Incidental Mutation 'R0049:Pax3'
ID 40842
Institutional Source Beutler Lab
Gene Symbol Pax3
Ensembl Gene ENSMUSG00000004872
Gene Name paired box 3
Synonyms Splchl2, Pax-3
MMRRC Submission 038343-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.822) question?
Stock # R0049 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 78077904-78173771 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 78080141 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 415 (L415P)
Ref Sequence ENSEMBL: ENSMUSP00000084320 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000004994] [ENSMUST00000087086]
AlphaFold P24610
Predicted Effect probably damaging
Transcript: ENSMUST00000004994
AA Change: L415P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000004994
Gene: ENSMUSG00000004872
AA Change: L415P

DomainStartEndE-ValueType
PAX 34 159 1.99e-91 SMART
low complexity region 164 185 N/A INTRINSIC
HOX 219 281 6.6e-27 SMART
Pfam:Pax7 347 391 5.9e-29 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000087086
AA Change: L415P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000084320
Gene: ENSMUSG00000004872
AA Change: L415P

DomainStartEndE-ValueType
PAX 34 159 1.99e-91 SMART
low complexity region 164 185 N/A INTRINSIC
HOX 219 281 6.6e-27 SMART
Pfam:Pax7 346 391 5.3e-27 PFAM
Meta Mutation Damage Score 0.2758 question?
Coding Region Coverage
  • 1x: 99.7%
  • 3x: 98.9%
  • 10x: 97.0%
  • 20x: 94.3%
Validation Efficiency 99% (114/115)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. Mutations in paired box gene 3 are associated with Waardenburg syndrome, craniofacial-deafness-hand syndrome, and alveolar rhabdomyosarcoma. The translocation t(2;13)(q35;q14), which represents a fusion between PAX3 and the forkhead gene, is a frequent finding in alveolar rhabdomyosarcoma. Alternative splicing results in transcripts encoding isoforms with different C-termini. [provided by RefSeq, Jul 2008]
PHENOTYPE: Effects on homozygotes for mutations in this gene vary in severity and include embryonic to perinatal death, malformations of neural tube, spinal ganglia, heart, vertebral column, hindbrain and limb musculature. Heterozygotes have white belly spots and variable spotting on the back and extremeties. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 110 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A2m A T 6: 121,615,267 (GRCm39) H9L possibly damaging Het
Aars1 T A 8: 111,779,083 (GRCm39) I739K possibly damaging Het
Abcb1b T A 5: 8,875,661 (GRCm39) H611Q probably damaging Het
Acod1 T A 14: 103,292,643 (GRCm39) I389K possibly damaging Het
Adgre1 T A 17: 57,709,841 (GRCm39) L166* probably null Het
Akap1 C A 11: 88,730,450 (GRCm39) probably null Het
Akna T A 4: 63,312,872 (GRCm39) Q417L probably damaging Het
Anxa7 T C 14: 20,512,678 (GRCm39) D285G probably damaging Het
Arhgap1 T C 2: 91,500,514 (GRCm39) Y308H probably damaging Het
Arhgef10 A C 8: 15,004,446 (GRCm39) R360S probably damaging Het
Arhgef11 T A 3: 87,636,500 (GRCm39) probably null Het
Arid3a A G 10: 79,766,899 (GRCm39) T58A possibly damaging Het
Atosb A T 4: 43,036,441 (GRCm39) S97T probably benign Het
Atp6v0a4 G A 6: 38,059,016 (GRCm39) R256C probably damaging Het
Camsap3 C A 8: 3,648,772 (GRCm39) S163R probably benign Het
Ccdc110 A T 8: 46,395,663 (GRCm39) E518V probably damaging Het
Ccdc180 G A 4: 45,930,119 (GRCm39) probably null Het
Ccnt1 T C 15: 98,462,960 (GRCm39) M71V probably benign Het
Celsr2 T A 3: 108,304,570 (GRCm39) Y2263F probably benign Het
Cfap36 A T 11: 29,196,514 (GRCm39) probably null Het
Cfap69 T C 5: 5,663,734 (GRCm39) T498A probably benign Het
Chadl T C 15: 81,578,213 (GRCm39) D6G probably benign Het
Clstn3 T A 6: 124,436,812 (GRCm39) I132F possibly damaging Het
Cnot4 A G 6: 35,028,212 (GRCm39) V468A probably benign Het
Crmp1 T G 5: 37,422,617 (GRCm39) D141E possibly damaging Het
Crtc1 A G 8: 70,844,509 (GRCm39) probably null Het
Cryz C A 3: 154,317,189 (GRCm39) A136D probably damaging Het
Dph6 A G 2: 114,353,525 (GRCm39) V221A probably benign Het
Dst A T 1: 34,314,862 (GRCm39) N4267Y probably damaging Het
Duox2 T A 2: 122,127,167 (GRCm39) D170V possibly damaging Het
Ecm2 A T 13: 49,677,922 (GRCm39) K403* probably null Het
Eif3d T C 15: 77,843,924 (GRCm39) N474S probably benign Het
Elf1 T C 14: 79,802,965 (GRCm39) L106P probably damaging Het
Exoc4 G C 6: 33,273,857 (GRCm39) probably null Het
F12 T C 13: 55,574,130 (GRCm39) D34G probably benign Het
Fam228b A T 12: 4,798,117 (GRCm39) F200Y probably damaging Het
Fgl2 T A 5: 21,580,661 (GRCm39) D334E possibly damaging Het
Fras1 T A 5: 96,924,481 (GRCm39) F3641I probably benign Het
Gabrb2 T G 11: 42,484,674 (GRCm39) Y244D probably damaging Het
Gcc1 A T 6: 28,421,268 (GRCm39) D16E probably benign Het
Gga3 C A 11: 115,477,915 (GRCm39) G558* probably null Het
Glt1d1 T C 5: 127,740,391 (GRCm39) probably benign Het
Gorasp2 T C 2: 70,521,067 (GRCm39) S346P possibly damaging Het
Hcn4 T C 9: 58,767,582 (GRCm39) S1048P probably damaging Het
Henmt1 T A 3: 108,861,105 (GRCm39) probably benign Het
Htt A C 5: 35,066,006 (GRCm39) K3060N probably damaging Het
Ibsp C T 5: 104,450,024 (GRCm39) L8F probably damaging Het
Kif27 A T 13: 58,451,378 (GRCm39) D983E probably damaging Het
Kif3a T A 11: 53,481,560 (GRCm39) probably benign Het
Kif3c A C 12: 3,417,090 (GRCm39) K370N possibly damaging Het
Loxhd1 T C 18: 77,468,256 (GRCm39) probably benign Het
Maz A T 7: 126,623,758 (GRCm39) D74E probably damaging Het
Med21 T C 6: 146,551,732 (GRCm39) S128P probably damaging Het
Mms19 A C 19: 41,943,607 (GRCm39) M374R probably damaging Het
Mprip T C 11: 59,657,571 (GRCm39) V801A probably damaging Het
Mrpl3 T C 9: 104,932,872 (GRCm39) V111A probably benign Het
Mtfr2 T A 10: 20,224,158 (GRCm39) Y31N probably damaging Het
Myh3 C T 11: 66,990,498 (GRCm39) R1677C probably damaging Het
Mynn T A 3: 30,661,230 (GRCm39) *61K probably null Het
Neb A C 2: 52,060,479 (GRCm39) M2286R possibly damaging Het
Ngf A T 3: 102,427,661 (GRCm39) R137* probably null Het
Nr1i3 T A 1: 171,041,982 (GRCm39) V22E probably damaging Het
Nxpe5 T C 5: 138,249,566 (GRCm39) V452A probably damaging Het
Oas1e C A 5: 120,933,395 (GRCm39) A57S probably benign Het
Or11g27 A T 14: 50,771,151 (GRCm39) K94M probably damaging Het
Or14j10 T A 17: 37,935,024 (GRCm39) R167S probably benign Het
Or5b105 G A 19: 13,080,642 (GRCm39) R3C possibly damaging Het
Pcnt G T 10: 76,205,655 (GRCm39) probably benign Het
Peg3 G T 7: 6,714,672 (GRCm39) D183E possibly damaging Het
Pglyrp1 G T 7: 18,623,313 (GRCm39) G120V probably damaging Het
Pnp2 T A 14: 51,196,990 (GRCm39) Y25* probably null Het
Pomt1 T A 2: 32,142,023 (GRCm39) H584Q possibly damaging Het
Ppp1r12a A G 10: 108,089,193 (GRCm39) N611D possibly damaging Het
Prkcq G A 2: 11,288,643 (GRCm39) G532E probably benign Het
Prl6a1 A T 13: 27,501,980 (GRCm39) I116F probably damaging Het
Ptprh T A 7: 4,576,361 (GRCm39) T300S possibly damaging Het
Pwp1 A G 10: 85,721,480 (GRCm39) T361A possibly damaging Het
Rab4a A T 8: 124,554,081 (GRCm39) H5L probably damaging Het
Raet1e C A 10: 22,056,761 (GRCm39) H112Q possibly damaging Het
Ramp1 T C 1: 91,124,592 (GRCm39) I51T possibly damaging Het
Raph1 G T 1: 60,565,058 (GRCm39) T143K probably benign Het
Rhpn1 A G 15: 75,581,088 (GRCm39) E110G possibly damaging Het
Rnf168 A T 16: 32,117,287 (GRCm39) T283S possibly damaging Het
Ros1 T A 10: 51,977,857 (GRCm39) Y1463F possibly damaging Het
Rtn4ip1 A G 10: 43,797,430 (GRCm39) Q223R probably null Het
Rtp4 G T 16: 23,431,679 (GRCm39) M70I probably benign Het
Sag C A 1: 87,762,340 (GRCm39) T335K probably damaging Het
Satb1 T A 17: 52,047,374 (GRCm39) Q647L probably benign Het
Sec31b T C 19: 44,508,847 (GRCm39) probably benign Het
Sgo1 C T 17: 53,986,691 (GRCm39) D167N probably damaging Het
Slco1a8 T C 6: 141,936,147 (GRCm39) T313A probably benign Het
Smchd1 T C 17: 71,738,231 (GRCm39) I545V probably benign Het
St6gal1 G T 16: 23,139,891 (GRCm39) A21S probably damaging Het
Stard9 C A 2: 120,530,300 (GRCm39) L2186I probably damaging Het
Sun2 T A 15: 79,611,810 (GRCm39) probably benign Het
Taf4 G A 2: 179,565,884 (GRCm39) T849M probably damaging Het
Tdrd5 A T 1: 156,129,473 (GRCm39) I79N probably damaging Het
Tdrd7 A G 4: 45,987,582 (GRCm39) I72V probably damaging Het
Tnxb T A 17: 34,928,542 (GRCm39) V2652E possibly damaging Het
Trim30a C T 7: 104,078,559 (GRCm39) probably null Het
Tshz3 A G 7: 36,469,534 (GRCm39) T508A probably damaging Het
Ttc21b A G 2: 66,053,908 (GRCm39) L757P probably damaging Het
Ubtd2 A C 11: 32,449,223 (GRCm39) probably null Het
Ubtd2 G T 11: 32,449,224 (GRCm39) probably null Het
Vmn1r218 C T 13: 23,321,225 (GRCm39) Q111* probably null Het
Vmn2r75 G A 7: 85,797,309 (GRCm39) Q835* probably null Het
Vwa8 T A 14: 79,331,179 (GRCm39) M1229K probably benign Het
Wdr76 C T 2: 121,349,932 (GRCm39) R111C probably damaging Het
Xcr1 T A 9: 123,684,940 (GRCm39) D274V possibly damaging Het
Ypel5 C T 17: 73,153,332 (GRCm39) T12I probably benign Het
Other mutations in Pax3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01642:Pax3 APN 1 78,173,300 (GRCm39) critical splice donor site probably null
IGL02249:Pax3 APN 1 78,171,962 (GRCm39) missense probably damaging 0.98
IGL02271:Pax3 APN 1 78,171,969 (GRCm39) missense probably damaging 1.00
IGL02376:Pax3 APN 1 78,108,929 (GRCm39) missense probably damaging 1.00
IGL02530:Pax3 APN 1 78,098,424 (GRCm39) missense possibly damaging 0.87
IGL02950:Pax3 APN 1 78,079,997 (GRCm39) missense probably benign 0.06
Nidoqueen UTSW 1 78,108,869 (GRCm39) missense probably damaging 1.00
Widget UTSW 1 78,099,227 (GRCm39) critical splice donor site probably null
R0049:Pax3 UTSW 1 78,080,141 (GRCm39) missense probably damaging 1.00
R0523:Pax3 UTSW 1 78,172,078 (GRCm39) missense possibly damaging 0.83
R1575:Pax3 UTSW 1 78,080,121 (GRCm39) missense probably benign 0.00
R1831:Pax3 UTSW 1 78,108,977 (GRCm39) missense probably damaging 1.00
R1934:Pax3 UTSW 1 78,080,117 (GRCm39) missense possibly damaging 0.90
R2420:Pax3 UTSW 1 78,173,501 (GRCm39) splice site probably null
R2473:Pax3 UTSW 1 78,099,227 (GRCm39) critical splice donor site probably null
R4430:Pax3 UTSW 1 78,171,961 (GRCm39) missense probably damaging 1.00
R4693:Pax3 UTSW 1 78,173,383 (GRCm39) missense probably benign 0.00
R4818:Pax3 UTSW 1 78,108,869 (GRCm39) missense probably damaging 1.00
R4860:Pax3 UTSW 1 78,169,093 (GRCm39) missense possibly damaging 0.78
R4860:Pax3 UTSW 1 78,169,093 (GRCm39) missense possibly damaging 0.78
R5302:Pax3 UTSW 1 78,098,249 (GRCm39) missense possibly damaging 0.88
R5475:Pax3 UTSW 1 78,080,055 (GRCm39) missense probably benign 0.06
R5855:Pax3 UTSW 1 78,098,288 (GRCm39) missense probably damaging 0.99
R6102:Pax3 UTSW 1 78,108,984 (GRCm39) missense probably damaging 1.00
R6190:Pax3 UTSW 1 78,169,186 (GRCm39) missense possibly damaging 0.63
R6856:Pax3 UTSW 1 78,109,056 (GRCm39) missense probably damaging 1.00
R7065:Pax3 UTSW 1 78,170,648 (GRCm39) splice site probably null
R7547:Pax3 UTSW 1 78,099,231 (GRCm39) nonsense probably null
R8059:Pax3 UTSW 1 78,080,003 (GRCm39) missense probably benign 0.04
R8224:Pax3 UTSW 1 78,098,327 (GRCm39) missense probably damaging 1.00
R8312:Pax3 UTSW 1 78,172,006 (GRCm39) missense probably damaging 1.00
R8324:Pax3 UTSW 1 78,170,426 (GRCm39) missense probably damaging 1.00
R9319:Pax3 UTSW 1 78,080,079 (GRCm39) missense probably benign
R9759:Pax3 UTSW 1 78,170,415 (GRCm39) missense probably damaging 1.00
Z1176:Pax3 UTSW 1 78,099,227 (GRCm39) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- TCCAGTTCCCCGTTCTCAAGCAAG -3'
(R):5'- TCAGAAAAGCTCCTCAATGGCTGTC -3'

Sequencing Primer
(F):5'- AGCAAGAGGTGATCTCTCTCC -3'
(R):5'- GCTCCTCAATGGCTGTCTAGAG -3'
Posted On 2013-05-23