Incidental Mutation 'R3778:Pax9'
ID 271921
Institutional Source Beutler Lab
Gene Symbol Pax9
Ensembl Gene ENSMUSG00000001497
Gene Name paired box 9
Synonyms Pax-9
MMRRC Submission 040750-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.950) question?
Stock # R3778 (G1)
Quality Score 191
Status Not validated
Chromosome 12
Chromosomal Location 56738552-56759607 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 56743533 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 60 (Y60C)
Ref Sequence ENSEMBL: ENSMUSP00000117928 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001538] [ENSMUST00000153250]
AlphaFold P47242
Predicted Effect probably damaging
Transcript: ENSMUST00000001538
AA Change: Y60C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000001538
Gene: ENSMUSG00000001497
AA Change: Y60C

DomainStartEndE-ValueType
PAX 4 128 6.81e-90 SMART
low complexity region 265 274 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152848
Predicted Effect probably damaging
Transcript: ENSMUST00000153250
AA Change: Y60C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000117928
Gene: ENSMUSG00000001497
AA Change: Y60C

DomainStartEndE-ValueType
PAX 4 128 6.81e-90 SMART
low complexity region 265 274 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000159874
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 94.8%
Validation Efficiency
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: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adcy8 A T 15: 64,618,846 (GRCm39) L769H probably damaging Het
Aldh1a7 A T 19: 20,696,675 (GRCm39) M106K possibly damaging Het
Ankfn1 G T 11: 89,332,220 (GRCm39) P442Q probably damaging Het
Aox1 A C 1: 58,092,862 (GRCm39) D158A possibly damaging Het
Apc A G 18: 34,446,134 (GRCm39) N976S probably damaging Het
Cfap54 C T 10: 92,740,206 (GRCm39) probably benign Het
Cldn1 C T 16: 26,190,216 (GRCm39) C54Y probably damaging Het
Col22a1 A T 15: 71,845,541 (GRCm39) I407N probably damaging Het
Cyp2e1 T C 7: 140,343,822 (GRCm39) V20A possibly damaging Het
Erp27 A T 6: 136,896,901 (GRCm39) N100K possibly damaging Het
Fbn1 C T 2: 125,159,006 (GRCm39) C2253Y probably damaging Het
Fhip1b T A 7: 105,037,435 (GRCm39) T383S probably damaging Het
Flnb G A 14: 7,915,353 (GRCm38) V1495I probably benign Het
Fscn3 A C 6: 28,430,031 (GRCm39) K67T possibly damaging Het
Gls A G 1: 52,208,071 (GRCm39) V571A probably benign Het
Gm14569 T A X: 35,696,085 (GRCm39) M875L probably benign Het
Gm4871 A G 5: 144,966,893 (GRCm39) S197P probably damaging Het
Gm7104 A T 12: 88,252,441 (GRCm39) noncoding transcript Het
Gp9 A T 6: 87,755,987 (GRCm39) M1L probably benign Het
Greb1l T A 18: 10,469,444 (GRCm39) L153H possibly damaging Het
H1f8 T C 6: 115,926,708 (GRCm39) probably null Het
Hadha A T 5: 30,325,127 (GRCm39) C688S probably damaging Het
Hif1an A G 19: 44,557,847 (GRCm39) D243G probably damaging Het
Hmcn1 A T 1: 150,678,575 (GRCm39) D515E possibly damaging Het
Hsfy2 A T 1: 56,675,847 (GRCm39) V230E possibly damaging Het
Ighv1-72 A T 12: 115,721,636 (GRCm39) S107T probably damaging Het
Inpp4b T A 8: 82,768,621 (GRCm39) V710D possibly damaging Het
Itpr3 A G 17: 27,314,446 (GRCm39) D632G possibly damaging Het
Kcnd3 C T 3: 105,566,082 (GRCm39) A421V probably damaging Het
Lrig2 A G 3: 104,365,277 (GRCm39) I625T probably benign Het
Lrp2 A T 2: 69,339,548 (GRCm39) M1121K probably benign Het
Man2b2 T C 5: 36,972,871 (GRCm39) N548D probably benign Het
Mei1 T C 15: 81,966,209 (GRCm39) L277P probably damaging Het
Mki67 A C 7: 135,297,859 (GRCm39) S2392A probably benign Het
Mycbp2 T A 14: 103,434,721 (GRCm39) I2241F probably damaging Het
Nalcn G A 14: 123,702,128 (GRCm39) T461M probably damaging Het
Ncoa6 A G 2: 155,263,115 (GRCm39) S440P probably damaging Het
Ncoa7 A G 10: 30,565,752 (GRCm39) Y632H probably damaging Het
Notch2 T C 3: 98,053,939 (GRCm39) S2201P probably damaging Het
Or10c1 T C 17: 37,522,649 (GRCm39) T32A probably benign Het
Or5p52 C A 7: 107,501,954 (GRCm39) A10E probably benign Het
Pard6g A T 18: 80,123,038 (GRCm39) probably null Het
Pask T A 1: 93,255,189 (GRCm39) I294F probably damaging Het
Pcdh15 G A 10: 73,782,983 (GRCm39) probably null Het
Pik3c2g A T 6: 139,599,385 (GRCm39) Y167F probably damaging Het
Ppfibp2 A G 7: 107,328,396 (GRCm39) T476A probably benign Het
Ppm1e T C 11: 87,139,754 (GRCm39) probably null Het
Rsph14 T G 10: 74,793,420 (GRCm39) Q360P possibly damaging Het
Rsph14 C G 10: 74,793,419 (GRCm39) Q360H possibly damaging Het
Sec24c A G 14: 20,733,375 (GRCm39) Q234R possibly damaging Het
Shcbp1 A T 8: 4,786,295 (GRCm39) N602K probably benign Het
Sirt5 A G 13: 43,536,583 (GRCm39) probably null Het
Slc66a1 T C 4: 139,026,293 (GRCm39) probably null Het
Sp8 G T 12: 118,812,750 (GRCm39) V202L possibly damaging Het
Tle6 G T 10: 81,431,987 (GRCm39) P86T probably benign Het
Tmem235 A T 11: 117,753,126 (GRCm39) H83L probably benign Het
Trappc10 A G 10: 78,036,636 (GRCm39) V861A possibly damaging Het
Trpm2 A C 10: 77,771,824 (GRCm39) L605R probably benign Het
Vat1l T C 8: 114,963,540 (GRCm39) probably null Het
Wnt6 A C 1: 74,821,941 (GRCm39) D174A possibly damaging Het
Wwox T C 8: 115,601,347 (GRCm39) C355R probably benign Het
Zfp229 A T 17: 21,964,183 (GRCm39) T138S probably benign Het
Other mutations in Pax9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00087:Pax9 APN 12 56,746,860 (GRCm39) missense probably benign
IGL02724:Pax9 APN 12 56,756,604 (GRCm39) missense possibly damaging 0.76
R0008:Pax9 UTSW 12 56,756,528 (GRCm39) missense probably benign
R0008:Pax9 UTSW 12 56,756,528 (GRCm39) missense probably benign
R1836:Pax9 UTSW 12 56,746,839 (GRCm39) missense probably benign 0.03
R1916:Pax9 UTSW 12 56,743,923 (GRCm39) missense possibly damaging 0.60
R2907:Pax9 UTSW 12 56,756,529 (GRCm39) missense probably benign 0.03
R4905:Pax9 UTSW 12 56,743,411 (GRCm39) missense probably damaging 1.00
R6247:Pax9 UTSW 12 56,756,480 (GRCm39) missense probably benign
R6469:Pax9 UTSW 12 56,743,648 (GRCm39) missense probably damaging 1.00
R6693:Pax9 UTSW 12 56,756,516 (GRCm39) missense probably benign 0.08
R7343:Pax9 UTSW 12 56,742,647 (GRCm39) start codon destroyed probably null 0.48
R7739:Pax9 UTSW 12 56,746,884 (GRCm39) missense probably benign 0.00
R7807:Pax9 UTSW 12 56,743,850 (GRCm39) missense possibly damaging 0.95
R8458:Pax9 UTSW 12 56,743,550 (GRCm39) missense possibly damaging 0.84
Predicted Primers PCR Primer
(F):5'- TGCTCCTTTTGCAGAGCCAG -3'
(R):5'- TCTTGTTGCGCAGAATACGGC -3'

Sequencing Primer
(F):5'- TTTGCAGAGCCAGCCTTCG -3'
(R):5'- ATACGGCTGATGGAACTCACCG -3'
Posted On 2015-03-25