Incidental Mutation 'R4764:Pax6'
ID 357078
Institutional Source Beutler Lab
Gene Symbol Pax6
Ensembl Gene ENSMUSG00000027168
Gene Name paired box 6
Synonyms Pax-6, Dickie's small eye, Gsfaey11, 1500038E17Rik, Dey, AEY11
MMRRC Submission 042405-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4764 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 105499245-105527709 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 105526847 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Glutamine at position 251 (P251Q)
Ref Sequence ENSEMBL: ENSMUSP00000106717 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000090391] [ENSMUST00000090397] [ENSMUST00000111082] [ENSMUST00000111083] [ENSMUST00000111085] [ENSMUST00000111086] [ENSMUST00000111087] [ENSMUST00000111088] [ENSMUST00000167211] [ENSMUST00000122965]
AlphaFold P63015
Predicted Effect probably benign
Transcript: ENSMUST00000090391
SMART Domains Protein: ENSMUSP00000087870
Gene: ENSMUSG00000027168

DomainStartEndE-ValueType
PAX 4 142 7.36e-86 SMART
low complexity region 188 199 N/A INTRINSIC
HOX 224 286 4.93e-26 SMART
low complexity region 295 308 N/A INTRINSIC
low complexity region 401 409 N/A INTRINSIC
low complexity region 412 426 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000090397
SMART Domains Protein: ENSMUSP00000087878
Gene: ENSMUSG00000027168

DomainStartEndE-ValueType
PAX 4 128 6.11e-92 SMART
low complexity region 174 185 N/A INTRINSIC
HOX 210 272 4.93e-26 SMART
low complexity region 281 294 N/A INTRINSIC
low complexity region 387 395 N/A INTRINSIC
low complexity region 398 412 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000111082
SMART Domains Protein: ENSMUSP00000106711
Gene: ENSMUSG00000027168

DomainStartEndE-ValueType
PAX 4 128 6.11e-92 SMART
low complexity region 174 185 N/A INTRINSIC
HOX 210 272 4.93e-26 SMART
low complexity region 281 294 N/A INTRINSIC
low complexity region 387 395 N/A INTRINSIC
low complexity region 398 412 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000111083
SMART Domains Protein: ENSMUSP00000106712
Gene: ENSMUSG00000027168

DomainStartEndE-ValueType
PAX 4 128 6.11e-92 SMART
low complexity region 174 185 N/A INTRINSIC
HOX 210 272 4.93e-26 SMART
low complexity region 281 294 N/A INTRINSIC
low complexity region 387 395 N/A INTRINSIC
low complexity region 398 412 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000111085
SMART Domains Protein: ENSMUSP00000106714
Gene: ENSMUSG00000027168

DomainStartEndE-ValueType
PAX 4 142 7.36e-86 SMART
low complexity region 188 199 N/A INTRINSIC
HOX 224 286 4.93e-26 SMART
low complexity region 295 308 N/A INTRINSIC
low complexity region 401 409 N/A INTRINSIC
low complexity region 412 426 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000111086
SMART Domains Protein: ENSMUSP00000106715
Gene: ENSMUSG00000027168

DomainStartEndE-ValueType
PAX 4 142 7.36e-86 SMART
low complexity region 188 199 N/A INTRINSIC
HOX 224 286 4.93e-26 SMART
low complexity region 295 308 N/A INTRINSIC
low complexity region 401 409 N/A INTRINSIC
low complexity region 412 426 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000111087
SMART Domains Protein: ENSMUSP00000106716
Gene: ENSMUSG00000027168

DomainStartEndE-ValueType
PAX 4 128 6.11e-92 SMART
low complexity region 174 185 N/A INTRINSIC
HOX 210 272 4.93e-26 SMART
low complexity region 281 294 N/A INTRINSIC
low complexity region 387 395 N/A INTRINSIC
low complexity region 398 412 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146803
SMART Domains Protein: ENSMUSP00000133346
Gene: ENSMUSG00000027168

DomainStartEndE-ValueType
Blast:PAX 1 62 1e-26 BLAST
HOX 74 136 4.93e-26 SMART
low complexity region 145 158 N/A INTRINSIC
Blast:PAX 186 234 3e-23 BLAST
low complexity region 251 259 N/A INTRINSIC
low complexity region 262 276 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000111088
AA Change: P251Q

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000106717
Gene: ENSMUSG00000027168
AA Change: P251Q

DomainStartEndE-ValueType
low complexity region 2 17 N/A INTRINSIC
HOX 39 101 4.93e-26 SMART
low complexity region 110 123 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140173
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154643
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135412
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138365
SMART Domains Protein: ENSMUSP00000117154
Gene: ENSMUSG00000027168

DomainStartEndE-ValueType
low complexity region 4 15 N/A INTRINSIC
PAX 33 192 4.87e-77 SMART
low complexity region 238 249 N/A INTRINSIC
SCOP:d1b72a_ 254 291 2e-4 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153011
SMART Domains Protein: ENSMUSP00000118457
Gene: ENSMUSG00000027168

DomainStartEndE-ValueType
PAX 2 109 4.98e-42 SMART
low complexity region 155 166 N/A INTRINSIC
Pfam:Homeobox 192 218 7.7e-9 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147946
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155081
Predicted Effect noncoding transcript
Transcript: ENSMUST00000145744
Predicted Effect noncoding transcript
Transcript: ENSMUST00000123063
SMART Domains Protein: ENSMUSP00000121345
Gene: ENSMUSG00000027168

DomainStartEndE-ValueType
HOX 9 71 2.5e-28 SMART
low complexity region 80 93 N/A INTRINSIC
Blast:PAX 121 169 6e-24 BLAST
low complexity region 186 194 N/A INTRINSIC
low complexity region 197 211 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000167211
SMART Domains Protein: ENSMUSP00000129344
Gene: ENSMUSG00000027168

DomainStartEndE-ValueType
PAX 4 142 7.36e-86 SMART
low complexity region 188 199 N/A INTRINSIC
HOX 224 286 4.93e-26 SMART
low complexity region 295 308 N/A INTRINSIC
low complexity region 401 409 N/A INTRINSIC
low complexity region 412 426 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000122965
SMART Domains Protein: ENSMUSP00000116575
Gene: ENSMUSG00000027167

DomainStartEndE-ValueType
Pfam:PAXNEB 28 422 4e-123 PFAM
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.9%
Validation Efficiency 99% (78/79)
MGI Phenotype FUNCTION: This gene encodes a homeobox-containing protein that functions as a regulator of transcription. It plays a key role in the development of neural tissues, particularly the eye. Activity of this protein is also required for expression of glucagon in the pancreas. This gene is regulated by multiple enhancers located up to tens or hundreds of kilobases upstream and downstream of the transcription start sites. Mutations in this gene or deletion of these regulatory elements results in severe defects in eye development. Alternative splicing and the use of alternative promoters results in multiple transcript variants, some of which encode proteins that lack the N-terminal paired domain. [provided by RefSeq, Jul 2015]
PHENOTYPE: Null and hypomorphic mutants show a range of phenotypes from viable with small eyes and lens/cornea fusion to microphthalmia and cataract to embryonic or perinatal lethality with anophthalmia and severe craniofacial and forebrain defects. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700001J03Rik T G 5: 146,122,029 (GRCm39) S18R probably benign Het
2010315B03Rik A C 9: 124,056,396 (GRCm39) V176G probably benign Het
Abcb1a T A 5: 8,765,732 (GRCm39) probably null Het
Acad11 C A 9: 103,953,076 (GRCm39) P102T probably damaging Het
Aggf1 T A 13: 95,501,221 (GRCm39) D387V probably damaging Het
Akr1c13 G A 13: 4,248,496 (GRCm39) V234I probably benign Het
Alg5 A G 3: 54,653,894 (GRCm39) Y210C possibly damaging Het
Arl8a C A 1: 135,074,837 (GRCm39) A41E probably benign Het
Axin1 C A 17: 26,392,730 (GRCm39) T337K possibly damaging Het
Bdp1 A G 13: 100,192,775 (GRCm39) L1353P probably damaging Het
Bptf A T 11: 106,934,520 (GRCm39) V2851E probably damaging Het
C9 A T 15: 6,489,124 (GRCm39) E160D probably damaging Het
Cbx6 T C 15: 79,712,881 (GRCm39) D182G probably damaging Het
Cep57l1 T C 10: 41,597,678 (GRCm39) R242G possibly damaging Het
Chst8 T C 7: 34,375,149 (GRCm39) D230G probably damaging Het
Col3a1 A C 1: 45,385,270 (GRCm39) D129A probably damaging Het
Cst12 A G 2: 148,631,393 (GRCm39) E38G possibly damaging Het
Disp1 G T 1: 182,869,660 (GRCm39) A920E probably damaging Het
Dtna T G 18: 23,668,206 (GRCm39) probably null Het
Elp3 T A 14: 65,820,378 (GRCm39) H97L probably damaging Het
Exoc8 A G 8: 125,624,314 (GRCm39) F18L possibly damaging Het
Extl3 T C 14: 65,314,769 (GRCm39) T138A probably benign Het
Foxi2 G T 7: 135,012,396 (GRCm39) G95C probably damaging Het
Foxj2 G T 6: 122,810,230 (GRCm39) Q196H probably benign Het
Frem1 A T 4: 82,907,426 (GRCm39) D811E probably damaging Het
Frmd4a A T 2: 4,608,259 (GRCm39) E709V probably damaging Het
Fscn3 T A 6: 28,436,200 (GRCm39) *499K probably null Het
Galc C T 12: 98,209,003 (GRCm39) G217D possibly damaging Het
Gm5592 G T 7: 40,865,542 (GRCm39) probably benign Het
Gm57858 T G 3: 36,064,809 (GRCm39) *521C probably null Het
Hnrnpul1 A G 7: 25,442,436 (GRCm39) S269P probably benign Het
Hrh1 T C 6: 114,457,496 (GRCm39) V259A probably benign Het
Lef1 T C 3: 130,978,382 (GRCm39) S167P probably benign Het
Mtf2 T C 5: 108,241,218 (GRCm39) I248T probably benign Het
Muc2 C T 7: 141,299,345 (GRCm39) T130M possibly damaging Het
Myo16 T C 8: 10,485,880 (GRCm39) F653S probably damaging Het
Myo1e T C 9: 70,250,417 (GRCm39) probably null Het
Myo5a G T 9: 75,023,618 (GRCm39) probably benign Het
Nlrp1b T A 11: 71,073,489 (GRCm39) D118V probably damaging Het
Npat T C 9: 53,483,920 (GRCm39) F1412S probably damaging Het
Onecut3 G T 10: 80,331,541 (GRCm39) A234S unknown Het
Or1ad1 G A 11: 50,875,602 (GRCm39) E25K probably benign Het
Or8b37 T G 9: 37,959,436 (GRCm39) L306R probably benign Het
Osbpl6 T A 2: 76,376,344 (GRCm39) I73K probably damaging Het
Otog C T 7: 45,937,943 (GRCm39) T1884I probably benign Het
Pias4 A G 10: 80,999,868 (GRCm39) Y62H possibly damaging Het
Pknox1 T A 17: 31,809,687 (GRCm39) V97D possibly damaging Het
Plekhf1 A G 7: 37,921,022 (GRCm39) V182A probably damaging Het
Plscr4 T C 9: 92,366,833 (GRCm39) V149A probably damaging Het
Polr2l A T 7: 141,053,309 (GRCm39) L35Q probably damaging Het
Ppp3ca T C 3: 136,596,250 (GRCm39) I305T probably damaging Het
Ptprg G A 14: 12,122,068 (GRCm38) A311T probably benign Het
Raet1e T G 10: 22,057,231 (GRCm39) I185R probably damaging Het
Rims1 A C 1: 22,518,543 (GRCm39) V520G probably damaging Het
Rp1 A T 1: 4,416,101 (GRCm39) D1670E probably damaging Het
Rps6ka1 A T 4: 133,587,868 (GRCm39) I352N probably damaging Het
Rtp3 T C 9: 110,816,418 (GRCm39) probably benign Het
Ryr3 T A 2: 112,563,376 (GRCm39) probably null Het
Sall3 A G 18: 81,017,691 (GRCm39) V79A probably damaging Het
Sdsl C T 5: 120,600,119 (GRCm39) V93M probably damaging Het
Slc7a13 A G 4: 19,819,390 (GRCm39) N197D probably benign Het
Slit1 T A 19: 41,709,483 (GRCm39) R137* probably null Het
Stxbp5 C A 10: 9,646,367 (GRCm39) R115L probably damaging Het
Tcea1 G A 1: 4,965,167 (GRCm39) R290H probably damaging Het
Tmem132e A T 11: 82,325,338 (GRCm39) T113S probably damaging Het
Tpp1 A T 7: 105,398,458 (GRCm39) I286N probably damaging Het
Trio G A 15: 27,732,624 (GRCm39) R3086* probably null Het
Usp22 T A 11: 61,051,462 (GRCm39) N294Y probably damaging Het
Usp44 T A 10: 93,681,933 (GRCm39) S128T probably benign Het
Zc3h7b T C 15: 81,653,384 (GRCm39) probably null Het
Zfhx2 T C 14: 55,304,372 (GRCm39) Y1204C possibly damaging Het
Other mutations in Pax6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02008:Pax6 APN 2 105,522,623 (GRCm39) critical splice donor site probably null
IGL02256:Pax6 APN 2 105,515,115 (GRCm39) missense probably benign 0.16
IGL02500:Pax6 APN 2 105,523,115 (GRCm39) missense probably benign 0.13
beady UTSW 2 105,522,036 (GRCm39) missense probably damaging 1.00
red_hots UTSW 2 105,525,705 (GRCm39) missense probably benign 0.00
G1citation:Pax6 UTSW 2 105,516,268 (GRCm39) missense probably benign 0.04
R1067:Pax6 UTSW 2 105,510,646 (GRCm39) missense probably benign 0.01
R1213:Pax6 UTSW 2 105,516,258 (GRCm39) missense probably benign 0.13
R1494:Pax6 UTSW 2 105,521,955 (GRCm39) missense probably benign 0.16
R1633:Pax6 UTSW 2 105,522,063 (GRCm39) missense probably damaging 1.00
R2291:Pax6 UTSW 2 105,516,228 (GRCm39) missense probably benign 0.09
R3834:Pax6 UTSW 2 105,526,795 (GRCm39) missense probably benign 0.00
R3835:Pax6 UTSW 2 105,526,795 (GRCm39) missense probably benign 0.00
R4665:Pax6 UTSW 2 105,514,343 (GRCm39) intron probably benign
R4714:Pax6 UTSW 2 105,525,745 (GRCm39) missense possibly damaging 0.74
R4747:Pax6 UTSW 2 105,526,847 (GRCm39) missense probably benign
R4767:Pax6 UTSW 2 105,525,705 (GRCm39) missense probably benign 0.00
R4771:Pax6 UTSW 2 105,526,847 (GRCm39) missense probably benign
R4772:Pax6 UTSW 2 105,526,847 (GRCm39) missense probably benign
R4816:Pax6 UTSW 2 105,514,129 (GRCm39) intron probably benign
R4819:Pax6 UTSW 2 105,522,622 (GRCm39) critical splice donor site probably null
R5418:Pax6 UTSW 2 105,521,910 (GRCm39) missense probably benign 0.00
R5683:Pax6 UTSW 2 105,516,252 (GRCm39) missense probably benign 0.06
R6041:Pax6 UTSW 2 105,514,247 (GRCm39) missense probably damaging 1.00
R6263:Pax6 UTSW 2 105,523,199 (GRCm39) critical splice donor site probably null
R6651:Pax6 UTSW 2 105,516,175 (GRCm39) missense probably benign 0.00
R6822:Pax6 UTSW 2 105,516,268 (GRCm39) missense probably benign 0.04
R7042:Pax6 UTSW 2 105,526,718 (GRCm39) missense probably benign
R7088:Pax6 UTSW 2 105,526,753 (GRCm39) missense probably benign 0.00
R7102:Pax6 UTSW 2 105,522,604 (GRCm39) missense probably damaging 0.98
R7294:Pax6 UTSW 2 105,515,246 (GRCm39) nonsense probably null
R7761:Pax6 UTSW 2 105,522,036 (GRCm39) missense probably damaging 1.00
R7948:Pax6 UTSW 2 105,516,222 (GRCm39) missense probably benign
R8882:Pax6 UTSW 2 105,521,963 (GRCm39) missense possibly damaging 0.96
R9151:Pax6 UTSW 2 105,523,097 (GRCm39) missense probably benign 0.10
R9796:Pax6 UTSW 2 105,522,541 (GRCm39) missense probably damaging 1.00
Z1177:Pax6 UTSW 2 105,516,161 (GRCm39) missense possibly damaging 0.64
Predicted Primers PCR Primer
(F):5'- ATGTCTCAGTACTGGCCTCG -3'
(R):5'- CATGGCAAATCTTGTCGATCATG -3'

Sequencing Primer
(F):5'- CAGTACTGGCCTCGATTACAG -3'
(R):5'- GCAAATCTTGTCGATCATGGTTTC -3'
Posted On 2015-11-11