Incidental Mutation 'R5888:Supt20'
ID 457773
Institutional Source Beutler Lab
Gene Symbol Supt20
Ensembl Gene ENSMUSG00000027751
Gene Name SPT20 SAGA complex component
Synonyms p38IP, Fam48a, p38 interacting protein, D3Ertd300e
MMRRC Submission 044089-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.929) question?
Stock # R5888 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 54600228-54636187 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 54619628 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tryptophan to Leucine at position 370 (W370L)
Ref Sequence ENSEMBL: ENSMUSP00000143059 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029315] [ENSMUST00000170552] [ENSMUST00000178832] [ENSMUST00000197502] [ENSMUST00000199674] [ENSMUST00000200439] [ENSMUST00000200441]
AlphaFold Q7TT00
Predicted Effect probably benign
Transcript: ENSMUST00000029315
SMART Domains Protein: ENSMUSP00000029315
Gene: ENSMUSG00000027751

DomainStartEndE-ValueType
low complexity region 65 78 N/A INTRINSIC
low complexity region 107 159 N/A INTRINSIC
coiled coil region 201 230 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000170552
AA Change: W371L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000131454
Gene: ENSMUSG00000027751
AA Change: W371L

DomainStartEndE-ValueType
Pfam:Spt20 63 229 6.8e-47 PFAM
low complexity region 425 441 N/A INTRINSIC
low complexity region 468 477 N/A INTRINSIC
low complexity region 488 502 N/A INTRINSIC
low complexity region 515 526 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000178832
Predicted Effect probably benign
Transcript: ENSMUST00000197502
AA Change: W370L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000143750
Gene: ENSMUSG00000027751
AA Change: W370L

DomainStartEndE-ValueType
low complexity region 45 56 N/A INTRINSIC
Pfam:Spt20 62 227 1.9e-43 PFAM
low complexity region 424 440 N/A INTRINSIC
low complexity region 467 476 N/A INTRINSIC
low complexity region 487 501 N/A INTRINSIC
low complexity region 512 532 N/A INTRINSIC
low complexity region 574 587 N/A INTRINSIC
low complexity region 632 680 N/A INTRINSIC
coiled coil region 722 751 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000198745
Predicted Effect probably benign
Transcript: ENSMUST00000199674
AA Change: W370L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000142948
Gene: ENSMUSG00000027751
AA Change: W370L

DomainStartEndE-ValueType
low complexity region 45 56 N/A INTRINSIC
Pfam:Spt20 59 227 3.3e-39 PFAM
low complexity region 424 442 N/A INTRINSIC
low complexity region 466 475 N/A INTRINSIC
low complexity region 486 500 N/A INTRINSIC
low complexity region 513 524 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000200439
AA Change: W370L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000143059
Gene: ENSMUSG00000027751
AA Change: W370L

DomainStartEndE-ValueType
low complexity region 45 56 N/A INTRINSIC
Pfam:Spt20 59 227 2.7e-42 PFAM
low complexity region 424 440 N/A INTRINSIC
low complexity region 467 476 N/A INTRINSIC
low complexity region 487 501 N/A INTRINSIC
low complexity region 514 525 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200450
Predicted Effect probably benign
Transcript: ENSMUST00000200441
SMART Domains Protein: ENSMUSP00000143231
Gene: ENSMUSG00000027751

DomainStartEndE-ValueType
low complexity region 65 78 N/A INTRINSIC
low complexity region 123 171 N/A INTRINSIC
coiled coil region 213 242 N/A INTRINSIC
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.2%
  • 20x: 94.9%
Validation Efficiency 94% (96/102)
MGI Phenotype PHENOTYPE: The incompletely penetrant homozygous phenotype of a splice-site mutation may include retinal epithelium expansion over the dorsal half of the eye, exencephaly, spina bifida, gastrulation defects and/or aberrant somite and mesoderm development. A few mutants survive postnatally and appear normal. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 92 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adcy1 T A 11: 7,089,095 (GRCm39) V503E possibly damaging Het
Alk C A 17: 72,181,938 (GRCm39) V1362L probably damaging Het
Ankrd55 T A 13: 112,492,453 (GRCm39) I208N possibly damaging Het
Asap2 T A 12: 21,268,191 (GRCm39) I319N probably damaging Het
Atp11b T C 3: 35,891,696 (GRCm39) I1036T probably benign Het
B4gat1 T C 19: 5,089,560 (GRCm39) F186L probably benign Het
C3 T A 17: 57,521,831 (GRCm39) T1079S probably damaging Het
Cacul1 G T 19: 60,525,902 (GRCm39) T287K possibly damaging Het
Cbr3 G C 16: 93,487,614 (GRCm39) G266R probably damaging Het
Cd63 T A 10: 128,748,160 (GRCm39) probably null Het
Chd7 G A 4: 8,866,382 (GRCm39) M851I probably damaging Het
Chst13 T A 6: 90,286,554 (GRCm39) H136L probably benign Het
Cyp2d22 T C 15: 82,258,014 (GRCm39) T179A probably benign Het
Dclre1b A T 3: 103,711,053 (GRCm39) V286E probably damaging Het
Defb45 G A 2: 152,435,154 (GRCm39) probably benign Het
Dlg1 T C 16: 31,610,704 (GRCm39) probably null Het
Dock3 A G 9: 106,901,002 (GRCm39) V321A probably benign Het
Dytn A T 1: 63,716,396 (GRCm39) V59E possibly damaging Het
Efcab3 T C 11: 104,612,227 (GRCm39) probably benign Het
Eif2ak1 A G 5: 143,823,733 (GRCm39) I393M probably damaging Het
Fam83g A T 11: 61,593,420 (GRCm39) E318V probably benign Het
Fbxo34 T A 14: 47,767,176 (GRCm39) F179I probably damaging Het
Fmo5 T A 3: 97,549,041 (GRCm39) Y230N probably benign Het
Fzd9 T G 5: 135,278,317 (GRCm39) probably null Het
Gata2 T C 6: 88,177,722 (GRCm39) S251P probably benign Het
Gigyf1 A G 5: 137,523,959 (GRCm39) D1043G probably damaging Het
Gm10322 T A 10: 59,452,125 (GRCm39) S81T probably benign Het
Gm15517 A T 7: 43,910,066 (GRCm39) probably benign Het
Haus4 T C 14: 54,781,676 (GRCm39) T232A probably benign Het
Hgfac A T 5: 35,202,751 (GRCm39) H417L probably damaging Het
Iqgap2 T C 13: 95,772,118 (GRCm39) K1354E possibly damaging Het
Kcnk12 C A 17: 88,054,077 (GRCm39) R195L probably benign Het
Kcnn2 A T 18: 45,725,412 (GRCm39) I303F probably damaging Het
Kcnt1 T C 2: 25,798,122 (GRCm39) F879S probably damaging Het
Kndc1 T C 7: 139,475,133 (GRCm39) F11L probably benign Het
Kpna7 A G 5: 144,926,605 (GRCm39) F449S probably damaging Het
Krt77 G T 15: 101,773,888 (GRCm39) N255K probably benign Het
Lair1 A T 7: 4,013,844 (GRCm39) D134E probably damaging Het
Loxhd1 T C 18: 77,490,211 (GRCm39) V1318A probably damaging Het
Marchf10 A T 11: 105,292,972 (GRCm39) V145D possibly damaging Het
Mcpt1 T A 14: 56,256,969 (GRCm39) M169K probably benign Het
Mdc1 T A 17: 36,158,712 (GRCm39) V364E probably benign Het
Mfsd11 T C 11: 116,762,210 (GRCm39) F270S probably damaging Het
Mfsd4b2 T G 10: 39,798,031 (GRCm39) D108A probably benign Het
Mink1 A T 11: 70,500,885 (GRCm39) probably benign Het
Mmp25 T C 17: 23,850,048 (GRCm39) Y504C probably damaging Het
Ms4a13 C T 19: 11,168,870 (GRCm39) V52I probably benign Het
Msh4 C T 3: 153,573,360 (GRCm39) probably null Het
Muc5b T G 7: 141,412,158 (GRCm39) S1701R unknown Het
Naalad2 A T 9: 18,241,937 (GRCm39) S656T probably benign Het
Ncapd2 T C 6: 125,164,052 (GRCm39) Y64C probably damaging Het
Ncapg2 T A 12: 116,389,420 (GRCm39) S347T possibly damaging Het
Ndufb11b T C 15: 81,864,872 (GRCm39) S38P probably benign Het
Nipal4 T C 11: 46,042,166 (GRCm39) T172A probably damaging Het
Nrros T C 16: 31,961,905 (GRCm39) K652R probably benign Het
Nrxn3 G T 12: 89,478,855 (GRCm39) A983S possibly damaging Het
Or4a76 T A 2: 89,461,143 (GRCm39) Y33F probably damaging Het
Or4ac1-ps1 T C 2: 88,370,588 (GRCm39) noncoding transcript Het
Or4c115 T A 2: 88,928,269 (GRCm39) M1L probably damaging Het
Or4k77 T C 2: 111,199,088 (GRCm39) M37T probably benign Het
Or51m1 A G 7: 103,578,239 (GRCm39) T70A possibly damaging Het
Or8g24 A T 9: 38,989,263 (GRCm39) Y259* probably null Het
Or8k37 A C 2: 86,469,488 (GRCm39) L188R probably damaging Het
P2rx4 T A 5: 122,857,228 (GRCm39) S155T probably benign Het
P2rx4 T G 5: 122,865,271 (GRCm39) Y299D probably damaging Het
Pcsk6 A T 7: 65,693,372 (GRCm39) L7F probably null Het
Pdss2 T C 10: 43,097,793 (GRCm39) silent Het
Pfkl A G 10: 77,827,204 (GRCm39) V494A possibly damaging Het
Prep G T 10: 44,943,460 (GRCm39) D12Y possibly damaging Het
Prg4 A G 1: 150,328,101 (GRCm39) F188S probably damaging Het
Ripor3 T C 2: 167,839,207 (GRCm39) Y98C probably damaging Het
Rnf216 T A 5: 143,054,069 (GRCm39) probably null Het
Rnf24 A G 2: 131,164,165 (GRCm39) probably benign Het
Rps18-ps6 G A 13: 97,896,901 (GRCm39) R66* probably null Het
Scn3a A G 2: 65,327,742 (GRCm39) M916T probably benign Het
Scnm1 T C 3: 95,037,596 (GRCm39) I157V probably benign Het
Sh2b3 C G 5: 121,967,084 (GRCm39) R10P possibly damaging Het
Slc25a27 T C 17: 43,960,585 (GRCm39) D211G probably damaging Het
Slc36a4 A T 9: 15,638,324 (GRCm39) Y250F probably damaging Het
Slc4a1 T A 11: 102,247,351 (GRCm39) E448V probably damaging Het
Slit1 C A 19: 41,731,735 (GRCm39) C38F probably damaging Het
Spock3 T A 8: 63,808,334 (GRCm39) N410K unknown Het
Tas2r139 T A 6: 42,118,430 (GRCm39) N187K probably damaging Het
Tbc1d9b G A 11: 50,031,311 (GRCm39) V111I probably benign Het
Thsd7b T A 1: 130,138,057 (GRCm39) Y1578* probably null Het
Tln2 T A 9: 67,136,685 (GRCm39) I1267F probably damaging Het
Tnk2 G A 16: 32,490,185 (GRCm39) V363I probably damaging Het
Ttc32 A G 12: 9,085,870 (GRCm39) K139R possibly damaging Het
Vmn1r30 G C 6: 58,412,550 (GRCm39) T94S possibly damaging Het
Vmn1r90 G A 7: 14,295,780 (GRCm39) T106I probably damaging Het
Zfp677 T A 17: 21,618,520 (GRCm39) C526S probably damaging Het
Zfp831 T G 2: 174,485,420 (GRCm39) S32A probably benign Het
Other mutations in Supt20
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00518:Supt20 APN 3 54,622,590 (GRCm39) missense probably damaging 0.98
IGL01781:Supt20 APN 3 54,602,626 (GRCm39) start codon destroyed probably null 0.47
IGL02510:Supt20 APN 3 54,622,945 (GRCm39) intron probably benign
IGL02656:Supt20 APN 3 54,615,816 (GRCm39) missense probably damaging 1.00
IGL02958:Supt20 APN 3 54,621,144 (GRCm39) intron probably benign
IGL03036:Supt20 APN 3 54,616,723 (GRCm39) nonsense probably null
IGL03128:Supt20 APN 3 54,615,708 (GRCm39) missense probably benign 0.05
IGL03164:Supt20 APN 3 54,620,609 (GRCm39) missense probably benign 0.01
FR4304:Supt20 UTSW 3 54,635,085 (GRCm39) nonsense probably null
FR4304:Supt20 UTSW 3 54,635,068 (GRCm39) small insertion probably benign
FR4304:Supt20 UTSW 3 54,635,083 (GRCm39) small insertion probably benign
FR4449:Supt20 UTSW 3 54,635,070 (GRCm39) small insertion probably benign
FR4548:Supt20 UTSW 3 54,635,094 (GRCm39) small insertion probably benign
FR4548:Supt20 UTSW 3 54,635,078 (GRCm39) small insertion probably benign
FR4548:Supt20 UTSW 3 54,635,085 (GRCm39) small insertion probably benign
FR4589:Supt20 UTSW 3 54,635,092 (GRCm39) small insertion probably benign
FR4589:Supt20 UTSW 3 54,635,072 (GRCm39) small insertion probably benign
FR4589:Supt20 UTSW 3 54,635,076 (GRCm39) small insertion probably benign
FR4737:Supt20 UTSW 3 54,635,082 (GRCm39) small insertion probably benign
FR4737:Supt20 UTSW 3 54,635,078 (GRCm39) small insertion probably benign
FR4737:Supt20 UTSW 3 54,635,079 (GRCm39) small insertion probably benign
R0383:Supt20 UTSW 3 54,610,570 (GRCm39) nonsense probably null
R0675:Supt20 UTSW 3 54,614,390 (GRCm39) missense probably damaging 1.00
R0744:Supt20 UTSW 3 54,622,122 (GRCm39) missense probably damaging 1.00
R0968:Supt20 UTSW 3 54,615,821 (GRCm39) intron probably benign
R1075:Supt20 UTSW 3 54,614,362 (GRCm39) nonsense probably null
R1689:Supt20 UTSW 3 54,619,583 (GRCm39) nonsense probably null
R1772:Supt20 UTSW 3 54,617,841 (GRCm39) missense probably damaging 1.00
R1779:Supt20 UTSW 3 54,622,164 (GRCm39) missense probably benign 0.00
R1829:Supt20 UTSW 3 54,635,079 (GRCm39) utr 3 prime probably benign
R3236:Supt20 UTSW 3 54,616,501 (GRCm39) missense possibly damaging 0.94
R3237:Supt20 UTSW 3 54,616,501 (GRCm39) missense possibly damaging 0.94
R4989:Supt20 UTSW 3 54,602,555 (GRCm39) utr 5 prime probably benign
R5180:Supt20 UTSW 3 54,616,506 (GRCm39) missense probably benign 0.00
R5188:Supt20 UTSW 3 54,617,849 (GRCm39) missense possibly damaging 0.87
R5423:Supt20 UTSW 3 54,616,746 (GRCm39) missense probably damaging 1.00
R5627:Supt20 UTSW 3 54,620,611 (GRCm39) missense possibly damaging 0.86
R5995:Supt20 UTSW 3 54,616,474 (GRCm39) missense probably damaging 0.97
R6316:Supt20 UTSW 3 54,635,069 (GRCm39) small insertion probably benign
R6623:Supt20 UTSW 3 54,625,715 (GRCm39) missense possibly damaging 0.93
R6713:Supt20 UTSW 3 54,606,022 (GRCm39) missense possibly damaging 0.89
R6874:Supt20 UTSW 3 54,635,175 (GRCm39) splice site probably null
R6988:Supt20 UTSW 3 54,606,018 (GRCm39) missense probably damaging 1.00
R7149:Supt20 UTSW 3 54,635,832 (GRCm39) missense unknown
R7592:Supt20 UTSW 3 54,614,543 (GRCm39) missense probably damaging 0.97
R7940:Supt20 UTSW 3 54,620,620 (GRCm39) missense probably benign 0.04
R8480:Supt20 UTSW 3 54,614,537 (GRCm39) missense probably damaging 1.00
R8550:Supt20 UTSW 3 54,623,063 (GRCm39) missense possibly damaging 0.48
R8935:Supt20 UTSW 3 54,634,988 (GRCm39) critical splice acceptor site probably null
R9412:Supt20 UTSW 3 54,635,069 (GRCm39) small deletion probably benign
R9414:Supt20 UTSW 3 54,610,504 (GRCm39) missense probably damaging 1.00
R9694:Supt20 UTSW 3 54,623,015 (GRCm39) missense probably benign 0.02
RF001:Supt20 UTSW 3 54,635,083 (GRCm39) small insertion probably benign
RF009:Supt20 UTSW 3 54,635,083 (GRCm39) small insertion probably benign
RF010:Supt20 UTSW 3 54,635,083 (GRCm39) small insertion probably benign
RF014:Supt20 UTSW 3 54,635,086 (GRCm39) small insertion probably benign
RF026:Supt20 UTSW 3 54,635,091 (GRCm39) nonsense probably null
RF026:Supt20 UTSW 3 54,635,068 (GRCm39) small insertion probably benign
RF032:Supt20 UTSW 3 54,635,087 (GRCm39) small insertion probably benign
RF038:Supt20 UTSW 3 54,635,068 (GRCm39) small insertion probably benign
RF045:Supt20 UTSW 3 54,635,087 (GRCm39) small insertion probably benign
RF052:Supt20 UTSW 3 54,635,086 (GRCm39) small insertion probably benign
Predicted Primers PCR Primer
(F):5'- CCTTTAGTGCCATGTATATAGCAGAC -3'
(R):5'- ACACACTGTTCTGTATCAGGTACC -3'

Sequencing Primer
(F):5'- CCATGTATATAGCAGACAGAAGTTAG -3'
(R):5'- TCATCAGCTAGCAAGCAG -3'
Posted On 2017-02-15