Mutagenetix > Incidental Mutation

Incidental Mutation 'R0744:Supt20'

70825

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

038925-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.939) question?

Stock #

R0744 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

54600228-54636187 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 54622122 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Asparagine at position 409 (Y409N)

Ref Sequence

ENSEMBL: ENSMUSP00000143750 (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

Domain	Start	End	E-Value	Type
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: Y410N

PolyPhen 2 Score 0.968 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000131454
Gene: ENSMUSG00000027751
AA Change: Y410N

Domain	Start	End	E-Value	Type
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: Y409N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000143750
Gene: ENSMUSG00000027751
AA Change: Y409N

Domain	Start	End	E-Value	Type
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

possibly damaging
Transcript: ENSMUST00000199674
AA Change: Y409N

PolyPhen 2 Score 0.955 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000142948
Gene: ENSMUSG00000027751
AA Change: Y409N

Domain	Start	End	E-Value	Type
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: Y409N

PolyPhen 2 Score 0.973 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000143059
Gene: ENSMUSG00000027751
AA Change: Y409N

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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

0.1715

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 94.8%

Validation Efficiency

98% (91/93)

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: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700113H08Rik	T	C	10: 87,000,931 (GRCm39)	L41P	probably damaging	Het
A930003A15Rik	T	C	16: 19,702,622 (GRCm39)		noncoding transcript	Het
Abca8a	A	T	11: 109,931,390 (GRCm39)	D1253E	possibly damaging	Het
Acsm3	T	C	7: 119,376,323 (GRCm39)	I350T	possibly damaging	Het
Adcy9	T	C	16: 4,237,135 (GRCm39)	D92G	possibly damaging	Het
Aebp2	T	G	6: 140,588,090 (GRCm39)		probably null	Het
AI987944	T	C	7: 41,026,283 (GRCm39)	Y6C	probably damaging	Het
Ascc3	T	C	10: 50,721,762 (GRCm39)	W2072R	probably benign	Het
Asxl3	A	G	18: 22,649,097 (GRCm39)	D362G	probably damaging	Het
Baiap2l1	T	A	5: 144,203,451 (GRCm39)	D479V	probably benign	Het
Bdp1	A	T	13: 100,172,333 (GRCm39)	H2094Q	probably benign	Het
Bptf	C	A	11: 107,001,638 (GRCm39)		probably null	Het
Camk4	G	T	18: 33,072,507 (GRCm39)	S20I	unknown	Het
Ccdc85a	T	A	11: 28,533,296 (GRCm39)	I83F	probably damaging	Het
Ccnt2	T	A	1: 127,730,131 (GRCm39)	M336K	probably benign	Het
Cd209e	G	T	8: 3,903,205 (GRCm39)	D62E	probably benign	Het
Cd226	A	C	18: 89,225,144 (GRCm39)		probably benign	Het
Clip1	T	C	5: 123,768,784 (GRCm39)	D605G	probably benign	Het
Crtc1	A	G	8: 70,845,663 (GRCm39)	V306A	probably benign	Het
D130043K22Rik	G	A	13: 25,047,563 (GRCm39)		probably benign	Het
Dmxl1	T	C	18: 49,966,215 (GRCm39)	V20A	probably damaging	Het
Dzip3	A	G	16: 48,780,038 (GRCm39)	Y301H	probably damaging	Het
Ephb4	T	A	5: 137,363,929 (GRCm39)	N600K	probably damaging	Het
Erich6	T	A	3: 58,543,543 (GRCm39)		probably benign	Het
Fbn1	T	C	2: 125,156,734 (GRCm39)		probably benign	Het
Fryl	A	T	5: 73,246,424 (GRCm39)		probably benign	Het
Galnt17	T	A	5: 131,179,754 (GRCm39)	D131V	probably damaging	Het
Gm6619	T	A	6: 131,467,297 (GRCm39)	L54Q	probably damaging	Het
Herc2	T	C	7: 55,855,784 (GRCm39)		probably benign	Het
Hic1	T	A	11: 75,056,627 (GRCm39)	Q754L	possibly damaging	Het
Hnf4g	A	T	3: 3,716,689 (GRCm39)	D286V	possibly damaging	Het
Iho1	A	T	9: 108,282,000 (GRCm39)	C563S	probably benign	Het
Itgb5	A	G	16: 33,720,953 (GRCm39)	K339R	probably damaging	Het
Itih1	A	T	14: 30,663,512 (GRCm39)	V164E	probably damaging	Het
Jak3	A	C	8: 72,136,622 (GRCm39)	N643T	probably damaging	Het
Lamp1	T	A	8: 13,222,654 (GRCm39)	F279L	probably damaging	Het
Lrfn5	A	C	12: 61,886,454 (GRCm39)	T81P	probably damaging	Het
Lrrc58	A	G	16: 37,698,935 (GRCm39)		probably benign	Het
Marchf6	T	C	15: 31,480,437 (GRCm39)	Y562C	probably benign	Het
Mark1	T	A	1: 184,653,805 (GRCm39)	I166F	probably damaging	Het
Mark2	A	G	19: 7,263,189 (GRCm39)	Y193H	probably damaging	Het
Mast4	C	G	13: 102,873,895 (GRCm39)	Q1632H	probably damaging	Het
Mcrs1	T	C	15: 99,141,330 (GRCm39)		probably benign	Het
Mgst3	A	G	1: 167,201,374 (GRCm39)	Y104H	probably damaging	Het
Mlxipl	C	T	5: 135,161,329 (GRCm39)	T416I	possibly damaging	Het
Mthfd2l	T	C	5: 91,094,801 (GRCm39)	V90A	probably damaging	Het
Mtnr1a	A	T	8: 45,540,974 (GRCm39)	I312F	probably benign	Het
Muc1	C	A	3: 89,137,635 (GRCm39)	P159Q	possibly damaging	Het
Myom2	A	T	8: 15,182,924 (GRCm39)	K1454*	probably null	Het
Myt1	TGAGGAGGAGGAGGAGGAGG	TGAGGAGGAGGAGGAGG	2: 181,439,298 (GRCm39)		probably benign	Het
Or10g3b	T	C	14: 52,586,835 (GRCm39)	I223V	probably benign	Het
Or2t29	T	A	11: 58,433,988 (GRCm39)	M105L	possibly damaging	Het
Or52ae9	T	C	7: 103,390,132 (GRCm39)	H105R	probably damaging	Het
Or56b1b	T	C	7: 108,164,205 (GRCm39)	T266A	possibly damaging	Het
Or8b1c	A	T	9: 38,384,081 (GRCm39)	I13F	probably benign	Het
Pdcd6	A	G	13: 74,464,443 (GRCm39)		probably benign	Het
Ppp1r16a	C	T	15: 76,577,869 (GRCm39)	Q328*	probably null	Het
Pramel23	A	T	4: 143,425,056 (GRCm39)	M129K	probably benign	Het
Pzp	A	G	6: 128,493,158 (GRCm39)		probably benign	Het
Rab27b	T	C	18: 70,120,112 (GRCm39)		probably benign	Het
Rapgef3	G	A	15: 97,659,466 (GRCm39)		probably benign	Het
Rapsn	T	C	2: 90,867,153 (GRCm39)	Y152H	probably damaging	Het
Rgs11	T	A	17: 26,422,292 (GRCm39)	M29K	probably damaging	Het
Rictor	A	G	15: 6,793,759 (GRCm39)		probably null	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Rims1	T	C	1: 22,497,709 (GRCm39)		probably null	Het
Samd9l	T	C	6: 3,372,725 (GRCm39)	E1512G	possibly damaging	Het
Sgsm1	C	T	5: 113,427,050 (GRCm39)	A127T	probably benign	Het
Slc22a28	T	C	19: 8,094,197 (GRCm39)	Y245C	possibly damaging	Het
Slc25a1	T	A	16: 17,745,300 (GRCm39)	H78L	probably benign	Het
Slc26a1	T	A	5: 108,821,389 (GRCm39)	T167S	probably benign	Het
Slc2a12	T	C	10: 22,577,915 (GRCm39)		probably benign	Het
Slc44a5	T	C	3: 153,971,111 (GRCm39)	S654P	probably damaging	Het
Slc51a	T	A	16: 32,294,667 (GRCm39)	T306S	probably benign	Het
Slc6a13	T	G	6: 121,279,826 (GRCm39)	W67G	probably damaging	Het
Sowahc	GGGAGGAGGAGGAGGAGGAGGAGGAGGA	GGGAGGAGGAGGAGGAGGAGGAGGA	10: 59,059,313 (GRCm39)		probably benign	Het
Sp100	A	T	1: 85,627,465 (GRCm39)	I86L	probably damaging	Het
Spata31e5	A	G	1: 28,816,902 (GRCm39)	S377P	possibly damaging	Het
Synrg	C	T	11: 83,915,131 (GRCm39)	Q1046*	probably null	Het
Tab2	T	C	10: 7,783,345 (GRCm39)		probably benign	Het
Tcof1	T	C	18: 60,978,904 (GRCm39)	D48G	probably damaging	Het
Tex24	A	T	8: 27,834,748 (GRCm39)	H92L	possibly damaging	Het
Tgm6	T	C	2: 129,993,681 (GRCm39)	V640A	probably benign	Het
Tle2	T	C	10: 81,424,781 (GRCm39)	F667L	probably damaging	Het
Tnfaip3	C	A	10: 18,878,697 (GRCm39)	A704S	probably benign	Het
Tomm34	T	C	2: 163,912,896 (GRCm39)	N22D	probably benign	Het
Trabd2b	A	G	4: 114,437,519 (GRCm39)	Q232R	probably benign	Het
Trim62	A	G	4: 128,778,008 (GRCm39)	S16G	probably damaging	Het
Ttc28	T	A	5: 111,378,947 (GRCm39)	I1144N	probably damaging	Het
Unc5a	C	A	13: 55,151,746 (GRCm39)	N56K	possibly damaging	Het
Ush2a	C	T	1: 188,546,603 (GRCm39)		probably benign	Het
Wrn	A	G	8: 33,785,034 (GRCm39)	I446T	possibly damaging	Het
Zbed5	T	A	5: 129,931,113 (GRCm39)	V354E	possibly damaging	Het
Zfp266	G	A	9: 20,411,095 (GRCm39)	H361Y	probably damaging	Het

Other mutations in Supt20

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
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'- AGTCTTGGTGTCTTGACCAGGCTC -3'
(R):5'- AGCCTTCTCAACCAGCCTTTAACAG -3'

Sequencing Primer
(F):5'- CTATGTGGCTGATGAGAATTCACC -3'
(R):5'- CTGTACCTATCTATCATTGAGGACG -3'

Posted On

2013-09-30