Incidental Mutation 'R5423:Supt20'
ID 426686
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 042989-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.939) question?
Stock # R5423 (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 54616746 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 306 (V306E)
Ref Sequence ENSEMBL: ENSMUSP00000143750 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029315] [ENSMUST00000170552] [ENSMUST00000178832] [ENSMUST00000197502] [ENSMUST00000199652] [ENSMUST00000199674] [ENSMUST00000200439] [ENSMUST00000199655] [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 damaging
Transcript: ENSMUST00000170552
AA Change: V307E

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000131454
Gene: ENSMUSG00000027751
AA Change: V307E

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: V306E

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000143750
Gene: ENSMUSG00000027751
AA Change: V306E

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 probably damaging
Transcript: ENSMUST00000199674
AA Change: V306E

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000142948
Gene: ENSMUSG00000027751
AA Change: V306E

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 damaging
Transcript: ENSMUST00000200439
AA Change: V306E

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000143059
Gene: ENSMUSG00000027751
AA Change: V306E

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: 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
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 0.4715 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.3%
Validation Efficiency 98% (60/61)
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: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acyp2 C T 11: 30,456,354 (GRCm39) E98K possibly damaging Het
Adam22 C A 5: 8,140,182 (GRCm39) G202W probably damaging Het
Adamts9 A G 6: 92,857,678 (GRCm39) I289T possibly damaging Het
Ak4 T G 4: 101,317,760 (GRCm39) I110S probably damaging Het
Arhgap9 T G 10: 127,165,418 (GRCm39) I609S probably damaging Het
Arid4a C A 12: 71,116,634 (GRCm39) S242* probably null Het
Ceacam1 T G 7: 25,173,951 (GRCm39) I235L probably benign Het
Chil3 T C 3: 106,055,978 (GRCm39) D365G probably damaging Het
Ckap2 A C 8: 22,667,212 (GRCm39) S216R probably benign Het
Cyp2e1 G T 7: 140,350,031 (GRCm39) V239L probably benign Het
Dnah7b T A 1: 46,397,431 (GRCm39) M3954K probably benign Het
Ercc6l2 A T 13: 64,020,072 (GRCm39) probably benign Het
Etv5 T C 16: 22,202,404 (GRCm39) D468G probably damaging Het
Fbxo44 T A 4: 148,238,686 (GRCm39) I213F probably benign Het
Gm5084 A G 13: 60,360,356 (GRCm39) noncoding transcript Het
Gpr17 G A 18: 32,080,694 (GRCm39) T123I probably damaging Het
Grin3a A G 4: 49,770,376 (GRCm39) probably benign Het
H2-D1 T G 17: 35,484,883 (GRCm39) L248R probably damaging Het
Hmcn1 T C 1: 150,577,723 (GRCm39) I2013V probably damaging Het
Hp1bp3 A T 4: 137,953,208 (GRCm39) D84V probably damaging Het
Ift140 T C 17: 25,252,059 (GRCm39) F33S probably damaging Het
Inhbc C G 10: 127,193,296 (GRCm39) C240S probably damaging Het
Iqgap1 T A 7: 80,449,610 (GRCm39) E62V probably damaging Het
Kcna4 G A 2: 107,126,151 (GRCm39) W295* probably null Het
Kdm4a C T 4: 117,996,105 (GRCm39) A975T probably damaging Het
Lrrtm3 T C 10: 63,923,931 (GRCm39) D412G possibly damaging Het
Midn A C 10: 79,991,027 (GRCm39) I346L probably benign Het
Ndufa10 C T 1: 92,390,042 (GRCm39) D259N probably benign Het
Nefh C A 11: 4,890,985 (GRCm39) A545S possibly damaging Het
Prpf8 A G 11: 75,399,784 (GRCm39) Y2281C probably damaging Het
Psip1 G A 4: 83,378,367 (GRCm39) probably benign Het
Ptpro G T 6: 137,419,705 (GRCm39) A184S probably damaging Het
Rab37 T A 11: 115,047,853 (GRCm39) I65K possibly damaging Het
Rasgrp4 T C 7: 28,844,561 (GRCm39) L247P probably damaging Het
Rnf20 T C 4: 49,644,620 (GRCm39) V295A probably damaging Het
Serpina3g A G 12: 104,204,253 (GRCm39) probably benign Het
Shox2 A G 3: 66,881,087 (GRCm39) probably benign Het
Skint6 T G 4: 112,707,937 (GRCm39) D977A possibly damaging Het
Slc25a23 C T 17: 57,360,597 (GRCm39) V248M probably damaging Het
Slco1a7 T A 6: 141,690,188 (GRCm39) K188N probably damaging Het
Smg1 A T 7: 117,745,294 (GRCm39) D3008E possibly damaging Het
St18 A G 1: 6,872,840 (GRCm39) S192G possibly damaging Het
T T C 17: 8,660,597 (GRCm39) Y403H probably damaging Het
Tars3 C A 7: 65,333,567 (GRCm39) N588K probably benign Het
Tmem132c T C 5: 127,640,907 (GRCm39) V1026A probably benign Het
Trpv4 T C 5: 114,774,506 (GRCm39) T193A probably benign Het
Ubqln4 A G 3: 88,470,506 (GRCm39) N326S probably damaging Het
Uggt2 G A 14: 119,256,898 (GRCm39) T1112I probably damaging Het
Vasn C T 16: 4,466,284 (GRCm39) P77L probably benign Het
Vps9d1 A C 8: 123,974,704 (GRCm39) probably null Het
Washc4 C A 10: 83,415,418 (GRCm39) Q803K possibly damaging Het
Zcchc2 C T 1: 105,958,430 (GRCm39) T967I probably damaging Het
Zfp874a G A 13: 67,590,473 (GRCm39) L404F possibly damaging Het
Zscan30 T C 18: 24,104,773 (GRCm39) noncoding transcript 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
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'- CTTGATTTCTTACAAAAGCGGAAGG -3'
(R):5'- TAACTGAGGCTGGATTGGCG -3'

Sequencing Primer
(F):5'- AAGCAGGCCAGCATTATGAC -3'
(R):5'- TGGATTGGCGGTCCACTCAATAC -3'
Posted On 2016-09-01