Incidental Mutation 'R1481:Gli3'
ID 164398
Institutional Source Beutler Lab
Gene Symbol Gli3
Ensembl Gene ENSMUSG00000021318
Gene Name GLI-Kruppel family member GLI3
Synonyms Bph, brachyphalangy
MMRRC Submission 039534-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1481 (G1)
Quality Score 225
Status Validated
Chromosome 13
Chromosomal Location 15638308-15904611 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 15788435 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Tyrosine at position 147 (H147Y)
Ref Sequence ENSEMBL: ENSMUSP00000106137 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000110510] [ENSMUST00000130065] [ENSMUST00000141194]
AlphaFold Q61602
Predicted Effect probably damaging
Transcript: ENSMUST00000110510
AA Change: H147Y

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000106137
Gene: ENSMUSG00000021318
AA Change: H147Y

DomainStartEndE-ValueType
low complexity region 120 136 N/A INTRINSIC
low complexity region 204 220 N/A INTRINSIC
low complexity region 324 341 N/A INTRINSIC
low complexity region 403 421 N/A INTRINSIC
ZnF_C2H2 480 505 1.53e-1 SMART
ZnF_C2H2 513 540 1.23e0 SMART
ZnF_C2H2 546 570 3.16e-3 SMART
ZnF_C2H2 576 601 4.17e-3 SMART
ZnF_C2H2 607 632 1.4e-4 SMART
low complexity region 703 726 N/A INTRINSIC
low complexity region 756 763 N/A INTRINSIC
low complexity region 849 880 N/A INTRINSIC
low complexity region 934 944 N/A INTRINSIC
low complexity region 1024 1038 N/A INTRINSIC
low complexity region 1081 1095 N/A INTRINSIC
low complexity region 1166 1175 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000130065
AA Change: H147Y

PolyPhen 2 Score 0.638 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000115989
Gene: ENSMUSG00000021318
AA Change: H147Y

DomainStartEndE-ValueType
low complexity region 120 136 N/A INTRINSIC
low complexity region 204 220 N/A INTRINSIC
low complexity region 324 341 N/A INTRINSIC
low complexity region 403 421 N/A INTRINSIC
ZnF_C2H2 480 505 1.53e-1 SMART
ZnF_C2H2 513 540 1.23e0 SMART
ZnF_C2H2 546 570 3.16e-3 SMART
ZnF_C2H2 576 596 1.45e2 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130535
Predicted Effect silent
Transcript: ENSMUST00000141194
Meta Mutation Damage Score 0.0755 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.3%
  • 20x: 92.6%
Validation Efficiency 100% (71/71)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein which belongs to the C2H2-type zinc finger proteins subclass of the Gli family. They are characterized as DNA-binding transcription factors and are mediators of Sonic hedgehog (Shh) signaling. The protein encoded by this gene localizes in the cytoplasm and activates patched Drosophila homolog (PTCH) gene expression. It is also thought to play a role during embryogenesis. Mutations in this gene have been associated with several diseases, including Greig cephalopolysyndactyly syndrome, Pallister-Hall syndrome, preaxial polydactyly type IV, and postaxial polydactyly types A1 and B. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutants die perinatally with gross polydactyly, multiple craniofacial defects, and frequently, exencephaly. Heterozygotes exhibit enlarged interfrontal bone and extra preaxial digits. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Arhgef5 A G 6: 43,251,568 (GRCm39) H773R probably damaging Het
Bltp1 T C 3: 37,062,583 (GRCm39) V3365A probably damaging Het
Bmp3 G A 5: 99,020,329 (GRCm39) V251M probably damaging Het
Ccdc175 C A 12: 72,148,722 (GRCm39) probably benign Het
Ccdc178 C T 18: 22,238,678 (GRCm39) G313D probably benign Het
Cd300ld2 T A 11: 114,903,459 (GRCm39) I129F probably benign Het
Cep170 T C 1: 176,609,951 (GRCm39) Q120R possibly damaging Het
Ckb T C 12: 111,637,696 (GRCm39) H145R probably benign Het
Cntnap5a T A 1: 116,045,393 (GRCm39) N336K probably damaging Het
Coil T A 11: 88,864,886 (GRCm39) C38S possibly damaging Het
Cps1 T C 1: 67,183,041 (GRCm39) V133A probably damaging Het
Cspg4 A G 9: 56,795,094 (GRCm39) E943G probably damaging Het
Cyp2c54 C T 19: 40,036,032 (GRCm39) D293N probably benign Het
Cyp2f2 T C 7: 26,821,302 (GRCm39) S72P probably benign Het
Dip2c G A 13: 9,601,902 (GRCm39) probably null Het
Dock6 T C 9: 21,731,918 (GRCm39) T1158A probably benign Het
Dscaml1 G A 9: 45,583,941 (GRCm39) V469I probably benign Het
Efcab14 A G 4: 115,613,714 (GRCm39) T221A probably benign Het
Ehbp1 T C 11: 21,956,782 (GRCm39) *1207W probably null Het
Eln T C 5: 134,735,426 (GRCm39) K786E probably damaging Het
Fyb1 C T 15: 6,649,128 (GRCm39) P385S probably benign Het
Galr1 A G 18: 82,423,866 (GRCm39) I137T possibly damaging Het
Gcm1 A T 9: 77,966,999 (GRCm39) K73* probably null Het
Gemin5 T C 11: 58,032,480 (GRCm39) N775D probably damaging Het
Gm10754 G T 10: 97,518,089 (GRCm39) probably benign Het
Gpr37 T C 6: 25,669,137 (GRCm39) D569G probably damaging Het
Grina T A 15: 76,133,289 (GRCm39) Y286N probably damaging Het
Gtf3c1 C A 7: 125,292,310 (GRCm39) probably null Het
Kcnc4 C T 3: 107,355,534 (GRCm39) V305M probably benign Het
Kntc1 T C 5: 123,916,338 (GRCm39) F724L probably benign Het
Kpnb1 T C 11: 97,069,136 (GRCm39) Y249C probably damaging Het
Krt6b T C 15: 101,586,809 (GRCm39) T269A probably benign Het
Lamc1 T C 1: 153,097,380 (GRCm39) K1555E probably damaging Het
Maneal T C 4: 124,755,650 (GRCm39) Y104C probably damaging Het
Map1b T C 13: 99,567,679 (GRCm39) T1681A unknown Het
Mettl17 T C 14: 52,128,160 (GRCm39) L272P probably benign Het
Mib2 T A 4: 155,741,456 (GRCm39) S357C probably benign Het
Mmp19 C A 10: 128,634,047 (GRCm39) T316K possibly damaging Het
Mroh9 C T 1: 162,854,078 (GRCm39) G774E probably damaging Het
Myh1 T C 11: 67,096,325 (GRCm39) probably benign Het
Ncor2 C A 5: 125,104,202 (GRCm39) E963* probably null Het
Nol6 T A 4: 41,123,596 (GRCm39) T51S probably benign Het
Nsun3 A T 16: 62,555,732 (GRCm39) C265S probably damaging Het
Nup214 C T 2: 31,924,478 (GRCm39) S1669F probably damaging Het
Nutm2 T A 13: 50,623,517 (GRCm39) N71K probably damaging Het
Or10a5 T G 7: 106,635,356 (GRCm39) L5R probably benign Het
Or5p73 C T 7: 108,065,167 (GRCm39) T212I probably benign Het
Orc3 T A 4: 34,607,228 (GRCm39) E34V possibly damaging Het
Pcdhb13 T A 18: 37,575,889 (GRCm39) L89Q probably damaging Het
Polr3a A T 14: 24,502,616 (GRCm39) V1241E probably null Het
Prpf39 C T 12: 65,100,088 (GRCm39) P135S probably damaging Het
Psrc1 T C 3: 108,292,309 (GRCm39) V34A probably benign Het
Rab27a G A 9: 72,989,684 (GRCm39) V52M probably benign Het
Rassf9 A G 10: 102,381,895 (GRCm39) T424A probably benign Het
Ripor3 G T 2: 167,842,297 (GRCm39) R61S possibly damaging Het
Ryr3 C T 2: 112,466,867 (GRCm39) probably benign Het
Samd4b C T 7: 28,113,435 (GRCm39) G177R probably damaging Het
Setbp1 C T 18: 78,826,516 (GRCm39) V1366M probably benign Het
Smad1 G A 8: 80,070,359 (GRCm39) A393V probably benign Het
Tctn2 T C 5: 124,745,826 (GRCm39) noncoding transcript Het
Tmem45a A T 16: 56,631,965 (GRCm39) F218I possibly damaging Het
Tpte A T 8: 22,845,487 (GRCm39) R512S probably damaging Het
Trim37 T A 11: 87,020,585 (GRCm39) L22* probably null Het
Ttc6 A G 12: 57,783,916 (GRCm39) N1792D probably damaging Het
Ttn A G 2: 76,775,960 (GRCm39) M1694T probably damaging Het
Vmn1r181 T A 7: 23,684,137 (GRCm39) W201R probably damaging Het
Wdr74 C T 19: 8,715,592 (GRCm39) L198F possibly damaging Het
Zfp560 T C 9: 20,260,086 (GRCm39) T259A probably benign Het
Other mutations in Gli3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00417:Gli3 APN 13 15,818,884 (GRCm39) missense probably damaging 1.00
IGL00471:Gli3 APN 13 15,898,354 (GRCm39) critical splice donor site probably null
IGL00484:Gli3 APN 13 15,818,977 (GRCm39) missense possibly damaging 0.84
IGL00588:Gli3 APN 13 15,818,977 (GRCm39) missense possibly damaging 0.84
IGL01161:Gli3 APN 13 15,722,983 (GRCm39) critical splice acceptor site probably null
IGL01633:Gli3 APN 13 15,823,219 (GRCm39) missense probably damaging 1.00
IGL01799:Gli3 APN 13 15,900,746 (GRCm39) missense probably benign 0.00
IGL01861:Gli3 APN 13 15,899,910 (GRCm39) missense probably damaging 1.00
IGL02063:Gli3 APN 13 15,900,957 (GRCm39) missense possibly damaging 0.94
IGL02112:Gli3 APN 13 15,837,099 (GRCm39) missense probably damaging 1.00
IGL02255:Gli3 APN 13 15,823,304 (GRCm39) missense probably damaging 1.00
IGL02270:Gli3 APN 13 15,901,371 (GRCm39) utr 3 prime probably benign
IGL02336:Gli3 APN 13 15,894,874 (GRCm39) missense probably damaging 1.00
IGL02346:Gli3 APN 13 15,898,278 (GRCm39) missense probably damaging 1.00
IGL02744:Gli3 APN 13 15,788,471 (GRCm39) critical splice donor site probably null
IGL02877:Gli3 APN 13 15,899,327 (GRCm39) missense probably damaging 1.00
IGL02975:Gli3 APN 13 15,899,153 (GRCm39) missense probably damaging 1.00
IGL03018:Gli3 APN 13 15,834,717 (GRCm39) missense probably damaging 1.00
IGL03378:Gli3 APN 13 15,819,005 (GRCm39) missense probably damaging 1.00
IGL03406:Gli3 APN 13 15,823,166 (GRCm39) missense probably damaging 1.00
Capone UTSW 13 15,889,619 (GRCm39) missense probably damaging 1.00
Carpals UTSW 13 15,888,235 (GRCm39) critical splice donor site probably null
Ness UTSW 13 15,898,140 (GRCm39) missense probably damaging 1.00
FR4737:Gli3 UTSW 13 15,818,942 (GRCm39) missense probably damaging 1.00
R0110:Gli3 UTSW 13 15,899,370 (GRCm39) missense probably damaging 1.00
R0329:Gli3 UTSW 13 15,898,143 (GRCm39) missense probably damaging 0.98
R0330:Gli3 UTSW 13 15,898,143 (GRCm39) missense probably damaging 0.98
R0360:Gli3 UTSW 13 15,899,349 (GRCm39) missense probably benign 0.32
R0364:Gli3 UTSW 13 15,899,349 (GRCm39) missense probably benign 0.32
R0469:Gli3 UTSW 13 15,899,370 (GRCm39) missense probably damaging 1.00
R0616:Gli3 UTSW 13 15,836,991 (GRCm39) missense possibly damaging 0.75
R0639:Gli3 UTSW 13 15,899,300 (GRCm39) missense probably damaging 1.00
R1072:Gli3 UTSW 13 15,888,190 (GRCm39) missense probably damaging 1.00
R1257:Gli3 UTSW 13 15,900,581 (GRCm39) nonsense probably null
R1270:Gli3 UTSW 13 15,898,329 (GRCm39) missense probably benign 0.02
R1424:Gli3 UTSW 13 15,900,899 (GRCm39) missense probably benign 0.00
R1596:Gli3 UTSW 13 15,900,056 (GRCm39) missense possibly damaging 0.74
R1628:Gli3 UTSW 13 15,900,897 (GRCm39) missense probably benign 0.00
R1721:Gli3 UTSW 13 15,900,882 (GRCm39) missense probably benign 0.27
R1797:Gli3 UTSW 13 15,888,097 (GRCm39) missense probably damaging 0.99
R1813:Gli3 UTSW 13 15,823,276 (GRCm39) missense probably damaging 1.00
R1819:Gli3 UTSW 13 15,900,377 (GRCm39) nonsense probably null
R1988:Gli3 UTSW 13 15,900,965 (GRCm39) missense probably benign
R2132:Gli3 UTSW 13 15,900,134 (GRCm39) missense possibly damaging 0.74
R2352:Gli3 UTSW 13 15,836,977 (GRCm39) missense probably benign 0.02
R3085:Gli3 UTSW 13 15,835,526 (GRCm39) missense probably damaging 1.00
R3177:Gli3 UTSW 13 15,900,567 (GRCm39) missense probably benign 0.28
R3277:Gli3 UTSW 13 15,900,567 (GRCm39) missense probably benign 0.28
R4162:Gli3 UTSW 13 15,899,700 (GRCm39) missense possibly damaging 0.93
R4497:Gli3 UTSW 13 15,898,156 (GRCm39) missense possibly damaging 0.74
R4526:Gli3 UTSW 13 15,888,216 (GRCm39) missense probably damaging 1.00
R4979:Gli3 UTSW 13 15,899,049 (GRCm39) missense possibly damaging 0.87
R5327:Gli3 UTSW 13 15,723,092 (GRCm39) missense probably damaging 0.99
R5395:Gli3 UTSW 13 15,889,535 (GRCm39) missense probably damaging 1.00
R5494:Gli3 UTSW 13 15,900,567 (GRCm39) missense probably benign 0.28
R5609:Gli3 UTSW 13 15,723,038 (GRCm39) missense possibly damaging 0.82
R5718:Gli3 UTSW 13 15,652,750 (GRCm39) critical splice donor site probably null
R5810:Gli3 UTSW 13 15,818,894 (GRCm39) missense probably damaging 0.99
R5896:Gli3 UTSW 13 15,900,765 (GRCm39) missense probably benign 0.00
R5930:Gli3 UTSW 13 15,723,210 (GRCm39) missense probably damaging 1.00
R5964:Gli3 UTSW 13 15,900,747 (GRCm39) nonsense probably null
R5985:Gli3 UTSW 13 15,898,140 (GRCm39) missense probably damaging 1.00
R6224:Gli3 UTSW 13 15,899,730 (GRCm39) missense probably benign
R6278:Gli3 UTSW 13 15,899,698 (GRCm39) missense possibly damaging 0.69
R6330:Gli3 UTSW 13 15,899,317 (GRCm39) missense probably damaging 1.00
R6383:Gli3 UTSW 13 15,898,140 (GRCm39) missense probably damaging 1.00
R6523:Gli3 UTSW 13 15,888,235 (GRCm39) critical splice donor site probably null
R7072:Gli3 UTSW 13 15,900,280 (GRCm39) missense possibly damaging 0.51
R7085:Gli3 UTSW 13 15,889,647 (GRCm39) missense probably damaging 1.00
R7228:Gli3 UTSW 13 15,899,087 (GRCm39) missense probably benign 0.00
R7327:Gli3 UTSW 13 15,900,144 (GRCm39) missense probably benign 0.02
R7451:Gli3 UTSW 13 15,900,876 (GRCm39) missense possibly damaging 0.50
R7974:Gli3 UTSW 13 15,900,841 (GRCm39) missense probably benign 0.00
R8167:Gli3 UTSW 13 15,900,228 (GRCm39) missense probably benign 0.00
R8170:Gli3 UTSW 13 15,894,793 (GRCm39) missense probably benign
R8199:Gli3 UTSW 13 15,900,576 (GRCm39) missense probably benign 0.08
R8247:Gli3 UTSW 13 15,901,360 (GRCm39) missense possibly damaging 0.82
R8332:Gli3 UTSW 13 15,888,133 (GRCm39) missense possibly damaging 0.58
R8347:Gli3 UTSW 13 15,898,110 (GRCm39) missense probably damaging 1.00
R8559:Gli3 UTSW 13 15,834,717 (GRCm39) missense probably damaging 1.00
R8676:Gli3 UTSW 13 15,889,619 (GRCm39) missense probably damaging 1.00
R8905:Gli3 UTSW 13 15,901,116 (GRCm39) missense probably benign 0.01
R9099:Gli3 UTSW 13 15,901,320 (GRCm39) missense probably damaging 1.00
R9260:Gli3 UTSW 13 15,899,675 (GRCm39) missense probably damaging 0.99
R9317:Gli3 UTSW 13 15,889,658 (GRCm39) missense probably damaging 1.00
R9475:Gli3 UTSW 13 15,900,296 (GRCm39) missense possibly damaging 0.87
R9546:Gli3 UTSW 13 15,788,443 (GRCm39) missense probably benign 0.00
R9571:Gli3 UTSW 13 15,900,858 (GRCm39) missense probably benign 0.00
R9621:Gli3 UTSW 13 15,901,253 (GRCm39) missense probably benign 0.01
R9704:Gli3 UTSW 13 15,898,058 (GRCm39) missense probably damaging 1.00
R9787:Gli3 UTSW 13 15,900,386 (GRCm39) missense probably damaging 0.96
RF010:Gli3 UTSW 13 15,900,954 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCCAGGGACTGACAGACAGGAT -3'
(R):5'- TGATTCAGTGACTCCAGGAGCAGAT -3'

Sequencing Primer
(F):5'- tgattttgagccgctggac -3'
(R):5'- ACTCCAGGAGCAGATAGAGC -3'
Posted On 2014-03-28