Incidental Mutation 'RF010:Supt20'
ID 603118
Institutional Source Beutler Lab
Gene Symbol Supt20
Ensembl Gene ENSMUSG00000027751
Gene Name SPT20 SAGA complex component
Synonyms p38IP, Fam48a, p38 interacting protein, D3Ertd300e
Accession Numbers
Essential gene? Probably essential (E-score: 0.939) question?
Stock # RF010 (G1)
Quality Score 217.468
Status Not validated
Chromosome 3
Chromosomal Location 54600228-54636187 bp(+) (GRCm39)
Type of Mutation small insertion (2 aa in frame mutation)
DNA Base Change (assembly) AGCAGC to AGCAGCGGCAGC at 54635083 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000143231 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029315] [ENSMUST00000029316] [ENSMUST00000200441] [ENSMUST00000197502] [ENSMUST00000199674] [ENSMUST00000200439] [ENSMUST00000154787] [ENSMUST00000153224]
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: ENSMUST00000029316
SMART Domains Protein: ENSMUSP00000029316
Gene: ENSMUSG00000027752

DomainStartEndE-ValueType
Pfam:RNase_PH 31 166 2.3e-29 PFAM
Pfam:RNase_PH_C 191 258 8.9e-15 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125632
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127112
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134892
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140935
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: ENSMUST00000197502
SMART Domains Protein: ENSMUSP00000143750
Gene: ENSMUSG00000027751

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 probably benign
Transcript: ENSMUST00000199674
SMART Domains Protein: ENSMUSP00000142948
Gene: ENSMUSG00000027751

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
SMART Domains Protein: ENSMUSP00000143059
Gene: ENSMUSG00000027751

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 probably benign
Transcript: ENSMUST00000154787
SMART Domains Protein: ENSMUSP00000115876
Gene: ENSMUSG00000027752

DomainStartEndE-ValueType
Pfam:RNase_PH 19 106 5.7e-18 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000153224
SMART Domains Protein: ENSMUSP00000118780
Gene: ENSMUSG00000027752

DomainStartEndE-ValueType
Pfam:RNase_PH 31 130 2e-16 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142377
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150923
Coding Region Coverage
  • 1x: 99.8%
  • 3x: 99.7%
  • 10x: 99.4%
  • 20x: 98.8%
Validation Efficiency
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: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2300002M23Rik GGGTTATGGTCAGTACCCCCCAGTAGGGACCTGGGGCGGTTATGGTCAGTACCCCCCAGTAGGGCCCTGGGGCGGTTATGGTCAGTACCCCCCAGTAGGGACCTGGGG GGGTTATGGTCAGTACCCCCCAGTAGGGCCCTGGGGCGGTTATGGTCAGTACCCCCCAGTAGGGACCTGGGG 17: 35,879,473 (GRCm39) probably benign Het
Acap3 CCTGGGCTGCTG CCTGGGCTGCTGCATACTGGGCTGCTG 4: 155,989,553 (GRCm39) probably benign Het
Ankrd28 A G 14: 31,500,943 (GRCm39) I16T probably damaging Het
AY761185 GCACTGTGGGC G 8: 21,433,927 (GRCm39) probably null Het
Bend3 T A 10: 43,386,180 (GRCm39) F191Y possibly damaging Het
Calhm1 GTGGC GTGGCTGTGGCTATGGC 19: 47,129,712 (GRCm39) probably benign Het
Camkv CGCTGCTGC CGC 9: 107,825,059 (GRCm39) probably benign Het
Cfap251 TCTCA T 5: 123,412,224 (GRCm39) probably benign Het
Chga GCA GCATCA 12: 102,527,662 (GRCm39) probably benign Het
Cngb1 CTCTGGCTCTGGCTCTGGCTCTG C 8: 96,030,278 (GRCm39) probably null Het
Cnot3 T C 7: 3,659,068 (GRCm39) V438A probably benign Het
Cntnap5c T A 17: 58,593,790 (GRCm39) W710R probably damaging Het
Dyrk1a A G 16: 94,478,422 (GRCm39) S404G probably benign Het
Efhd2 GCCGCC GCCGCCTCCGCC 4: 141,602,075 (GRCm39) probably benign Het
Flywch1 GTGT GTGTGGGGAGGCTACGTACTCACCCACACCTGTTGT 17: 23,981,149 (GRCm39) probably null Het
Fmn2 T A 1: 174,409,581 (GRCm39) S605T unknown Het
Gab3 TCT TCTGCT X: 74,043,617 (GRCm39) probably benign Het
Gabre GCTC GCTCCGTCTC X: 71,313,666 (GRCm39) probably benign Het
Gli3 A G 13: 15,900,954 (GRCm39) Y1447C probably damaging Het
Hibch T C 1: 52,952,891 (GRCm39) V297A probably benign Het
Ifi213 C G 1: 173,409,719 (GRCm39) D462H probably damaging Het
Kcnh8 G A 17: 53,285,267 (GRCm39) R1079H probably benign Het
Lce1m GCTGCTGCC GCTGCTGCCCCCACTGCTGCC 3: 92,925,597 (GRCm39) probably benign Het
Lpo A G 11: 87,711,928 (GRCm39) V43A probably benign Het
Map1a A AGCTCCAGCTCCAGCCCCACCTCCAGCTCCC 2: 121,136,799 (GRCm39) probably benign Het
Mapk9 A G 11: 49,745,083 (GRCm39) probably benign Het
Mep1a G A 17: 43,797,126 (GRCm39) H314Y probably damaging Het
Myh3 ATTAC ATTACTTAC 11: 66,977,182 (GRCm39) probably null Het
Myh3 AC ACTTCC 11: 66,977,185 (GRCm39) probably null Het
Nusap1 ACGTTAGCAGTGAGGAGCAA ACGTTAGCAGTGAGGAGCAAACTGAGATACTCGTTAGCAGTGAGGAGCAA 2: 119,458,065 (GRCm39) probably benign Het
Or10ag56 T A 2: 87,139,184 (GRCm39) V37E possibly damaging Het
Or14a259 T C 7: 86,012,594 (GRCm39) Q317R probably benign Het
Pdcd11 AGGAGG A 19: 47,101,890 (GRCm39) probably null Het
Pfkm T A 15: 98,027,674 (GRCm39) I651N possibly damaging Het
Phldb3 CCCCCGCCCC CCCCC 7: 24,325,920 (GRCm39) probably null Het
Polr1has CACCACCAC CACCACCACCACCACCACCACTACCACCAC 17: 37,275,955 (GRCm39) probably benign Het
Prkce T C 17: 86,795,627 (GRCm39) V288A probably damaging Het
Pxmp4 A G 2: 154,434,183 (GRCm39) S93P probably damaging Het
Rfc4 T C 16: 22,946,232 (GRCm39) T17A probably benign Het
Rfx4 CTCTCTCT CTCTCTCTCTCTCTCTATCTCTCT 10: 84,694,351 (GRCm39) probably benign Het
Ryr3 G T 2: 112,606,015 (GRCm39) A2415E probably damaging Het
Sbp ACAAAGATGCTGACAACAAAGATGCTGACA ACAAAGATGCTGACACCAAAGATGCTGACAACAAAGATGCTGACA 17: 24,164,325 (GRCm39) probably benign Het
Sec24c T A 14: 20,738,783 (GRCm39) probably null Het
Sec63 C A 10: 42,682,620 (GRCm39) A437E probably benign Het
Six3 GCG GCGTCG 17: 85,928,783 (GRCm39) probably benign Het
Slco5a1 G A 1: 12,942,171 (GRCm39) T825I probably damaging Het
Spmap2l CAG CAGCGATCCTCCCCAGTCCCGCAAGGCGAG 5: 77,164,274 (GRCm39) probably benign Het
Stard8 GGA GGAAGA X: 98,110,123 (GRCm39) probably benign Het
Stxbp1 A G 2: 32,711,927 (GRCm39) V30A probably benign Het
Syne1 T A 10: 5,196,386 (GRCm39) D3882V possibly damaging Het
T A G 17: 8,660,540 (GRCm39) T384A probably benign Het
Tbc1d12 CGGGGCGG CG 19: 38,825,384 (GRCm39) probably benign Het
Tcof1 CAG CAGAAG 18: 60,968,816 (GRCm39) probably benign Het
Tcstv5 A T 13: 120,411,582 (GRCm39) V8E probably benign Het
Tfeb GCA GCAACA 17: 48,097,019 (GRCm39) probably benign Het
Tfeb CAG CAGAAG 17: 48,097,032 (GRCm39) probably benign Het
Thumpd3 C T 6: 113,033,006 (GRCm39) A248V probably damaging Het
Tlcd4 T A 3: 121,022,533 (GRCm39) I103L probably benign Het
Tmem181a T C 17: 6,330,978 (GRCm39) probably null Het
Trim41 A T 11: 48,698,165 (GRCm39) H600Q probably damaging Het
Ttbk2 A T 2: 120,620,820 (GRCm39) C147* probably null Het
Ttll2 C T 17: 7,618,737 (GRCm39) A397T probably benign Het
Unc79 T A 12: 103,079,046 (GRCm39) L1737Q probably benign Het
Usp47 T A 7: 111,692,145 (GRCm39) V869E probably damaging Het
Vmn1r231 T A 17: 21,110,255 (GRCm39) Q220L probably damaging Het
Vmn2r26 C T 6: 124,016,448 (GRCm39) T304I possibly damaging Het
Wrn T C 8: 33,778,793 (GRCm39) N839S probably benign Het
Zfp384 GCCCAGGCCCAGGCCCAGGCCCAG GCCCAGGCCCAGTCCCAGGCCCAGGCCCAGGCCCAG 6: 125,013,434 (GRCm39) probably benign Het
Zfp384 GGCCCAGG GGCCCAGGAGCACGCCCAGG 6: 125,013,451 (GRCm39) probably benign Het
Zfyve26 C T 12: 79,302,112 (GRCm39) C1828Y 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
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
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
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'- GCTAGAATGTCCAGGAATCAGTG -3'
(R):5'- AGCTGACTGGCTTTTAACATGTC -3'

Sequencing Primer
(F):5'- TGTCCAGGAATCAGTGATATACCC -3'
(R):5'- GACTGGCTTTTAACATGTCAGACTC -3'
Posted On 2019-12-04