Incidental Mutation 'RF014:Supt20'
| ID |
603389 |
| 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)
|
| Stock # |
RF014 (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 54635086 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000143231
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029315]
[ENSMUST00000029316]
[ENSMUST00000153224]
[ENSMUST00000154787]
[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 benign
Transcript: ENSMUST00000029316
|
| SMART Domains |
Protein: ENSMUSP00000029316
Gene: ENSMUSG00000027752
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RNase_PH
|
31 |
166 |
2.3e-29 |
PFAM |
|
Pfam:RNase_PH_C
|
191 |
258 |
8.9e-15 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000153224
|
| SMART Domains |
Protein: ENSMUSP00000118780
Gene: ENSMUSG00000027752
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RNase_PH
|
31 |
130 |
2e-16 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000154787
|
| SMART Domains |
Protein: ENSMUSP00000115876
Gene: ENSMUSG00000027752
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RNase_PH
|
19 |
106 |
5.7e-18 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000197502
|
| SMART Domains |
Protein: ENSMUSP00000143750
Gene: ENSMUSG00000027751
| 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 |
probably benign
Transcript: ENSMUST00000199674
|
| SMART Domains |
Protein: ENSMUSP00000142948
Gene: ENSMUSG00000027751
| 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 benign
Transcript: ENSMUST00000200439
|
| SMART Domains |
Protein: ENSMUSP00000143059
Gene: ENSMUSG00000027751
| 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 |
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 |
|
| Coding Region Coverage |
- 1x: 99.8%
- 3x: 99.7%
- 10x: 99.4%
- 20x: 98.6%
|
| Validation Efficiency |
98% (49/50) |
| 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: 69 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 5430401F13Rik |
AGAAAGGAAAAGGTGGCCAGCAAAAACAGAAAGGAAAAGGTGGCCAG |
AGAAAGGAAAAGGTGGCCAGCAAAAACAGAAAGGAAAAGGTGGCCAGCAAAAACAGAAAGGAAAAGGTGGCCAG |
6: 131,529,820 (GRCm39) |
|
probably benign |
Het |
| A2ml1 |
T |
C |
6: 128,547,031 (GRCm39) |
N366S |
probably damaging |
Het |
| Abca5 |
T |
C |
11: 110,170,580 (GRCm39) |
|
probably null |
Het |
| Acaca |
T |
C |
11: 84,122,550 (GRCm39) |
V323A |
probably benign |
Het |
| Agbl3 |
T |
A |
6: 34,776,293 (GRCm39) |
D266E |
possibly damaging |
Het |
| Aggf1 |
A |
T |
13: 95,507,276 (GRCm39) |
S170T |
possibly damaging |
Het |
| Amhr2 |
A |
T |
15: 102,361,589 (GRCm39) |
S467C |
probably benign |
Het |
| Begain |
GCCGCC |
GCCGCCACCGCC |
12: 108,999,348 (GRCm39) |
|
probably benign |
Het |
| Best3 |
A |
T |
10: 116,840,410 (GRCm39) |
Q280L |
probably damaging |
Het |
| Calhm1 |
CTGTGGCTGTGG |
CTGTGGCTGTGGGTGTGGCTGTGG |
19: 47,129,704 (GRCm39) |
|
probably benign |
Het |
| Ccdc186 |
A |
G |
19: 56,801,904 (GRCm39) |
L71S |
probably benign |
Het |
| Ces1d |
C |
A |
8: 93,902,793 (GRCm39) |
|
probably null |
Het |
| Chga |
AGC |
AGCGGC |
12: 102,527,652 (GRCm39) |
|
probably benign |
Het |
| Chga |
AGC |
AGCTGC |
12: 102,527,664 (GRCm39) |
|
probably benign |
Het |
| Clstn3 |
T |
A |
6: 124,436,225 (GRCm39) |
K212* |
probably null |
Het |
| Col16a1 |
TTTTT |
TTTTTCTTTT |
4: 129,986,860 (GRCm39) |
|
probably benign |
Het |
| Cpxm2 |
G |
T |
7: 131,672,592 (GRCm39) |
T319K |
possibly damaging |
Het |
| Cyb5r4 |
TGCCCAGGGATGTGACAGACACAC |
TGCCCAGGGATGTGACAGACACACCGCCCAGGGATGTGACAGACACAC |
9: 86,922,468 (GRCm39) |
|
probably benign |
Het |
| Dst |
T |
C |
1: 34,286,760 (GRCm39) |
S3364P |
probably benign |
Het |
| Edc4 |
C |
T |
8: 106,611,232 (GRCm39) |
T61M |
probably benign |
Het |
| Fndc5 |
A |
G |
4: 129,035,960 (GRCm39) |
H199R |
probably benign |
Het |
| Gm43302 |
T |
A |
5: 105,422,623 (GRCm39) |
I470F |
possibly damaging |
Het |
| Gne |
G |
T |
4: 44,060,045 (GRCm39) |
A147D |
probably damaging |
Het |
| Igkv12-89 |
G |
GCAACGCCAC |
6: 68,812,270 (GRCm39) |
|
probably benign |
Het |
| Irf9 |
C |
T |
14: 55,843,334 (GRCm39) |
R179* |
probably null |
Het |
| Jakmip1 |
A |
T |
5: 37,331,870 (GRCm39) |
K850M |
possibly damaging |
Het |
| Kalrn |
G |
A |
16: 33,860,303 (GRCm39) |
T1884I |
probably benign |
Het |
| Krtap28-10 |
CCACCACAGCCACAGCCACCACAGCCACAG |
CCACCACAGCCACAGACACCACAGCCACAGCCACCACAGCCACAG |
1: 83,019,972 (GRCm39) |
|
probably benign |
Het |
| Las1l |
CTCCTCCTTCTCCTCTTCCTC |
CTCCTC |
X: 94,984,263 (GRCm39) |
|
probably benign |
Het |
| Lctl |
A |
G |
9: 64,026,212 (GRCm39) |
Y89C |
probably damaging |
Het |
| Lpgat1 |
GCC |
GCCTCC |
1: 191,450,665 (GRCm39) |
|
probably benign |
Het |
| Luzp2 |
A |
T |
7: 54,821,953 (GRCm39) |
I157F |
probably damaging |
Het |
| Lyz3 |
A |
G |
10: 117,070,322 (GRCm39) |
*152Q |
probably null |
Het |
| Mamld1 |
GCA |
GCACCA |
X: 70,162,451 (GRCm39) |
|
probably benign |
Het |
| Map1a |
GCTCCAGCTCCAGCTCCAGCTCCA |
GCTCCAGCTCCAGCTCCAGCTCCAGCTCCACCTCCAGCTCCAGCTCCAGCTCCA |
2: 121,136,776 (GRCm39) |
|
probably benign |
Het |
| Mbd3l1 |
A |
T |
9: 18,396,296 (GRCm39) |
E140D |
possibly damaging |
Het |
| Mlh3 |
T |
A |
12: 85,314,803 (GRCm39) |
Q461L |
probably benign |
Het |
| Mto1 |
G |
T |
9: 78,355,598 (GRCm39) |
R7L |
probably benign |
Het |
| Muc4 |
A |
T |
16: 32,570,676 (GRCm39) |
S579C |
probably damaging |
Het |
| Ngfr |
T |
C |
11: 95,469,027 (GRCm39) |
Y117C |
probably damaging |
Het |
| Or10aa3 |
A |
T |
1: 173,878,553 (GRCm39) |
I205F |
possibly damaging |
Het |
| Or13a23-ps1 |
A |
T |
7: 140,118,690 (GRCm39) |
M87L |
probably benign |
Het |
| Or8d2b |
C |
A |
9: 38,789,196 (GRCm39) |
H241Q |
probably benign |
Het |
| Plch2 |
A |
G |
4: 155,091,577 (GRCm39) |
S179P |
probably damaging |
Het |
| Pogz |
T |
G |
3: 94,785,558 (GRCm39) |
S838A |
possibly damaging |
Het |
| Polr1has |
CACCACCACCAC |
CACCACCACCACCACCACCACGACCACCACCAC |
17: 37,275,952 (GRCm39) |
|
probably benign |
Het |
| Pot1b |
T |
A |
17: 55,981,106 (GRCm39) |
T303S |
probably benign |
Het |
| Pou2f2 |
T |
A |
7: 24,815,162 (GRCm39) |
I72L |
unknown |
Het |
| Ptpn4 |
A |
G |
1: 119,612,195 (GRCm39) |
|
probably null |
Het |
| Ptprs |
A |
T |
17: 56,723,935 (GRCm39) |
I1686N |
probably damaging |
Het |
| Rfx4 |
CTCTCT |
CTCTCTCTCTCTCTCTTTCTCT |
10: 84,694,353 (GRCm39) |
|
probably benign |
Het |
| Rnf14 |
T |
A |
18: 38,442,623 (GRCm39) |
V308E |
probably damaging |
Het |
| Setd1a |
TGGTGGTGG |
TGGTGGTGGGGGTGGTGG |
7: 127,384,518 (GRCm39) |
|
probably benign |
Het |
| Sgo2b |
T |
C |
8: 64,384,439 (GRCm39) |
T186A |
possibly damaging |
Het |
| Six3 |
CGG |
CGGTGG |
17: 85,928,784 (GRCm39) |
|
probably benign |
Het |
| Six4 |
TG |
T |
12: 73,150,356 (GRCm39) |
|
probably null |
Het |
| Spmap2l |
CAGCGATCCTCCCCAGTCCCGCA |
CAGCGATCCTCCCCAGTCCCGCAGGGCGAGCGATCCTCCCCAGTCCCGCA |
5: 77,164,247 (GRCm39) |
|
probably benign |
Het |
| Stox1 |
T |
A |
10: 62,500,025 (GRCm39) |
H845L |
probably benign |
Het |
| Trappc9 |
A |
AGCTGCTGCTGCTGCT |
15: 72,673,132 (GRCm39) |
|
probably benign |
Het |
| Trim33 |
T |
C |
3: 103,236,408 (GRCm39) |
V506A |
possibly damaging |
Het |
| Uckl1 |
T |
C |
2: 181,211,987 (GRCm39) |
D373G |
probably benign |
Het |
| Vmn2r94 |
G |
T |
17: 18,473,549 (GRCm39) |
C492* |
probably null |
Het |
| Wdr33 |
A |
G |
18: 32,014,326 (GRCm39) |
D396G |
probably damaging |
Het |
| Ypel1 |
C |
T |
16: 16,915,282 (GRCm39) |
V109M |
probably damaging |
Het |
| Zbtb11 |
A |
T |
16: 55,800,960 (GRCm39) |
I105L |
probably damaging |
Het |
| Zbtb40 |
A |
T |
4: 136,744,617 (GRCm39) |
C268S |
probably benign |
Het |
| Zfp36l1 |
T |
A |
12: 80,156,518 (GRCm39) |
M288L |
probably benign |
Het |
| Zfp384 |
CC |
CCAAGGCCCAGGAC |
6: 125,013,429 (GRCm39) |
|
probably benign |
Het |
| Zfp87 |
A |
G |
13: 74,523,173 (GRCm39) |
F15S |
probably benign |
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 |
|
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 |
|
|
RF010:Supt20
|
UTSW |
3 |
54,635,083 (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'- TGGCTAGAATGTCCAGGAATCAG -3'
(R):5'- TGACTGGCTTTTAACATGTCAGAC -3'
Sequencing Primer
(F):5'- TGTCCAGGAATCAGTGATATACCC -3'
(R):5'- AGGCAGTGTACGGTACTT -3'
|
| Posted On |
2019-12-04 |
Incidental Mutation