Incidental Mutation 'R6003:Hoxc9'
ID 478478
Institutional Source Beutler Lab
Gene Symbol Hoxc9
Ensembl Gene ENSMUSG00000036139
Gene Name homeobox C9
Synonyms Hox-3.2
MMRRC Submission 043252-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6003 (G1)
Quality Score 203.462
Status Not validated
Chromosome 15
Chromosomal Location 102885467-102893324 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 102890311 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 76 (V76A)
Ref Sequence ENSEMBL: ENSMUSP00000001706 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001706] [ENSMUST00000173306]
AlphaFold P09633
Predicted Effect probably benign
Transcript: ENSMUST00000001706
AA Change: V76A

PolyPhen 2 Score 0.149 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000001706
Gene: ENSMUSG00000036139
AA Change: V76A

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
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.4%
  • 10x: 97.2%
  • 20x: 90.9%
Validation Efficiency
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: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A4galt T C 15: 83,112,312 (GRCm39) E157G probably benign Het
Abcb11 T C 2: 69,073,811 (GRCm39) K1238R probably benign Het
Ankar T A 1: 72,738,046 (GRCm39) E45D probably damaging Het
Antxrl G T 14: 33,797,592 (GRCm39) K522N possibly damaging Het
Ap1m1 A G 8: 73,003,011 (GRCm39) Y93C probably damaging Het
As3mt C T 19: 46,696,567 (GRCm39) T35M possibly damaging Het
Aspg T C 12: 112,079,476 (GRCm39) S85P probably damaging Het
Cachd1 T C 4: 100,809,216 (GRCm39) S234P possibly damaging Het
Ccdc3 T C 2: 5,146,218 (GRCm39) probably null Het
Cnpy1 T C 5: 28,450,759 (GRCm39) T16A probably benign Het
Cope T C 8: 70,757,285 (GRCm39) L43P probably benign Het
E2f8 T C 7: 48,520,525 (GRCm39) M599V probably benign Het
Eif3a A T 19: 60,755,319 (GRCm39) D954E unknown Het
Gfpt1 T A 6: 87,065,230 (GRCm39) probably null Het
Ggps1 T G 13: 14,228,587 (GRCm39) S145R probably benign Het
Gon4l A G 3: 88,803,400 (GRCm39) D1337G probably damaging Het
Gtf2a1l G T 17: 89,001,531 (GRCm39) G82V probably damaging Het
Gucy1b1 C A 3: 81,965,584 (GRCm39) L87F probably damaging Het
Ints2 T C 11: 86,129,294 (GRCm39) E460G probably damaging Het
Kdm4b C T 17: 56,703,916 (GRCm39) R756W probably damaging Het
Lax1 T A 1: 133,611,834 (GRCm39) I34F probably benign Het
Marveld3 A T 8: 110,680,960 (GRCm39) C312S probably damaging Het
Ncoa2 T C 1: 13,237,254 (GRCm39) D824G possibly damaging Het
Nrxn2 C A 19: 6,548,358 (GRCm39) A17D possibly damaging Het
Nup133 A T 8: 124,665,031 (GRCm39) I220N probably damaging Het
Nup205 T C 6: 35,189,751 (GRCm39) V984A probably benign Het
Nup54 A T 5: 92,570,853 (GRCm39) D318E probably damaging Het
Obp2a A T 2: 25,591,151 (GRCm39) K94N probably damaging Het
Or2ak5 A T 11: 58,611,196 (GRCm39) I226N probably benign Het
Or5b3 T C 19: 13,388,403 (GRCm39) S157P probably benign Het
Pappa2 T C 1: 158,763,820 (GRCm39) I564V probably benign Het
Parpbp A G 10: 87,969,020 (GRCm39) V142A possibly damaging Het
Rdh16f2 A T 10: 127,712,201 (GRCm39) R219S probably benign Het
Rfx6 C T 10: 51,584,683 (GRCm39) R228C probably damaging Het
Rpap2 A G 5: 107,749,767 (GRCm39) probably null Het
Rskr T G 11: 78,183,846 (GRCm39) probably null Het
Slc15a2 T C 16: 36,574,910 (GRCm39) I531V probably benign Het
Srebf1 T C 11: 60,097,930 (GRCm39) E58G possibly damaging Het
Tmem214 C A 5: 31,028,068 (GRCm39) T96K possibly damaging Het
Usp19 T C 9: 108,373,579 (GRCm39) Y691H probably damaging Het
Vmn1r86 C T 7: 12,836,125 (GRCm39) W200* probably null Het
Vmn2r8 A T 5: 108,945,248 (GRCm39) S786R probably damaging Het
Vps52 T A 17: 34,175,068 (GRCm39) M1K probably null Het
Zzef1 T A 11: 72,714,891 (GRCm39) 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
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
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
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'- ACTATTACGTGGACTCGCTCATCTC -3'
(R):5'- ACATGTAGTCCGGGTAGCTG -3'

Sequencing Primer
(F):5'- TCGCTCATCTCTCACGACAATGAAG -3'
(R):5'- CTTGAGGGCGTAGTGACGG -3'
Posted On 2017-06-26