Incidental Mutation 'R6693:Pax9'
ID 528179
Institutional Source Beutler Lab
Gene Symbol Pax9
Ensembl Gene ENSMUSG00000001497
Gene Name paired box 9
Synonyms Pax-9
MMRRC Submission 044811-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.944) question?
Stock # R6693 (G1)
Quality Score 225.009
Status Validated
Chromosome 12
Chromosomal Location 56691767-56712822 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to A at 56709731 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 285 (S285T)
Ref Sequence ENSEMBL: ENSMUSP00000117928 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001538] [ENSMUST00000044634] [ENSMUST00000110680] [ENSMUST00000153250] [ENSMUST00000217690]
AlphaFold P47242
Predicted Effect probably benign
Transcript: ENSMUST00000001538
AA Change: S285T

PolyPhen 2 Score 0.075 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000001538
Gene: ENSMUSG00000001497
AA Change: S285T

PAX 4 128 6.81e-90 SMART
low complexity region 265 274 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000044634
SMART Domains Protein: ENSMUSP00000039289
Gene: ENSMUSG00000035472

Pfam:Mito_carr 10 104 2.3e-24 PFAM
Pfam:Mito_carr 107 200 1.3e-16 PFAM
Pfam:Mito_carr 202 298 3.4e-20 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000110680
SMART Domains Protein: ENSMUSP00000106308
Gene: ENSMUSG00000035472

Pfam:Mito_carr 28 111 4.7e-21 PFAM
Pfam:Mito_carr 114 207 7.7e-17 PFAM
Pfam:Mito_carr 209 305 2e-20 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152848
Predicted Effect probably benign
Transcript: ENSMUST00000153250
AA Change: S285T

PolyPhen 2 Score 0.075 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000117928
Gene: ENSMUSG00000001497
AA Change: S285T

PAX 4 128 6.81e-90 SMART
low complexity region 265 274 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000217690
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 97.8%
  • 20x: 93.3%
Validation Efficiency 100% (37/37)
MGI Phenotype FUNCTION: This gene is a member of the paired box (PAX) family of transcription factors. Members of this gene family typically contain a paired box domain, an octapeptide, and a paired-type homeodomain. These genes play critical roles during fetal development and cancer growth. Mice lacking this gene exhibit impaired development of organs, musculature and the skeleton, including absent and abnormally developed teeth, and neonatal lethality. Mutations in the human gene are associated with selective tooth agenesis-3. [provided by RefSeq, Sep 2015]
PHENOTYPE: Homozygous inactivation of this gene results in abnormal tooth development and absent teeth and may lead to lack of pharyngeal pouch derivatives, athymia, craniofacial and limb anomalies, a small tympanic ring, various defects of the skeleton and musculature, and neonatal lethality. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 35 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik T C 3: 138,069,154 (GRCm38) V1368A probably benign Het
Aak1 C T 6: 86,965,515 (GRCm38) S680L unknown Het
Adam25 A T 8: 40,754,531 (GRCm38) N278I probably damaging Het
Adamtsl1 C A 4: 86,342,886 (GRCm38) H1111Q probably benign Het
Adgrg7 T A 16: 56,770,224 (GRCm38) N195Y probably damaging Het
Arhgap23 A G 11: 97,466,517 (GRCm38) N436S probably damaging Het
Cfap65 T C 1: 74,917,286 (GRCm38) I1045V probably benign Het
Chrm3 T C 13: 9,877,422 (GRCm38) N526S probably benign Het
Cpeb2 A T 5: 43,285,912 (GRCm38) D982V probably damaging Het
Fbxw27 T C 9: 109,788,044 (GRCm38) I130V probably benign Het
Glb1l T C 1: 75,209,101 (GRCm38) D61G probably damaging Het
Herc1 G A 9: 66,478,976 (GRCm38) C3737Y probably damaging Het
Kcnt2 A T 1: 140,351,227 (GRCm38) M39L probably benign Het
Kif17 C A 4: 138,286,480 (GRCm38) Q236K probably benign Het
Klhl25 T C 7: 75,866,813 (GRCm38) V184A possibly damaging Het
Lmf1 A T 17: 25,645,278 (GRCm38) M287L probably benign Het
Macf1 T C 4: 123,473,808 (GRCm38) T822A possibly damaging Het
Mmp13 A T 9: 7,280,245 (GRCm38) T392S probably benign Het
Myo6 T A 9: 80,245,731 (GRCm38) N215K probably damaging Het
Nedd1 T C 10: 92,698,337 (GRCm38) K317R possibly damaging Het
Or8g17 C T 9: 39,018,801 (GRCm38) A247T probably damaging Het
Or9m1 A G 2: 87,903,308 (GRCm38) Y123H probably damaging Het
Pcdhb15 A T 18: 37,474,341 (GRCm38) T209S probably benign Het
Pdpk1 A T 17: 24,111,126 (GRCm38) probably null Het
Rbak T C 5: 143,174,111 (GRCm38) K396E probably damaging Het
Rps6ka5 A G 12: 100,573,829 (GRCm38) V545A probably benign Het
Scg2 G T 1: 79,436,020 (GRCm38) Q329K probably benign Het
Shroom3 G A 5: 92,940,758 (GRCm38) A456T possibly damaging Het
Slc12a7 G T 13: 73,797,537 (GRCm38) A489S probably benign Het
Slc16a4 T C 3: 107,303,064 (GRCm38) I350T probably damaging Het
Slc25a45 T C 19: 5,880,134 (GRCm38) V44A possibly damaging Het
Sucla2 T A 14: 73,568,667 (GRCm38) L102* probably null Het
Tgif1 T A 17: 70,850,890 (GRCm38) probably benign Het
Tmem8b A G 4: 43,669,837 (GRCm38) E111G probably benign Het
Zfp971 G T 2: 178,033,431 (GRCm38) K274N probably benign Het
Other mutations in Pax9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00087:Pax9 APN 12 56,700,075 (GRCm38) missense probably benign
IGL02724:Pax9 APN 12 56,709,819 (GRCm38) missense possibly damaging 0.76
R0008:Pax9 UTSW 12 56,709,743 (GRCm38) missense probably benign
R0008:Pax9 UTSW 12 56,709,743 (GRCm38) missense probably benign
R1836:Pax9 UTSW 12 56,700,054 (GRCm38) missense probably benign 0.03
R1916:Pax9 UTSW 12 56,697,138 (GRCm38) missense possibly damaging 0.60
R2907:Pax9 UTSW 12 56,709,744 (GRCm38) missense probably benign 0.03
R3778:Pax9 UTSW 12 56,696,748 (GRCm38) missense probably damaging 1.00
R4905:Pax9 UTSW 12 56,696,626 (GRCm38) missense probably damaging 1.00
R6247:Pax9 UTSW 12 56,709,695 (GRCm38) missense probably benign
R6469:Pax9 UTSW 12 56,696,863 (GRCm38) missense probably damaging 1.00
R7343:Pax9 UTSW 12 56,695,862 (GRCm38) start codon destroyed probably null 0.48
R7739:Pax9 UTSW 12 56,700,099 (GRCm38) missense probably benign 0.00
R7807:Pax9 UTSW 12 56,697,065 (GRCm38) missense possibly damaging 0.95
R8458:Pax9 UTSW 12 56,696,765 (GRCm38) missense possibly damaging 0.84
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2018-07-24