Incidental Mutation 'R2414:Hoxc9'
ID 250119
Institutional Source Beutler Lab
Gene Symbol Hoxc9
Ensembl Gene ENSMUSG00000036139
Gene Name homeobox C9
Synonyms Hox-3.2
MMRRC Submission 040378-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2414 (G1)
Quality Score 225
Status Validated
Chromosome 15
Chromosomal Location 102885467-102893324 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 102892540 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Isoleucine at position 251 (N251I)
Ref Sequence ENSEMBL: ENSMUSP00000001706 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001706] [ENSMUST00000173306]
AlphaFold P09633
Predicted Effect probably damaging
Transcript: ENSMUST00000001706
AA Change: N251I

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000001706
Gene: ENSMUSG00000036139
AA Change: N251I

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 0.2729 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 93.9%
Validation Efficiency 100% (38/38)
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: 33 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ackr2 C A 9: 121,738,040 (GRCm39) S138R probably damaging Het
Alpk3 C A 7: 80,742,501 (GRCm39) P773T probably benign Het
Arfgef2 A G 2: 166,687,424 (GRCm39) E216G probably benign Het
Aspscr1 T C 11: 120,580,048 (GRCm39) S196P probably benign Het
AU040320 A T 4: 126,762,484 (GRCm39) probably null Het
BC002059 T C 17: 17,193,932 (GRCm39) noncoding transcript Het
Cep112 A G 11: 108,643,408 (GRCm39) N799S possibly damaging Het
Cilp A G 9: 65,181,927 (GRCm39) probably benign Het
Cpn2 T C 16: 30,079,392 (GRCm39) E103G probably benign Het
Cpt1b G A 15: 89,304,283 (GRCm39) probably benign Het
Epor T A 9: 21,870,785 (GRCm39) D365V probably damaging Het
H2bc21 T A 3: 96,128,750 (GRCm39) I90N possibly damaging Het
Hip1r T C 5: 124,139,306 (GRCm39) Y900H probably damaging Het
Hpd C T 5: 123,315,587 (GRCm39) probably null Het
Lrrc34 T A 3: 30,688,711 (GRCm39) I197L probably benign Het
Msi2 A G 11: 88,607,373 (GRCm39) V78A probably damaging Het
Myh4 A G 11: 67,141,594 (GRCm39) I818V probably benign Het
Nol4 T C 18: 22,956,629 (GRCm39) probably null Het
Plekha5 A G 6: 140,496,582 (GRCm39) N362S probably damaging Het
Polr1b A G 2: 128,945,054 (GRCm39) probably benign Het
Rc3h2 A T 2: 37,289,831 (GRCm39) probably null Het
Sgsm3 A G 15: 80,890,946 (GRCm39) N136D probably benign Het
Slco1a5 A G 6: 142,181,976 (GRCm39) C583R probably damaging Het
Surf1 A G 2: 26,806,295 (GRCm39) W13R probably damaging Het
Tesk2 T C 4: 116,658,954 (GRCm39) W276R possibly damaging Het
Tmem8b A G 4: 43,673,892 (GRCm39) probably benign Het
Togaram2 T G 17: 72,023,304 (GRCm39) probably benign Het
Ttll11 A G 2: 35,869,546 (GRCm39) S31P unknown Het
Ttll8 A G 15: 88,820,336 (GRCm39) probably benign Het
Tub A G 7: 108,626,240 (GRCm39) K259E probably damaging Het
Ube2o T C 11: 116,439,683 (GRCm39) I162M probably benign Het
Vamp8 C T 6: 72,365,326 (GRCm39) M1I probably null Het
Zfp503 C A 14: 22,036,032 (GRCm39) G295* probably null 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
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
R4824:Hoxc9 UTSW 15 102,890,225 (GRCm39) nonsense probably null
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'- TCCACAAGGAAGAAGCGCTG -3'
(R):5'- CCTCCTCGATGGATAGAACTAACTC -3'

Sequencing Primer
(F):5'- GAAGAAGCGCTGCCCCTAC -3'
(R):5'- CGATGGATAGAACTAACTCTAAACAC -3'
Posted On 2014-11-12