Incidental Mutation 'R1772:Supt20'
ID 196665
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 039803-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.939) question?
Stock # R1772 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 54600228-54636187 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 54617841 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 314 (V314E)
Ref Sequence ENSEMBL: ENSMUSP00000143750 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029315] [ENSMUST00000170552] [ENSMUST00000178832] [ENSMUST00000197502] [ENSMUST00000199652] [ENSMUST00000199674] [ENSMUST00000200439] [ENSMUST00000200441] [ENSMUST00000199655]
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 possibly damaging
Transcript: ENSMUST00000170552
AA Change: V315E

PolyPhen 2 Score 0.833 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000131454
Gene: ENSMUSG00000027751
AA Change: V315E

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 damaging
Transcript: ENSMUST00000197502
AA Change: V314E

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000143750
Gene: ENSMUSG00000027751
AA Change: V314E

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: ENSMUST00000199652
SMART Domains Protein: ENSMUSP00000142648
Gene: ENSMUSG00000027751

DomainStartEndE-ValueType
low complexity region 45 56 N/A INTRINSIC
Pfam:Spt20 59 181 1.2e-25 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000199674
AA Change: V314E

PolyPhen 2 Score 0.881 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000142948
Gene: ENSMUSG00000027751
AA Change: V314E

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: V314E

PolyPhen 2 Score 0.064 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000143059
Gene: ENSMUSG00000027751
AA Change: V314E

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
Predicted Effect probably benign
Transcript: ENSMUST00000199655
SMART Domains Protein: ENSMUSP00000143520
Gene: ENSMUSG00000027751

DomainStartEndE-ValueType
low complexity region 45 56 N/A INTRINSIC
Pfam:Spt20 62 140 5.3e-17 PFAM
Meta Mutation Damage Score 0.0897 question?
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 97.0%
  • 10x: 95.6%
  • 20x: 93.5%
Validation Efficiency 97% (107/110)
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: 106 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgb G T 10: 10,258,465 (GRCm39) probably benign Het
Aldh1a7 T C 19: 20,693,383 (GRCm39) K179E probably damaging Het
Angptl7 G A 4: 148,581,883 (GRCm39) R168C probably damaging Het
Atp8b1 T A 18: 64,706,563 (GRCm39) I208F possibly damaging Het
Bco1 A G 8: 117,857,347 (GRCm39) Y438C probably benign Het
Bltp1 T C 3: 37,013,581 (GRCm39) S1937P probably damaging Het
Btrc A C 19: 45,501,100 (GRCm39) K218Q probably damaging Het
Cct8l1 G A 5: 25,722,697 (GRCm39) V471M probably damaging Het
Cd180 C T 13: 102,842,750 (GRCm39) L599F probably benign Het
Cd300e T C 11: 114,945,344 (GRCm39) N150S probably benign Het
Clcn1 C A 6: 42,271,079 (GRCm39) T281K probably damaging Het
Cnnm3 T C 1: 36,558,038 (GRCm39) S417P probably damaging Het
Cspg4 T A 9: 56,804,776 (GRCm39) S1862R probably benign Het
Cspg5 A T 9: 110,091,206 (GRCm39) N432Y probably damaging Het
Cyp2r1 T A 7: 114,152,451 (GRCm39) I169F probably damaging Het
D130043K22Rik T A 13: 25,059,982 (GRCm39) S618T probably damaging Het
Diaph3 G A 14: 87,202,985 (GRCm39) P635L probably damaging Het
Dlg1 A G 16: 31,484,485 (GRCm39) I38V possibly damaging Het
Dlk1 T G 12: 109,425,685 (GRCm39) V186G probably damaging Het
Dmxl2 T C 9: 54,330,508 (GRCm39) probably benign Het
Dnajc17 G A 2: 119,014,164 (GRCm39) R132* probably null Het
Dock9 G T 14: 121,847,210 (GRCm39) N1042K probably benign Het
Dok7 A T 5: 35,243,994 (GRCm39) Q511L probably damaging Het
Espnl G A 1: 91,272,325 (GRCm39) E562K possibly damaging Het
Evi5 G A 5: 107,943,707 (GRCm39) T562I probably benign Het
Exd2 T A 12: 80,536,253 (GRCm39) D294E probably benign Het
Fbn1 A T 2: 125,245,148 (GRCm39) D246E possibly damaging Het
Fbxw16 A T 9: 109,268,650 (GRCm39) W247R possibly damaging Het
Fcer1a A G 1: 173,053,004 (GRCm39) I64T probably benign Het
Fcgbp C A 7: 27,804,600 (GRCm39) Q1903K possibly damaging Het
Fmn1 A G 2: 113,195,700 (GRCm39) S467G unknown Het
Fndc7 T A 3: 108,777,850 (GRCm39) T369S probably damaging Het
Fnta T C 8: 26,490,994 (GRCm39) probably benign Het
Gak A T 5: 108,754,758 (GRCm39) H289Q probably damaging Het
Gas2l3 A G 10: 89,252,876 (GRCm39) probably benign Het
Gbp8 T C 5: 105,163,987 (GRCm39) N437S probably benign Het
Gk5 G A 9: 96,032,850 (GRCm39) probably null Het
Hid1 A T 11: 115,239,299 (GRCm39) V788E probably damaging Het
Hmcn1 T C 1: 150,439,319 (GRCm39) T5505A probably damaging Het
Igf1r T A 7: 67,844,822 (GRCm39) M865K probably benign Het
Katnal2 G A 18: 77,090,233 (GRCm39) T258I probably damaging Het
Kdm3b A T 18: 34,936,557 (GRCm39) I280L probably benign Het
Kif24 A G 4: 41,409,787 (GRCm39) V382A probably damaging Het
Kif2a A T 13: 107,114,640 (GRCm39) probably benign Het
Klhl10 A G 11: 100,333,022 (GRCm39) I56V probably benign Het
Klk6 C T 7: 43,478,695 (GRCm39) Q201* probably null Het
Klra3 A T 6: 130,300,671 (GRCm39) S233T probably benign Het
Krt9 A T 11: 100,082,131 (GRCm39) M223K probably damaging Het
Lama4 G A 10: 38,936,220 (GRCm39) E632K probably benign Het
Lamb1 T C 12: 31,328,524 (GRCm39) Y163H probably damaging Het
Lipo3 A G 19: 33,764,821 (GRCm39) I11T probably benign Het
Lix1l T A 3: 96,531,207 (GRCm39) H333Q possibly damaging Het
Mal2 T A 15: 54,451,783 (GRCm39) M68K probably damaging Het
Map2k2 T C 10: 80,956,934 (GRCm39) I104T probably damaging Het
Matn2 T C 15: 34,428,931 (GRCm39) V765A probably damaging Het
Mptx2 T A 1: 173,102,040 (GRCm39) K216N probably damaging Het
Mup5 C T 4: 61,750,578 (GRCm39) probably null Het
Mycbp2 A G 14: 103,419,855 (GRCm39) Y2494H probably damaging Het
Myh3 G A 11: 66,990,220 (GRCm39) D1622N probably benign Het
Myo6 T C 9: 80,177,331 (GRCm39) I609T possibly damaging Het
Ndst1 G A 18: 60,835,909 (GRCm39) T458I probably damaging Het
Neb A T 2: 52,125,689 (GRCm39) Y3622N probably damaging Het
Ntm A G 9: 29,090,396 (GRCm39) Y108H probably benign Het
Or13c3 T G 4: 52,855,730 (GRCm39) K261T probably benign Het
Or1a1b T C 11: 74,097,398 (GRCm39) I215V probably benign Het
Or52e19 T C 7: 102,959,449 (GRCm39) Y174H possibly damaging Het
Pappa2 T A 1: 158,641,938 (GRCm39) I1373F possibly damaging Het
Pear1 A G 3: 87,661,799 (GRCm39) probably benign Het
Phc3 C T 3: 31,015,969 (GRCm39) A81T probably damaging Het
Pmepa1 A G 2: 173,076,153 (GRCm39) S105P probably damaging Het
Ppp6r1 T C 7: 4,645,030 (GRCm39) I248V probably benign Het
Prdm4 G A 10: 85,729,256 (GRCm39) T717I probably damaging Het
Prom1 T C 5: 44,168,566 (GRCm39) T669A probably benign Het
Ptpn5 T A 7: 46,740,516 (GRCm39) I96F probably benign Het
Ptpro T C 6: 137,407,741 (GRCm39) L922P probably damaging Het
Reck A T 4: 43,890,982 (GRCm39) H40L probably benign Het
Rreb1 T A 13: 38,114,899 (GRCm39) C753S probably benign Het
Sacs T C 14: 61,448,346 (GRCm39) L3464P probably damaging Het
Samsn1 A T 16: 75,667,663 (GRCm39) D304E probably benign Het
Scgb2b3 T C 7: 31,059,621 (GRCm39) N51S possibly damaging Het
Shroom3 T C 5: 93,088,515 (GRCm39) S341P probably damaging Het
Siglece T C 7: 43,308,717 (GRCm39) D212G probably damaging Het
Sirpa A G 2: 129,458,376 (GRCm39) T331A probably damaging Het
Spata21 T C 4: 140,838,607 (GRCm39) S553P possibly damaging Het
Speer4b T A 5: 27,705,236 (GRCm39) probably benign Het
Srgap2 T C 1: 131,247,376 (GRCm39) D552G probably damaging Het
Stab2 A G 10: 86,790,098 (GRCm39) I556T probably benign Het
Strip1 C T 3: 107,534,047 (GRCm39) probably null Het
Stxbp6 T A 12: 44,949,653 (GRCm39) D92V probably damaging Het
Styx A G 14: 45,594,215 (GRCm39) K46E probably damaging Het
Syne2 T A 12: 75,985,503 (GRCm39) D1650E probably benign Het
Szt2 T A 4: 118,262,714 (GRCm39) K21M probably damaging Het
Tbx4 A T 11: 85,802,033 (GRCm39) H222L probably damaging Het
Tcstv1b T A 13: 120,634,725 (GRCm39) D2E probably benign Het
Tmx3 A T 18: 90,551,121 (GRCm39) I254L probably benign Het
Tns2 C T 15: 102,017,369 (GRCm39) R281C probably damaging Het
Trpv2 A T 11: 62,485,052 (GRCm39) probably benign Het
Ubap2 A G 4: 41,202,380 (GRCm39) S683P probably benign Het
Ube2d3 C T 3: 135,170,972 (GRCm39) R139W probably benign Het
Ubox5 G T 2: 130,433,794 (GRCm39) Q518K probably benign Het
Usp42 T C 5: 143,702,857 (GRCm39) N588S probably damaging Het
Vars2 G A 17: 35,970,976 (GRCm39) T618M probably damaging Het
Wfdc17 A T 11: 83,595,730 (GRCm39) N65Y probably damaging Het
Zbtb38 G A 9: 96,570,094 (GRCm39) P330L probably damaging Het
Zfp385a C T 15: 103,224,308 (GRCm39) probably null Het
Zfp637 T A 6: 117,822,373 (GRCm39) L167H probably damaging 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
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
R5888:Supt20 UTSW 3 54,619,628 (GRCm39) missense probably benign
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'- CATCTGTAGTCCCACATGCGACAC -3'
(R):5'- ATTTTCCTGAAGCCCACAAGTACTCC -3'

Sequencing Primer
(F):5'- CTGCTAGTTGAGACCCTTGT -3'
(R):5'- tgggcagtgaaagccag -3'
Posted On 2014-05-23