hoxc9 APN 15 102,892,522 (GRCm39) missense probably damaging 1.00
R0498:Hoxc9 UTSW 15 102,892,359 (GRCm39) missense probably damaging 1.00
R1436:Hoxc9 UTSW 15 102,890,304 (GRCm39) missense probably benign 0.03
R2059:Hoxc9 UTSW 15 102,892,555 (GRCm39) missense probably benign 0.01
R2414:Hoxc9 UTSW 15 102,892,540 (GRCm39) missense probably damaging 1.00
R2900:Hoxc9 UTSW 15 102,890,185 (GRCm39) missense probably benign 0.00
R3807:Hoxc9 UTSW 15 102,890,116 (GRCm39) missense possibly damaging 0.94
R3821:Hoxc9 UTSW 15 102,890,596 (GRCm39) missense probably benign 0.32
R5165:Hoxc9 UTSW 15 102,892,432 (GRCm39) missense probably damaging 1.00
R5700:Hoxc9 UTSW 15 102,890,313 (GRCm39) missense possibly damaging 0.65
R5701:Hoxc9 UTSW 15 102,890,313 (GRCm39) missense possibly damaging 0.65
R6003:Hoxc9 UTSW 15 102,890,311 (GRCm39) missense probably benign 0.15
R6145:Hoxc9 UTSW 15 102,892,391 (GRCm39) missense probably damaging 1.00
R6570:Hoxc9 UTSW 15 102,890,185 (GRCm39) missense probably benign 0.00
R7312:Hoxc9 UTSW 15 102,890,593 (GRCm39) missense probably benign 0.02
R7434:Hoxc9 UTSW 15 102,892,414 (GRCm39) missense probably damaging 1.00
R8080:Hoxc9 UTSW 15 102,890,551 (GRCm39) missense probably benign 0.22
R8519:Hoxc9 UTSW 15 102,892,341 (GRCm39) missense probably damaging 1.00
R8792:Hoxc9 UTSW 15 102,890,226 (GRCm39) missense probably benign 0.00
R9705:Hoxc9 UTSW 15 102,890,362 (GRCm39) missense possibly damaging 0.80
R9717:Hoxc9 UTSW 15 102,890,551 (GRCm39) missense probably benign 0.22
Predicted Primers PCR Primer
(F):5'- AATTACCTGCCTTGATTGTTCTGTG -3'
(R):5'- ACATGTAGTCCGGGTAGCTG -3'

Sequencing Primer
(F):5'- CCTTGATTGTTCTGTGAGCAG -3'
(R):5'- GCTTGAGGGCGTAGTGAC -3'
Posted On 2016-03-01