Incidental Mutation 'R6469:Pax9'
ID 520282
Institutional Source Beutler Lab
Gene Symbol Pax9
Ensembl Gene ENSMUSG00000001497
Gene Name paired box 9
Synonyms Pax-9
MMRRC Submission 044602-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.950) question?
Stock # R6469 (G1)
Quality Score 225.009
Status Validated
Chromosome 12
Chromosomal Location 56738552-56759607 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 56743648 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 98 (F98L)
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: F98L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000001538
Gene: ENSMUSG00000001497
AA Change: F98L

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: F98L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000117928
Gene: ENSMUSG00000001497
AA Change: F98L

DomainStartEndE-ValueType
PAX 4 128 6.81e-90 SMART
low complexity region 265 274 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000159874
Meta Mutation Damage Score 0.9543 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.4%
  • 10x: 97.2%
  • 20x: 91.3%
Validation Efficiency 100% (43/43)
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: 41 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik T G 3: 137,772,736 (GRCm39) S642A probably damaging Het
Aadacl2 A T 3: 59,932,210 (GRCm39) T242S probably benign Het
Adprh T C 16: 38,270,671 (GRCm39) M45V probably benign Het
Akr1c13 T C 13: 4,246,511 (GRCm39) probably null Het
Ap3d1 A C 10: 80,547,992 (GRCm39) V900G probably benign Het
Bak1 G A 17: 27,240,293 (GRCm39) R125C probably damaging Het
Bmpr1b T C 3: 141,562,222 (GRCm39) T322A possibly damaging Het
Camsap3 T A 8: 3,653,941 (GRCm39) L521Q possibly damaging Het
Col6a6 A T 9: 105,575,890 (GRCm39) F2157I probably damaging Het
Dcun1d4 G A 5: 73,691,957 (GRCm39) M155I probably damaging Het
Diaph3 T C 14: 86,893,974 (GRCm39) S12G possibly damaging Het
Enpp5 G A 17: 44,396,155 (GRCm39) G356S probably damaging Het
Fan1 T A 7: 64,022,234 (GRCm39) N340Y probably damaging Het
Fgb A T 3: 82,953,449 (GRCm39) L107* probably null Het
Ganab T C 19: 8,879,996 (GRCm39) probably null Het
Gba1 C T 3: 89,111,388 (GRCm39) P51L probably benign Het
Glb1l2 T C 9: 26,707,828 (GRCm39) D60G probably benign Het
Idh3b AG AGCACCACAACTG 2: 130,121,593 (GRCm39) probably null Het
Itih2 A G 2: 10,128,224 (GRCm39) V159A possibly damaging Het
Kif1b T C 4: 149,277,053 (GRCm39) M1337V probably benign Het
Lrch1 C T 14: 75,054,525 (GRCm39) R323Q probably damaging Het
Lrrc30 T C 17: 67,938,860 (GRCm39) N240S probably benign Het
Mrgpra9 T C 7: 46,884,854 (GRCm39) Y271C probably benign Het
Ncor1 T C 11: 62,234,128 (GRCm39) H682R probably damaging Het
Or14j4 A T 17: 37,921,204 (GRCm39) V146E probably damaging Het
Phlpp1 G A 1: 106,214,833 (GRCm39) R585Q probably damaging Het
Prkdc A G 16: 15,612,939 (GRCm39) T3166A probably benign Het
Prr11 T A 11: 86,988,003 (GRCm39) Q300L possibly damaging Het
Rad50 T A 11: 53,575,062 (GRCm39) E620D probably benign Het
Rpl3 A T 15: 79,967,546 (GRCm39) probably null Het
Sacs G T 14: 61,428,697 (GRCm39) G252V probably damaging Het
Serpina3i T A 12: 104,232,776 (GRCm39) V227E probably damaging Het
Smap2 GACTCTAC GAC 4: 120,830,282 (GRCm39) probably benign Het
Snx19 T C 9: 30,339,039 (GRCm39) V59A possibly damaging Het
St3gal1 A G 15: 66,983,195 (GRCm39) V187A possibly damaging Het
Tcstv2c T A 13: 120,616,349 (GRCm39) W63R probably damaging Het
Tsc1 G A 2: 28,561,898 (GRCm39) probably null Het
Vmn2r61 C T 7: 41,915,283 (GRCm39) Q77* probably null Het
Wdr72 A G 9: 74,120,643 (GRCm39) H954R probably benign Het
Zbtb21 T C 16: 97,757,972 (GRCm39) M20V probably benign Het
Zkscan16 A T 4: 58,956,483 (GRCm39) D255V 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
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
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'- CTTCGCATCGTGGAATTAGC -3'
(R):5'- AAATGTGGTTGTAGGGCAGC -3'

Sequencing Primer
(F):5'- TCGTGGAATTAGCCCAACTG -3'
(R):5'- TTGTAGGGCAGCGCGGG -3'
Posted On 2018-06-06