Incidental Mutation 'R4905:Pax9'
ID 378120
Institutional Source Beutler Lab
Gene Symbol Pax9
Ensembl Gene ENSMUSG00000001497
Gene Name paired box 9
Synonyms Pax-9
Accession Numbers
Essential gene? Probably essential (E-score: 0.950) question?
Stock # R4905 (G1)
Quality Score 225
Status Not validated
Chromosome 12
Chromosomal Location 56738552-56759607 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 56743411 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Serine at position 19 (R19S)
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: R19S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000001538
Gene: ENSMUSG00000001497
AA Change: R19S

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: R19S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000117928
Gene: ENSMUSG00000001497
AA Change: R19S

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: 98.9%
  • 3x: 98.0%
  • 10x: 95.0%
  • 20x: 87.5%
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700017N19Rik A T 10: 100,448,680 (GRCm39) probably null Het
2700049A03Rik G T 12: 71,211,320 (GRCm39) E685* probably null Het
2700049A03Rik A T 12: 71,211,321 (GRCm39) E685V possibly damaging Het
Abcc5 A G 16: 20,218,678 (GRCm39) S235P probably damaging Het
Abcc6 T C 7: 45,644,649 (GRCm39) N842S probably benign Het
Acbd6 G A 1: 155,500,669 (GRCm39) V210I probably benign Het
Ahctf1 A T 1: 179,576,192 (GRCm39) V2130D probably damaging Het
Akap5 A G 12: 76,375,207 (GRCm39) E213G probably damaging Het
Alyref T G 11: 120,486,879 (GRCm39) probably null Het
Anapc5 G T 5: 122,955,973 (GRCm39) N152K probably benign Het
Atp8b2 A T 3: 89,856,315 (GRCm39) D416E probably benign Het
AW551984 A T 9: 39,508,454 (GRCm39) V354E probably damaging Het
Bag6 A G 17: 35,364,162 (GRCm39) E844G probably damaging Het
Bmp1 C T 14: 70,728,802 (GRCm39) R590H probably benign Het
Ccnh T C 13: 85,354,254 (GRCm39) S233P possibly damaging Het
Cdca7 TGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA TGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 2: 72,312,205 (GRCm39) probably benign Het
Col6a6 A G 9: 105,644,623 (GRCm39) S1222P probably damaging Het
Dhfr G A 13: 92,502,282 (GRCm39) G118S probably damaging Het
Dnah9 G A 11: 65,764,950 (GRCm39) R1414* probably null Het
Dnai1 A G 4: 41,614,269 (GRCm39) D315G probably benign Het
Eogt T C 6: 97,119,792 (GRCm39) R139G probably benign Het
Fcgbpl1 A T 7: 27,856,408 (GRCm39) K2065M possibly damaging Het
Fh1 C T 1: 175,446,639 (GRCm39) G79E probably damaging Het
Gabrg3 A G 7: 56,374,304 (GRCm39) Y421H probably damaging Het
Glipr1 C A 10: 111,821,545 (GRCm39) R219L probably damaging Het
Gm1123 T C 9: 98,891,369 (GRCm39) D360G probably benign Het
Ift81 C T 5: 122,729,142 (GRCm39) probably null Het
Itsn2 A G 12: 4,684,583 (GRCm39) probably benign Het
Kri1 A T 9: 21,198,998 (GRCm39) H55Q probably benign Het
Mcidas C T 13: 113,134,038 (GRCm39) T174M possibly damaging Het
Mcidas C A 13: 113,130,951 (GRCm39) A92E possibly damaging Het
Mmp25 C A 17: 23,863,022 (GRCm39) G130* probably null Het
Myh11 G A 16: 14,068,387 (GRCm39) T211M probably benign Het
Myo10 A G 15: 25,800,298 (GRCm39) D1458G probably damaging Het
Ncf4 A G 15: 78,139,104 (GRCm39) T154A probably damaging Het
Nfatc4 T C 14: 56,068,039 (GRCm39) I620T probably benign Het
Nos3 A T 5: 24,572,329 (GRCm39) Y134F probably benign Het
Nup50l T A 6: 96,142,911 (GRCm39) R44S possibly damaging Het
Or13c3 T C 4: 52,855,613 (GRCm39) N300S probably damaging Het
Or51a6 A T 7: 102,604,721 (GRCm39) I36N probably damaging Het
Or5b106 C A 19: 13,123,541 (GRCm39) A161S probably benign Het
Or6c209 T A 10: 129,483,792 (GRCm39) V265E possibly damaging Het
Pcdha9 T C 18: 37,131,945 (GRCm39) I338T probably damaging Het
Plxnb2 G T 15: 89,041,614 (GRCm39) T1730K probably damaging Het
Rac1 A G 5: 143,502,907 (GRCm39) probably null Het
Samsn1 G T 16: 75,673,353 (GRCm39) F174L possibly damaging Het
Scaf1 G A 7: 44,662,129 (GRCm39) T86M probably damaging Het
Smc1b A G 15: 84,950,428 (GRCm39) Y1199H probably damaging Het
Svep1 A G 4: 58,069,308 (GRCm39) I2826T probably benign Het
Tex36 A G 7: 133,189,182 (GRCm39) V130A probably damaging Het
Tigd5 A G 15: 75,783,252 (GRCm39) H538R probably damaging Het
Tlr3 C A 8: 45,852,260 (GRCm39) probably null Het
Tubb2b A T 13: 34,312,187 (GRCm39) I202N probably damaging Het
Unc13c A G 9: 73,587,674 (GRCm39) V1453A probably benign Het
Unc5c A T 3: 141,507,071 (GRCm39) T608S probably benign Het
Vrk1 C A 12: 106,018,087 (GRCm39) H119N probably damaging Het
Wdr53 T A 16: 32,075,476 (GRCm39) M227K probably benign Het
Xpo4 T C 14: 57,875,746 (GRCm39) D129G possibly damaging Het
Zcchc4 T C 5: 52,953,992 (GRCm39) I224T probably damaging Het
Zdhhc1 T A 8: 106,210,326 (GRCm39) E30D probably damaging Het
Zscan29 C G 2: 120,991,864 (GRCm39) R540T possibly 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
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
R3778:Pax9 UTSW 12 56,743,533 (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'- GGCAACCCCAGTCCTTATAG -3'
(R):5'- TGGGTCCCTCTGCTTGTAAG -3'

Sequencing Primer
(F):5'- AGGGTGTCATAACCCTGC -3'
(R):5'- GTAAGTCCGGATGTGTTTCACCAC -3'
Posted On 2016-04-15