Incidental Mutation 'R3835:Stag1'
ID |
275591 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Stag1
|
Ensembl Gene |
ENSMUSG00000037286 |
Gene Name |
STAG1 cohesin complex component |
Synonyms |
SA-1, Scc3 |
MMRRC Submission |
040890-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R3835 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
9 |
Chromosomal Location |
100479762-100840597 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 100620035 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Isoleucine
at position 46
(T46I)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000116597
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000041418]
[ENSMUST00000123302]
[ENSMUST00000124487]
[ENSMUST00000129269]
[ENSMUST00000133388]
[ENSMUST00000138405]
[ENSMUST00000146312]
[ENSMUST00000155108]
|
AlphaFold |
Q9D3E6 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000041418
AA Change: T46I
PolyPhen 2
Score 0.048 (Sensitivity: 0.94; Specificity: 0.83)
|
SMART Domains |
Protein: ENSMUSP00000040724 Gene: ENSMUSG00000037286 AA Change: T46I
Domain | Start | End | E-Value | Type |
low complexity region
|
32 |
44 |
N/A |
INTRINSIC |
low complexity region
|
59 |
72 |
N/A |
INTRINSIC |
Pfam:STAG
|
157 |
276 |
1.5e-50 |
PFAM |
SCOP:d1qbkb_
|
279 |
850 |
4e-5 |
SMART |
low complexity region
|
1062 |
1081 |
N/A |
INTRINSIC |
low complexity region
|
1107 |
1120 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000123302
AA Change: T46I
PolyPhen 2
Score 0.116 (Sensitivity: 0.93; Specificity: 0.86)
|
SMART Domains |
Protein: ENSMUSP00000117879 Gene: ENSMUSG00000037286 AA Change: T46I
Domain | Start | End | E-Value | Type |
low complexity region
|
32 |
44 |
N/A |
INTRINSIC |
low complexity region
|
59 |
72 |
N/A |
INTRINSIC |
Pfam:STAG
|
157 |
276 |
2.9e-51 |
PFAM |
low complexity region
|
303 |
315 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000124487
AA Change: T46I
PolyPhen 2
Score 0.018 (Sensitivity: 0.95; Specificity: 0.80)
|
SMART Domains |
Protein: ENSMUSP00000123595 Gene: ENSMUSG00000037286 AA Change: T46I
Domain | Start | End | E-Value | Type |
low complexity region
|
32 |
44 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000129269
AA Change: T46I
PolyPhen 2
Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)
|
SMART Domains |
Protein: ENSMUSP00000116205 Gene: ENSMUSG00000037286 AA Change: T46I
Domain | Start | End | E-Value | Type |
low complexity region
|
32 |
44 |
N/A |
INTRINSIC |
low complexity region
|
59 |
72 |
N/A |
INTRINSIC |
Pfam:STAG
|
160 |
274 |
3.8e-41 |
PFAM |
SCOP:d1qbkb_
|
279 |
850 |
3e-5 |
SMART |
low complexity region
|
1062 |
1081 |
N/A |
INTRINSIC |
low complexity region
|
1107 |
1120 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000133388
AA Change: T46I
PolyPhen 2
Score 0.165 (Sensitivity: 0.92; Specificity: 0.87)
|
SMART Domains |
Protein: ENSMUSP00000119637 Gene: ENSMUSG00000037286 AA Change: T46I
Domain | Start | End | E-Value | Type |
low complexity region
|
32 |
44 |
N/A |
INTRINSIC |
low complexity region
|
59 |
72 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000138405
AA Change: T46I
PolyPhen 2
Score 0.048 (Sensitivity: 0.94; Specificity: 0.83)
|
SMART Domains |
Protein: ENSMUSP00000116322 Gene: ENSMUSG00000037286 AA Change: T46I
Domain | Start | End | E-Value | Type |
low complexity region
|
32 |
44 |
N/A |
INTRINSIC |
low complexity region
|
59 |
72 |
N/A |
INTRINSIC |
Pfam:STAG
|
157 |
276 |
1.5e-51 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143816
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000146312
AA Change: T46I
PolyPhen 2
Score 0.967 (Sensitivity: 0.77; Specificity: 0.95)
|
SMART Domains |
Protein: ENSMUSP00000116597 Gene: ENSMUSG00000037286 AA Change: T46I
Domain | Start | End | E-Value | Type |
low complexity region
|
32 |
44 |
N/A |
INTRINSIC |
low complexity region
|
59 |
72 |
N/A |
INTRINSIC |
Pfam:STAG
|
99 |
196 |
4.2e-46 |
PFAM |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000155108
AA Change: T46I
PolyPhen 2
Score 0.625 (Sensitivity: 0.87; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000118952 Gene: ENSMUSG00000037286 AA Change: T46I
Domain | Start | End | E-Value | Type |
low complexity region
|
32 |
44 |
N/A |
INTRINSIC |
low complexity region
|
59 |
72 |
N/A |
INTRINSIC |
|
Meta Mutation Damage Score |
0.1017 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.9%
|
Validation Efficiency |
98% (43/44) |
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the SCC3 family and is expressed in the nucleus. It encodes a component of cohesin, a multisubunit protein complex that provides sister chromatid cohesion along the length of a chromosome from DNA replication through prophase and prometaphase, after which it is dissociated in preparation for segregation during anaphase. [provided by RefSeq, Jul 2008] PHENOTYPE: Mouse embryos homozygous for a null mutation show developmental delay and die before birth. Heterozygous animals have shorter lifespan and earlier onset of tumourigenesis. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 44 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adgrl4 |
T |
C |
3: 151,216,254 (GRCm39) |
I479T |
probably damaging |
Het |
Adh6a |
G |
A |
3: 138,033,275 (GRCm39) |
|
probably null |
Het |
Anapc7 |
A |
G |
5: 122,581,940 (GRCm39) |
T528A |
possibly damaging |
Het |
Ap5b1 |
A |
G |
19: 5,618,918 (GRCm39) |
T113A |
possibly damaging |
Het |
Apaf1 |
G |
A |
10: 90,895,449 (GRCm39) |
R439C |
probably benign |
Het |
Apoa5 |
A |
T |
9: 46,181,878 (GRCm39) |
H318L |
probably damaging |
Het |
Bltp2 |
A |
G |
11: 78,169,911 (GRCm39) |
R1545G |
probably benign |
Het |
Btnl9 |
T |
G |
11: 49,071,512 (GRCm39) |
T104P |
probably damaging |
Het |
Cimip3 |
AC |
A |
17: 47,744,348 (GRCm39) |
|
probably benign |
Het |
Dennd5a |
T |
C |
7: 109,533,449 (GRCm39) |
K107R |
probably benign |
Het |
Dthd1 |
A |
T |
5: 63,007,128 (GRCm39) |
R610W |
probably damaging |
Het |
Eno1 |
T |
C |
4: 150,331,119 (GRCm39) |
S186P |
probably benign |
Het |
Gipc2 |
C |
A |
3: 151,833,823 (GRCm39) |
V153F |
probably damaging |
Het |
Gpt |
A |
G |
15: 76,582,783 (GRCm39) |
Y295C |
probably damaging |
Het |
Kcnh5 |
T |
A |
12: 74,945,044 (GRCm39) |
Q735L |
probably benign |
Het |
Lrrc10 |
A |
G |
10: 116,881,691 (GRCm39) |
N122D |
possibly damaging |
Het |
Lrrc37 |
C |
A |
11: 103,510,836 (GRCm39) |
L377F |
unknown |
Het |
Meis2 |
T |
C |
2: 115,752,228 (GRCm39) |
H301R |
probably damaging |
Het |
Muc5b |
A |
T |
7: 141,412,918 (GRCm39) |
I1955F |
unknown |
Het |
Nalcn |
A |
T |
14: 123,530,834 (GRCm39) |
|
probably benign |
Het |
Nmt2 |
T |
C |
2: 3,315,723 (GRCm39) |
|
probably benign |
Het |
Nnt |
C |
T |
13: 119,509,031 (GRCm39) |
G403R |
probably damaging |
Het |
Or4a79 |
T |
G |
2: 89,551,799 (GRCm39) |
I219L |
possibly damaging |
Het |
Or4d6 |
T |
A |
19: 12,086,764 (GRCm39) |
I49F |
possibly damaging |
Het |
Or5b109 |
A |
T |
19: 13,212,103 (GRCm39) |
D163V |
probably benign |
Het |
Ovgp1 |
A |
G |
3: 105,893,631 (GRCm39) |
E468G |
probably benign |
Het |
Pax6 |
G |
A |
2: 105,526,795 (GRCm39) |
E234K |
probably benign |
Het |
Prkdc |
A |
G |
16: 15,609,810 (GRCm39) |
E3138G |
probably damaging |
Het |
Prmt6 |
T |
C |
3: 110,158,121 (GRCm39) |
D56G |
possibly damaging |
Het |
Ptprt |
A |
G |
2: 161,389,307 (GRCm39) |
V1261A |
probably damaging |
Het |
Qtrt2 |
A |
G |
16: 43,701,435 (GRCm39) |
S42P |
probably damaging |
Het |
Rab9b |
C |
T |
X: 135,762,259 (GRCm39) |
R47Q |
possibly damaging |
Het |
Rpgrip1 |
A |
G |
14: 52,384,710 (GRCm39) |
E606G |
probably damaging |
Het |
Setx |
C |
T |
2: 29,035,072 (GRCm39) |
S519L |
possibly damaging |
Het |
Slc15a2 |
A |
T |
16: 36,592,490 (GRCm39) |
C191* |
probably null |
Het |
Snrk |
T |
C |
9: 121,966,069 (GRCm39) |
|
probably benign |
Het |
St6galnac1 |
T |
C |
11: 116,657,109 (GRCm39) |
D422G |
probably damaging |
Het |
Tagln |
T |
C |
9: 45,843,008 (GRCm39) |
I18V |
probably benign |
Het |
Tasor2 |
T |
C |
13: 3,625,292 (GRCm39) |
T1553A |
probably benign |
Het |
Tbx18 |
C |
A |
9: 87,611,689 (GRCm39) |
A114S |
probably benign |
Het |
Ttc16 |
T |
C |
2: 32,659,322 (GRCm39) |
D259G |
probably damaging |
Het |
Vldlr |
A |
G |
19: 27,212,214 (GRCm39) |
D76G |
probably damaging |
Het |
Vmn2r24 |
G |
T |
6: 123,764,412 (GRCm39) |
D430Y |
probably benign |
Het |
Xlr3a |
T |
C |
X: 72,138,644 (GRCm39) |
E5G |
probably damaging |
Het |
|
Other mutations in Stag1 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00649:Stag1
|
APN |
9 |
100,658,861 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01010:Stag1
|
APN |
9 |
100,827,986 (GRCm39) |
missense |
probably benign |
0.06 |
IGL01012:Stag1
|
APN |
9 |
100,737,912 (GRCm39) |
missense |
possibly damaging |
0.47 |
IGL01025:Stag1
|
APN |
9 |
100,833,710 (GRCm39) |
missense |
possibly damaging |
0.95 |
IGL01307:Stag1
|
APN |
9 |
100,833,841 (GRCm39) |
intron |
probably benign |
|
IGL02149:Stag1
|
APN |
9 |
100,769,442 (GRCm39) |
missense |
probably benign |
0.09 |
IGL02608:Stag1
|
APN |
9 |
100,639,822 (GRCm39) |
missense |
probably null |
0.99 |
IGL03008:Stag1
|
APN |
9 |
100,658,844 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL03210:Stag1
|
APN |
9 |
100,727,129 (GRCm39) |
missense |
possibly damaging |
0.63 |
eto_o
|
UTSW |
9 |
100,678,769 (GRCm39) |
missense |
probably damaging |
1.00 |
PIT4280001:Stag1
|
UTSW |
9 |
100,824,769 (GRCm39) |
missense |
possibly damaging |
0.95 |
R0070:Stag1
|
UTSW |
9 |
100,838,461 (GRCm39) |
missense |
probably null |
1.00 |
R0070:Stag1
|
UTSW |
9 |
100,838,461 (GRCm39) |
missense |
probably null |
1.00 |
R0349:Stag1
|
UTSW |
9 |
100,658,837 (GRCm39) |
missense |
probably damaging |
0.98 |
R0479:Stag1
|
UTSW |
9 |
100,810,144 (GRCm39) |
missense |
probably benign |
0.00 |
R0531:Stag1
|
UTSW |
9 |
100,836,300 (GRCm39) |
makesense |
probably null |
|
R0962:Stag1
|
UTSW |
9 |
100,678,880 (GRCm39) |
missense |
probably damaging |
1.00 |
R0976:Stag1
|
UTSW |
9 |
100,812,069 (GRCm39) |
critical splice donor site |
probably null |
|
R0976:Stag1
|
UTSW |
9 |
100,658,877 (GRCm39) |
missense |
probably damaging |
0.98 |
R1170:Stag1
|
UTSW |
9 |
100,770,506 (GRCm39) |
intron |
probably benign |
|
R1499:Stag1
|
UTSW |
9 |
100,769,426 (GRCm39) |
intron |
probably benign |
|
R1499:Stag1
|
UTSW |
9 |
100,737,885 (GRCm39) |
missense |
possibly damaging |
0.77 |
R1644:Stag1
|
UTSW |
9 |
100,762,953 (GRCm39) |
intron |
probably benign |
|
R1747:Stag1
|
UTSW |
9 |
100,770,353 (GRCm39) |
missense |
probably benign |
|
R1799:Stag1
|
UTSW |
9 |
100,835,515 (GRCm39) |
splice site |
probably null |
|
R1807:Stag1
|
UTSW |
9 |
100,790,719 (GRCm39) |
missense |
probably benign |
0.34 |
R1978:Stag1
|
UTSW |
9 |
100,770,139 (GRCm39) |
missense |
probably benign |
0.03 |
R2029:Stag1
|
UTSW |
9 |
100,668,740 (GRCm39) |
missense |
probably damaging |
1.00 |
R2161:Stag1
|
UTSW |
9 |
100,771,648 (GRCm39) |
missense |
probably damaging |
1.00 |
R2300:Stag1
|
UTSW |
9 |
100,594,553 (GRCm39) |
missense |
possibly damaging |
0.92 |
R2327:Stag1
|
UTSW |
9 |
100,668,666 (GRCm39) |
missense |
possibly damaging |
0.81 |
R2426:Stag1
|
UTSW |
9 |
100,727,169 (GRCm39) |
critical splice donor site |
probably null |
|
R2448:Stag1
|
UTSW |
9 |
100,770,462 (GRCm39) |
missense |
probably benign |
0.42 |
R2504:Stag1
|
UTSW |
9 |
100,748,263 (GRCm39) |
missense |
probably damaging |
0.99 |
R3713:Stag1
|
UTSW |
9 |
100,771,671 (GRCm39) |
missense |
probably benign |
0.01 |
R3862:Stag1
|
UTSW |
9 |
100,826,838 (GRCm39) |
missense |
probably benign |
0.02 |
R4398:Stag1
|
UTSW |
9 |
100,838,659 (GRCm39) |
utr 3 prime |
probably benign |
|
R4568:Stag1
|
UTSW |
9 |
100,730,722 (GRCm39) |
missense |
probably damaging |
1.00 |
R4651:Stag1
|
UTSW |
9 |
100,678,769 (GRCm39) |
missense |
probably damaging |
1.00 |
R4652:Stag1
|
UTSW |
9 |
100,678,769 (GRCm39) |
missense |
probably damaging |
1.00 |
R4653:Stag1
|
UTSW |
9 |
100,678,769 (GRCm39) |
missense |
probably damaging |
1.00 |
R4675:Stag1
|
UTSW |
9 |
100,730,758 (GRCm39) |
missense |
probably damaging |
1.00 |
R4709:Stag1
|
UTSW |
9 |
100,620,092 (GRCm39) |
missense |
probably damaging |
0.99 |
R4924:Stag1
|
UTSW |
9 |
100,678,808 (GRCm39) |
missense |
possibly damaging |
0.67 |
R5018:Stag1
|
UTSW |
9 |
100,833,672 (GRCm39) |
missense |
probably benign |
0.00 |
R5435:Stag1
|
UTSW |
9 |
100,835,603 (GRCm39) |
missense |
probably benign |
0.03 |
R5460:Stag1
|
UTSW |
9 |
100,838,506 (GRCm39) |
splice site |
probably null |
|
R5805:Stag1
|
UTSW |
9 |
100,678,831 (GRCm39) |
missense |
probably damaging |
1.00 |
R6127:Stag1
|
UTSW |
9 |
100,833,750 (GRCm39) |
missense |
probably benign |
0.05 |
R6313:Stag1
|
UTSW |
9 |
100,639,786 (GRCm39) |
missense |
probably damaging |
1.00 |
R6597:Stag1
|
UTSW |
9 |
100,769,473 (GRCm39) |
missense |
probably benign |
0.01 |
R6807:Stag1
|
UTSW |
9 |
100,826,903 (GRCm39) |
missense |
probably damaging |
1.00 |
R7099:Stag1
|
UTSW |
9 |
100,826,879 (GRCm39) |
missense |
probably benign |
0.02 |
R7167:Stag1
|
UTSW |
9 |
100,827,942 (GRCm39) |
missense |
probably benign |
0.05 |
R7395:Stag1
|
UTSW |
9 |
100,678,781 (GRCm39) |
missense |
probably damaging |
0.99 |
R7504:Stag1
|
UTSW |
9 |
100,770,381 (GRCm39) |
missense |
probably benign |
0.09 |
R7663:Stag1
|
UTSW |
9 |
100,620,191 (GRCm39) |
missense |
probably damaging |
0.98 |
R7769:Stag1
|
UTSW |
9 |
100,826,880 (GRCm39) |
missense |
possibly damaging |
0.86 |
R8245:Stag1
|
UTSW |
9 |
100,811,946 (GRCm39) |
missense |
probably benign |
0.01 |
R8343:Stag1
|
UTSW |
9 |
100,639,819 (GRCm39) |
missense |
possibly damaging |
0.95 |
R8473:Stag1
|
UTSW |
9 |
100,762,840 (GRCm39) |
missense |
probably damaging |
1.00 |
R8709:Stag1
|
UTSW |
9 |
100,772,975 (GRCm39) |
intron |
probably benign |
|
R8925:Stag1
|
UTSW |
9 |
100,587,298 (GRCm39) |
missense |
possibly damaging |
0.46 |
R8927:Stag1
|
UTSW |
9 |
100,587,298 (GRCm39) |
missense |
possibly damaging |
0.46 |
R8951:Stag1
|
UTSW |
9 |
100,762,854 (GRCm39) |
missense |
probably damaging |
1.00 |
R9138:Stag1
|
UTSW |
9 |
100,829,335 (GRCm39) |
missense |
probably benign |
0.01 |
R9233:Stag1
|
UTSW |
9 |
100,812,024 (GRCm39) |
missense |
probably benign |
0.00 |
R9246:Stag1
|
UTSW |
9 |
100,770,329 (GRCm39) |
missense |
probably benign |
0.00 |
R9419:Stag1
|
UTSW |
9 |
100,811,967 (GRCm39) |
missense |
probably benign |
|
R9442:Stag1
|
UTSW |
9 |
100,836,306 (GRCm39) |
missense |
probably damaging |
1.00 |
R9694:Stag1
|
UTSW |
9 |
100,810,151 (GRCm39) |
missense |
probably benign |
0.05 |
R9740:Stag1
|
UTSW |
9 |
100,587,288 (GRCm39) |
missense |
probably damaging |
0.98 |
|
Predicted Primers |
PCR Primer
(F):5'- TAGGCTCTCAAATTGCAGGAG -3'
(R):5'- TGTGAAGATTACCTGCATTGCAC -3'
Sequencing Primer
(F):5'- CTCAAATTGCAGGAGAGTATATTGAG -3'
(R):5'- GAAGATTACCTGCATTGCACTCTTC -3'
|
Posted On |
2015-04-06 |