Incidental Mutation 'R1836:Pax9'
ID 205318
Institutional Source Beutler Lab
Gene Symbol Pax9
Ensembl Gene ENSMUSG00000001497
Gene Name paired box 9
Synonyms Pax-9
MMRRC Submission 039863-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.950) question?
Stock # R1836 (G1)
Quality Score 189
Status Not validated
Chromosome 12
Chromosomal Location 56738552-56759607 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 56746839 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 225 (E225G)
Ref Sequence ENSEMBL: ENSMUSP00000117928 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001538] [ENSMUST00000153250]
AlphaFold P47242
Predicted Effect probably benign
Transcript: ENSMUST00000001538
AA Change: E225G

PolyPhen 2 Score 0.028 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000001538
Gene: ENSMUSG00000001497
AA Change: E225G

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 benign
Transcript: ENSMUST00000153250
AA Change: E225G

PolyPhen 2 Score 0.028 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000117928
Gene: ENSMUSG00000001497
AA Change: E225G

DomainStartEndE-ValueType
PAX 4 128 6.81e-90 SMART
low complexity region 265 274 N/A INTRINSIC
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.8%
  • 10x: 95.1%
  • 20x: 91.8%
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: 108 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2210408I21Rik A G 13: 77,471,493 (GRCm39) E966G probably benign Het
9330159F19Rik T C 10: 29,097,795 (GRCm39) V64A probably damaging Het
Abcb5 G T 12: 118,831,696 (GRCm39) Q1219K possibly damaging Het
Acox2 A T 14: 8,248,059 (GRCm38) C408S possibly damaging Het
Acsf3 T A 8: 123,506,922 (GRCm39) Y72N probably damaging Het
Acss2 T A 2: 155,400,550 (GRCm39) Y530N probably damaging Het
Adam28 T C 14: 68,886,870 (GRCm39) E48G possibly damaging Het
Adgrv1 A C 13: 81,652,232 (GRCm39) M2957R probably benign Het
Adi1 C A 12: 28,729,562 (GRCm39) D138E probably benign Het
Alk A C 17: 72,198,032 (GRCm39) L1228R probably damaging Het
Alms1 T A 6: 85,655,485 (GRCm39) S3344T possibly damaging Het
Aox1 G A 1: 58,348,150 (GRCm39) A623T probably benign Het
Arhgef2 C T 3: 88,546,766 (GRCm39) T545I probably damaging Het
Atp8a2 T A 14: 60,243,815 (GRCm39) N630I possibly damaging Het
Bcl9 G T 3: 97,113,186 (GRCm39) Q1090K probably damaging Het
Bdp1 A G 13: 100,171,653 (GRCm39) S2152P probably benign Het
Birc6 T A 17: 74,921,385 (GRCm39) S2155T probably benign Het
Camk2b T C 11: 5,922,384 (GRCm39) E488G probably damaging Het
Capn9 T A 8: 125,332,304 (GRCm39) probably null Het
Cd209f A G 8: 4,154,491 (GRCm39) S119P probably damaging Het
Cep78 T C 19: 15,946,533 (GRCm39) E433G probably damaging Het
Chid1 G T 7: 141,106,409 (GRCm39) probably null Het
Cldnd2 T C 7: 43,092,349 (GRCm39) S129P possibly damaging Het
Cobll1 A T 2: 64,956,580 (GRCm39) F289Y probably damaging Het
Creb1 C T 1: 64,590,109 (GRCm39) Q32* probably null Het
Creb3l4 G T 3: 90,146,210 (GRCm39) S182Y probably benign Het
Dgcr2 A T 16: 17,667,584 (GRCm39) C292S probably damaging Het
Dnah8 T C 17: 31,093,901 (GRCm39) V4665A possibly damaging Het
Dnah9 A T 11: 66,009,667 (GRCm39) M740K probably benign Het
Dnmt1 G A 9: 20,829,542 (GRCm39) T687I probably damaging Het
Ece1 C T 4: 137,685,312 (GRCm39) R601W probably damaging Het
Echdc2 C A 4: 108,022,732 (GRCm39) R3S probably damaging Het
Ep400 A T 5: 110,852,920 (GRCm39) L1275Q unknown Het
Epha6 A T 16: 60,026,108 (GRCm39) W445R probably damaging Het
Ercc5 T A 1: 44,220,035 (GRCm39) S1102R probably benign Het
Fam228a T G 12: 4,765,620 (GRCm39) T264P probably damaging Het
Fzd6 T A 15: 38,897,315 (GRCm39) I488N probably damaging Het
Gabrg3 T G 7: 56,379,389 (GRCm39) N338H probably damaging Het
Gde1 A G 7: 118,294,357 (GRCm39) F39L possibly damaging Het
Gjb3 G A 4: 127,220,224 (GRCm39) R103W probably damaging Het
Gm4781 T A 10: 100,232,582 (GRCm39) noncoding transcript Het
Gm4846 T A 1: 166,311,492 (GRCm39) T456S probably benign Het
Gpx5 A G 13: 21,471,624 (GRCm39) I193T probably benign Het
H3c2 T A 13: 23,936,715 (GRCm39) V118D probably damaging Het
Herc2 A T 7: 55,804,853 (GRCm39) K2294* probably null Het
Iqgap3 T A 3: 88,015,675 (GRCm39) V19D probably damaging Het
Itga5 T C 15: 103,254,441 (GRCm39) I1006V probably damaging Het
Lamb1 C T 12: 31,351,093 (GRCm39) T781I probably benign Het
Lias A G 5: 65,549,686 (GRCm39) T57A probably benign Het
Lin37 C A 7: 30,256,368 (GRCm39) R108L probably damaging Het
Lrrd1 A T 5: 3,915,709 (GRCm39) T769S probably benign Het
Mamstr T C 7: 45,294,387 (GRCm39) W414R probably damaging Het
Mtmr11 T G 3: 96,072,103 (GRCm39) S233R probably damaging Het
Myh1 A T 11: 67,095,648 (GRCm39) I266F probably damaging Het
Myt1 C A 2: 181,439,068 (GRCm39) Q197K probably benign Het
Naip5 G T 13: 100,356,195 (GRCm39) T1140K probably benign Het
Ncf2 G A 1: 152,683,822 (GRCm39) V14M probably damaging Het
Ndufb11b T C 15: 81,865,068 (GRCm39) V103A probably damaging Het
Nhsl1 G T 10: 18,400,653 (GRCm39) R626S possibly damaging Het
Nol12 T A 15: 78,822,089 (GRCm39) V108E probably damaging Het
Nr1i2 G T 16: 38,069,644 (GRCm39) P420Q probably damaging Het
Nup155 A G 15: 8,184,464 (GRCm39) I1286M possibly damaging Het
Ocrl T A X: 47,050,993 (GRCm39) I74N probably damaging Het
Or4c10b A C 2: 89,711,629 (GRCm39) H153P probably damaging Het
Or51b17 A G 7: 103,542,592 (GRCm39) S117P probably damaging Het
Or5ak23 A G 2: 85,244,749 (GRCm39) V158A probably benign Het
Pard3b C T 1: 62,676,763 (GRCm39) S999L probably benign Het
Pdcd4 T G 19: 53,914,650 (GRCm39) L335R probably damaging Het
Pdgfra T A 5: 75,343,675 (GRCm39) M732K possibly damaging Het
Pkhd1 G T 1: 20,187,293 (GRCm39) Q3672K probably benign Het
Pold2 A G 11: 5,823,454 (GRCm39) L325P possibly damaging Het
Pom121l2 A T 13: 22,167,954 (GRCm39) T742S probably benign Het
Ppfia1 C T 7: 144,073,368 (GRCm39) E208K probably benign Het
Prex2 A T 1: 11,207,004 (GRCm39) R521W probably damaging Het
Prr23a4 C A 9: 98,785,535 (GRCm39) R67S probably benign Het
Rhpn2 T C 7: 35,071,813 (GRCm39) L226P probably benign Het
Rps12 C A 10: 23,661,527 (GRCm39) D95Y probably damaging Het
Sardh T A 2: 27,105,194 (GRCm39) D643V possibly damaging Het
Sars1 T C 3: 108,343,260 (GRCm39) D77G probably benign Het
Scin C A 12: 40,174,697 (GRCm39) V129F probably damaging Het
Semp2l1 T G 1: 32,584,758 (GRCm39) D384A probably damaging Het
Sftpa1 T A 14: 40,854,803 (GRCm39) M66K possibly damaging Het
Sgo1 T C 17: 53,994,799 (GRCm39) K28E probably damaging Het
Sim2 G T 16: 93,924,436 (GRCm39) probably null Het
Srp54b T A 12: 55,296,945 (GRCm39) probably null Het
Stard7 T C 2: 127,137,480 (GRCm39) V310A probably benign Het
Tasp1 T C 2: 139,793,477 (GRCm39) D233G probably damaging Het
Tdrd6 G T 17: 43,936,480 (GRCm39) L1523M probably benign Het
Tle3 A G 9: 61,321,305 (GRCm39) D639G probably damaging Het
Tmem128 A G 5: 38,417,750 (GRCm39) D2G probably damaging Het
Tmem163 A G 1: 127,605,246 (GRCm39) S41P probably benign Het
Ttn C T 2: 76,559,505 (GRCm39) S29632N probably damaging Het
Tuba4a A G 1: 75,192,754 (GRCm39) S287P probably benign Het
Ubn1 G C 16: 4,895,255 (GRCm39) G767A probably benign Het
Ugdh A T 5: 65,577,634 (GRCm39) C288* probably null Het
Upf2 T A 2: 6,055,135 (GRCm39) probably null Het
Vmn1r2 T C 4: 3,172,836 (GRCm39) S252P probably damaging Het
Vmn1r28 A C 6: 58,242,237 (GRCm39) T27P probably damaging Het
Vmn1r77 T C 7: 11,775,338 (GRCm39) I38T probably benign Het
Vmn2r51 C A 7: 9,832,090 (GRCm39) E499* probably null Het
Vmn2r51 G T 7: 9,832,091 (GRCm39) Y498* probably null Het
Vmn2r53 A T 7: 12,334,812 (GRCm39) W283R probably damaging Het
Vpreb1a T A 16: 16,686,933 (GRCm39) T15S probably benign Het
Vps13b T C 15: 35,910,378 (GRCm39) S3381P probably damaging Het
Wnt2 A T 6: 18,023,234 (GRCm39) D138E probably damaging Het
Zdhhc22 A G 12: 87,030,204 (GRCm39) V248A probably benign Het
Zfp30 T A 7: 29,492,805 (GRCm39) I434N probably damaging Het
Zfp316 A G 5: 143,239,178 (GRCm39) L947P probably damaging 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
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
R3778:Pax9 UTSW 12 56,743,533 (GRCm39) missense probably damaging 1.00
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'- AGTCTATGCTTAGGCCCAGC -3'
(R):5'- CCTTGGCTTGACTAAACCCG -3'

Sequencing Primer
(F):5'- TTAGGCCCAGCGTCCCTAG -3'
(R):5'- TTGACTAAACCCGGCTGGC -3'
Posted On 2014-06-23