Incidental Mutation 'R7739:Pax9'
ID 596445
Institutional Source Beutler Lab
Gene Symbol Pax9
Ensembl Gene ENSMUSG00000001497
Gene Name paired box 9
Synonyms Pax-9
MMRRC Submission 045795-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.950) question?
Stock # R7739 (G1)
Quality Score 225.009
Status Not validated
Chromosome 12
Chromosomal Location 56738552-56759607 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 56746884 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Leucine at position 240 (H240L)
Ref Sequence ENSEMBL: ENSMUSP00000001538 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001538] [ENSMUST00000153250]
AlphaFold P47242
Predicted Effect probably benign
Transcript: ENSMUST00000001538
AA Change: H240L

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000001538
Gene: ENSMUSG00000001497
AA Change: H240L

DomainStartEndE-ValueType
PAX 4 128 6.81e-90 SMART
low complexity region 265 274 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000153250
AA Change: H240L

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000117928
Gene: ENSMUSG00000001497
AA Change: H240L

DomainStartEndE-ValueType
PAX 4 128 6.81e-90 SMART
low complexity region 265 274 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.8%
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9130401M01Rik C A 15: 57,885,875 (GRCm39) A336S probably benign Het
Abca8b A G 11: 109,865,417 (GRCm39) S347P probably benign Het
Acvr1 T C 2: 58,352,983 (GRCm39) T326A possibly damaging Het
Atp13a4 A G 16: 29,275,419 (GRCm39) I355T Het
Atp2a2 G A 5: 122,607,768 (GRCm39) T247I probably damaging Het
Atp2b1 T A 10: 98,837,227 (GRCm39) D555E probably benign Het
Aurkb G T 11: 68,939,058 (GRCm39) G94* probably null Het
B130006D01Rik A T 11: 95,616,986 (GRCm39) H37L unknown Het
Cabin1 A G 10: 75,494,492 (GRCm39) L1629P probably damaging Het
Ccdc168 G A 1: 44,095,578 (GRCm39) T1840I possibly damaging Het
Ccdc80 A C 16: 44,916,186 (GRCm39) D314A probably benign Het
Cdc42bpg T A 19: 6,360,845 (GRCm39) I201N probably damaging Het
Chd9 T C 8: 91,761,653 (GRCm39) L2246P probably damaging Het
Cpsf1 T A 15: 76,484,511 (GRCm39) M657L probably benign Het
Dmtf1 A G 5: 9,190,453 (GRCm39) V87A probably damaging Het
Drd5 G T 5: 38,477,421 (GRCm39) W138L probably damaging Het
Dspp G A 5: 104,326,012 (GRCm39) D792N unknown Het
Fat2 C A 11: 55,171,957 (GRCm39) E2919* probably null Het
Fgf20 A G 8: 40,732,937 (GRCm39) V167A probably damaging Het
Grm5 T C 7: 87,779,266 (GRCm39) V934A possibly damaging Het
Gtf3c3 G T 1: 54,444,198 (GRCm39) A730D possibly damaging Het
H2-T24 A G 17: 36,325,483 (GRCm39) V335A probably benign Het
Havcr2 T G 11: 46,347,384 (GRCm39) N120K probably damaging Het
Hmcn2 T C 2: 31,348,038 (GRCm39) F4895L possibly damaging Het
Igsf3 T C 3: 101,342,847 (GRCm39) Y475H probably damaging Het
Lonp1 T C 17: 56,933,620 (GRCm39) D85G probably benign Het
Lrrc49 T C 9: 60,500,975 (GRCm39) S657G probably benign Het
Lrrk2 T A 15: 91,584,816 (GRCm39) Y382N probably damaging Het
Macf1 T C 4: 123,279,391 (GRCm39) D3870G probably damaging Het
Mtf1 T A 4: 124,718,081 (GRCm39) C260S probably damaging Het
Naa35 A G 13: 59,747,598 (GRCm39) D110G probably damaging Het
Npas3 A T 12: 54,115,501 (GRCm39) T808S probably damaging Het
Or5a1 A G 19: 12,097,909 (GRCm39) W56R probably damaging Het
Pik3c2a T C 7: 115,993,529 (GRCm39) T413A probably benign Het
Pik3r1 A G 13: 101,846,205 (GRCm39) V127A probably benign Het
Pik3r5 A G 11: 68,381,324 (GRCm39) E170G probably damaging Het
Polr1a T C 6: 71,931,819 (GRCm39) I966T possibly damaging Het
Prelid2 A G 18: 42,045,433 (GRCm39) probably null Het
Rab29 T A 1: 131,799,923 (GRCm39) M166K probably damaging Het
Rab2b T C 14: 52,503,717 (GRCm39) E135G probably damaging Het
Rnf103 T A 6: 71,486,463 (GRCm39) S365T possibly damaging Het
Rnf213 G A 11: 119,301,687 (GRCm39) E387K Het
Sh3d19 T C 3: 86,031,038 (GRCm39) V734A probably benign Het
Spata31e5 T A 1: 28,816,689 (GRCm39) T448S possibly damaging Het
Spmip3 T A 1: 177,570,828 (GRCm39) I54K probably damaging Het
Ssbp1 T G 6: 40,454,914 (GRCm39) N124K probably damaging Het
Tbc1d31 C T 15: 57,799,494 (GRCm39) R227* probably null Het
Tcerg1 A G 18: 42,657,039 (GRCm39) T174A unknown Het
Tenm2 T C 11: 35,960,388 (GRCm39) S980G possibly damaging Het
Trim30a T C 7: 104,079,386 (GRCm39) I156M possibly damaging Het
Trim39 T C 17: 36,571,396 (GRCm39) D454G possibly damaging Het
Trpc7 A T 13: 56,921,579 (GRCm39) *863K probably null Het
Tubgcp3 A G 8: 12,707,561 (GRCm39) Y143H probably benign Het
Vmn1r33 C T 6: 66,589,357 (GRCm39) D66N probably benign Het
Vmn2r8 A T 5: 108,950,043 (GRCm39) I268N probably damaging Het
Vmn2r91 A C 17: 18,356,080 (GRCm39) E582D probably benign Het
Vtcn1 T C 3: 100,791,211 (GRCm39) F83S probably damaging Het
Wdr81 G T 11: 75,332,811 (GRCm39) D684E Het
Wipi1 A G 11: 109,470,535 (GRCm39) S295P probably damaging Het
Zfp27 A T 7: 29,593,699 (GRCm39) H755Q possibly damaging Het
Zfp963 A G 8: 70,195,533 (GRCm39) F307L 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
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
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'- TCTTAGCCTAGGACCTTTGTGG -3'
(R):5'- CCTTGGCTTGACTAAACCCG -3'

Sequencing Primer
(F):5'- CCTTTGTGGTCTTGTCTCAGGAG -3'
(R):5'- TTGACTAAACCCGGCTGGC -3'
Posted On 2019-11-26