Incidental Mutation 'R6682:Smc4'
| ID |
527528 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smc4
|
| Ensembl Gene |
ENSMUSG00000034349 |
| Gene Name |
structural maintenance of chromosomes 4 |
| Synonyms |
Smc4l1, 2500002A22Rik |
| MMRRC Submission |
044801-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.972)
|
| Stock # |
R6682 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
68912071-68941956 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 68914574 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Arginine
at position 62
(S62R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000047872
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000042901]
[ENSMUST00000107803]
[ENSMUST00000107812]
[ENSMUST00000136502]
[ENSMUST00000195525]
[ENSMUST00000148385]
[ENSMUST00000169064]
[ENSMUST00000148031]
[ENSMUST00000154741]
|
| AlphaFold |
Q8CG47 |
| PDB Structure |
Crystal Structure of the Mouse Condensin Hinge Domain [X-RAY DIFFRACTION]
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000042901
AA Change: S62R
PolyPhen 2
Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000047872
Gene: ENSMUSG00000034349
AA Change: S62R
| Domain | Start | End | E-Value | Type |
|---|
|
PDB:1W1W|D
|
89 |
238 |
1e-17 |
PDB |
|
Blast:AAA
|
104 |
238 |
3e-6 |
BLAST |
|
low complexity region
|
408 |
427 |
N/A |
INTRINSIC |
|
low complexity region
|
447 |
460 |
N/A |
INTRINSIC |
|
low complexity region
|
473 |
482 |
N/A |
INTRINSIC |
|
low complexity region
|
545 |
567 |
N/A |
INTRINSIC |
|
SMC_hinge
|
611 |
726 |
1.12e-31 |
SMART |
|
low complexity region
|
870 |
881 |
N/A |
INTRINSIC |
|
low complexity region
|
942 |
953 |
N/A |
INTRINSIC |
|
Blast:AAA
|
1102 |
1276 |
5e-26 |
BLAST |
|
PDB:3KTA|D
|
1125 |
1276 |
3e-30 |
PDB |
|
SCOP:d1e69a_
|
1188 |
1263 |
3e-5 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000083646
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000083672
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000107803
|
| SMART Domains |
Protein: ENSMUSP00000103433
Gene: ENSMUSG00000034349
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:AAA_23
|
59 |
329 |
1.3e-12 |
PFAM |
|
Pfam:AAA_21
|
81 |
199 |
5.2e-7 |
PFAM |
|
coiled coil region
|
369 |
482 |
N/A |
INTRINSIC |
|
coiled coil region
|
511 |
563 |
N/A |
INTRINSIC |
|
SMC_hinge
|
586 |
701 |
8.6e-36 |
SMART |
|
Pfam:SMC_N
|
738 |
1247 |
1.1e-35 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000107812
|
| SMART Domains |
Protein: ENSMUSP00000103442
Gene: ENSMUSG00000027778
| Domain | Start | End | E-Value | Type |
|---|
|
WD40
|
4 |
41 |
1.43e0 |
SMART |
|
Blast:WD40
|
46 |
93 |
4e-9 |
BLAST |
|
WD40
|
95 |
134 |
9.38e-5 |
SMART |
|
WD40
|
136 |
176 |
2.75e1 |
SMART |
|
WD40
|
177 |
216 |
1.42e-4 |
SMART |
|
WD40
|
219 |
256 |
1.56e-1 |
SMART |
|
WD40
|
258 |
297 |
2.75e1 |
SMART |
|
low complexity region
|
429 |
440 |
N/A |
INTRINSIC |
|
Blast:WD40
|
496 |
533 |
4e-18 |
BLAST |
|
low complexity region
|
764 |
772 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000136448
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000136502
AA Change: S62R
PolyPhen 2
Score 0.938 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000115033
Gene: ENSMUSG00000034349
AA Change: S62R
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SMC_N
|
81 |
303 |
1.2e-42 |
PFAM |
|
Pfam:AAA_23
|
84 |
336 |
2.6e-16 |
PFAM |
|
Pfam:AAA_21
|
106 |
227 |
1e-9 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000195525
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000148385
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000169064
|
| SMART Domains |
Protein: ENSMUSP00000133263
Gene: ENSMUSG00000027778
| Domain | Start | End | E-Value | Type |
|---|
|
WD40
|
4 |
41 |
1.43e0 |
SMART |
|
Blast:WD40
|
46 |
93 |
4e-9 |
BLAST |
|
WD40
|
95 |
134 |
9.38e-5 |
SMART |
|
WD40
|
136 |
176 |
2.75e1 |
SMART |
|
WD40
|
177 |
216 |
1.42e-4 |
SMART |
|
WD40
|
219 |
256 |
1.56e-1 |
SMART |
|
WD40
|
258 |
297 |
2.75e1 |
SMART |
|
low complexity region
|
429 |
440 |
N/A |
INTRINSIC |
|
Blast:WD40
|
496 |
533 |
4e-18 |
BLAST |
|
low complexity region
|
764 |
772 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000176135
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000192467
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000148031
|
| SMART Domains |
Protein: ENSMUSP00000122919
Gene: ENSMUSG00000027778
| Domain | Start | End | E-Value | Type |
|---|
|
WD40
|
4 |
41 |
1.43e0 |
SMART |
|
Blast:WD40
|
46 |
93 |
3e-10 |
BLAST |
|
WD40
|
95 |
134 |
9.38e-5 |
SMART |
|
Blast:WD40
|
136 |
159 |
1e-8 |
BLAST |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000152502
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000154741
|
| SMART Domains |
Protein: ENSMUSP00000118406
Gene: ENSMUSG00000027778
| Domain | Start | End | E-Value | Type |
|---|
|
WD40
|
4 |
41 |
1.43e0 |
SMART |
|
Blast:WD40
|
46 |
93 |
9e-10 |
BLAST |
|
WD40
|
95 |
134 |
9.38e-5 |
SMART |
|
WD40
|
136 |
176 |
2.75e1 |
SMART |
|
WD40
|
177 |
209 |
2.12e2 |
SMART |
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.4%
- 20x: 95.6%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the 'structural maintenance of chromosomes' (SMC) gene family. Members of this gene family play a role in two changes in chromosome structure during mitotic segregation of chromosomes- chromosome condensation and sister chromatid cohesion. The protein encoded by this gene is likely a subunit of the 13S condensin complex, which is involved in chromosome condensation. A pseudogene related to this gene is located on chromosome 2. [provided by RefSeq, Jun 2016]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 39 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aspm |
T |
C |
1: 139,385,460 (GRCm39) |
V368A |
possibly damaging |
Het |
| Bcl9l |
A |
G |
9: 44,412,400 (GRCm39) |
T92A |
possibly damaging |
Het |
| Celsr2 |
A |
T |
3: 108,307,817 (GRCm39) |
|
probably null |
Het |
| Cndp2 |
T |
C |
18: 84,695,455 (GRCm39) |
K149E |
probably benign |
Het |
| Cnpy4 |
T |
C |
5: 138,185,984 (GRCm39) |
|
probably null |
Het |
| Cox6c |
A |
T |
15: 35,938,319 (GRCm39) |
|
probably null |
Het |
| Cpt2 |
G |
T |
4: 107,761,627 (GRCm39) |
S158R |
probably damaging |
Het |
| Dlgap1 |
A |
G |
17: 71,094,118 (GRCm39) |
K813R |
probably damaging |
Het |
| Dock10 |
A |
C |
1: 80,490,338 (GRCm39) |
L1927R |
probably damaging |
Het |
| Gak |
T |
A |
5: 108,746,742 (GRCm39) |
K430I |
probably damaging |
Het |
| Grik3 |
T |
A |
4: 125,544,259 (GRCm39) |
Y327N |
probably damaging |
Het |
| Ldb3 |
T |
A |
14: 34,274,221 (GRCm39) |
T334S |
possibly damaging |
Het |
| Ldlr |
A |
G |
9: 21,643,671 (GRCm39) |
D85G |
probably benign |
Het |
| Med26 |
T |
A |
8: 73,249,927 (GRCm39) |
T391S |
probably benign |
Het |
| Mmp27 |
A |
G |
9: 7,573,606 (GRCm39) |
T233A |
probably benign |
Het |
| Mob1a |
A |
G |
6: 83,311,132 (GRCm39) |
Y117C |
possibly damaging |
Het |
| Mrps35 |
A |
T |
6: 146,949,777 (GRCm39) |
E97V |
possibly damaging |
Het |
| Msln |
A |
T |
17: 25,971,993 (GRCm39) |
S75T |
probably damaging |
Het |
| Myoz1 |
C |
T |
14: 20,703,687 (GRCm39) |
|
probably null |
Het |
| Nim1k |
A |
G |
13: 120,173,724 (GRCm39) |
I390T |
probably benign |
Het |
| Or10k2 |
A |
G |
8: 84,268,187 (GRCm39) |
H138R |
probably benign |
Het |
| Or4k51 |
C |
T |
2: 111,584,980 (GRCm39) |
P129S |
probably damaging |
Het |
| Pclo |
A |
C |
5: 14,589,893 (GRCm39) |
Q731P |
unknown |
Het |
| Prl3d3 |
G |
A |
13: 27,345,023 (GRCm39) |
E132K |
probably benign |
Het |
| Pth1r |
C |
T |
9: 110,556,319 (GRCm39) |
|
probably null |
Het |
| Ptpru |
T |
C |
4: 131,548,093 (GRCm39) |
M135V |
probably benign |
Het |
| Slc12a9 |
A |
T |
5: 137,325,663 (GRCm39) |
L316Q |
probably damaging |
Het |
| Slc35f6 |
G |
A |
5: 30,814,764 (GRCm39) |
M177I |
possibly damaging |
Het |
| Tmem179 |
C |
T |
12: 112,469,714 (GRCm39) |
D29N |
probably benign |
Het |
| Togaram2 |
A |
T |
17: 72,011,749 (GRCm39) |
D476V |
probably benign |
Het |
| Trpc4ap |
C |
T |
2: 155,479,687 (GRCm39) |
|
probably null |
Het |
| Trpm8 |
C |
A |
1: 88,254,224 (GRCm39) |
T149K |
probably damaging |
Het |
| Uhmk1 |
C |
T |
1: 170,039,804 (GRCm39) |
|
probably null |
Het |
| Vmn2r79 |
C |
A |
7: 86,653,370 (GRCm39) |
T545K |
possibly damaging |
Het |
| Vmn2r95 |
C |
A |
17: 18,660,489 (GRCm39) |
N300K |
probably damaging |
Het |
| Wdr41 |
G |
A |
13: 95,149,639 (GRCm39) |
G419D |
probably damaging |
Het |
| Zc3hav1 |
A |
T |
6: 38,302,130 (GRCm39) |
H597Q |
probably benign |
Het |
| Zfp704 |
T |
C |
3: 9,630,253 (GRCm39) |
E36G |
probably benign |
Het |
| Zfp9 |
A |
G |
6: 118,444,202 (GRCm39) |
V47A |
possibly damaging |
Het |
|
| Other mutations in Smc4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00401:Smc4
|
APN |
3 |
68,937,712 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL00542:Smc4
|
APN |
3 |
68,935,771 (GRCm39) |
splice site |
probably benign |
|
|
IGL01104:Smc4
|
APN |
3 |
68,934,917 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL01380:Smc4
|
APN |
3 |
68,933,161 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01397:Smc4
|
APN |
3 |
68,938,877 (GRCm39) |
missense |
probably benign |
|
|
IGL02441:Smc4
|
APN |
3 |
68,913,544 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02629:Smc4
|
APN |
3 |
68,933,206 (GRCm39) |
missense |
probably damaging |
0.96 |
|
IGL03220:Smc4
|
APN |
3 |
68,916,875 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
pyrrhic
|
UTSW |
3 |
68,934,835 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0452:Smc4
|
UTSW |
3 |
68,915,361 (GRCm39) |
nonsense |
probably null |
|
|
R0523:Smc4
|
UTSW |
3 |
68,933,221 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0568:Smc4
|
UTSW |
3 |
68,929,794 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0571:Smc4
|
UTSW |
3 |
68,931,622 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0602:Smc4
|
UTSW |
3 |
68,916,871 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0925:Smc4
|
UTSW |
3 |
68,913,548 (GRCm39) |
critical splice donor site |
probably benign |
|
|
R0963:Smc4
|
UTSW |
3 |
68,933,259 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1540:Smc4
|
UTSW |
3 |
68,924,105 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1755:Smc4
|
UTSW |
3 |
68,941,441 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1920:Smc4
|
UTSW |
3 |
68,940,401 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4226:Smc4
|
UTSW |
3 |
68,938,800 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4510:Smc4
|
UTSW |
3 |
68,923,980 (GRCm39) |
splice site |
probably null |
|
|
R4511:Smc4
|
UTSW |
3 |
68,923,980 (GRCm39) |
splice site |
probably null |
|
|
R4899:Smc4
|
UTSW |
3 |
68,939,144 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R4967:Smc4
|
UTSW |
3 |
68,925,572 (GRCm39) |
intron |
probably benign |
|
|
R5096:Smc4
|
UTSW |
3 |
68,928,612 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5101:Smc4
|
UTSW |
3 |
68,935,845 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5588:Smc4
|
UTSW |
3 |
68,933,190 (GRCm39) |
missense |
probably benign |
|
|
R5631:Smc4
|
UTSW |
3 |
68,937,645 (GRCm39) |
missense |
probably benign |
0.16 |
|
R5633:Smc4
|
UTSW |
3 |
68,915,443 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6229:Smc4
|
UTSW |
3 |
68,937,580 (GRCm39) |
nonsense |
probably null |
|
|
R6300:Smc4
|
UTSW |
3 |
68,935,224 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6554:Smc4
|
UTSW |
3 |
68,936,848 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6596:Smc4
|
UTSW |
3 |
68,933,226 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6603:Smc4
|
UTSW |
3 |
68,929,794 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6727:Smc4
|
UTSW |
3 |
68,924,105 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6955:Smc4
|
UTSW |
3 |
68,931,642 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R7037:Smc4
|
UTSW |
3 |
68,925,528 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
R7051:Smc4
|
UTSW |
3 |
68,934,835 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7454:Smc4
|
UTSW |
3 |
68,925,457 (GRCm39) |
missense |
probably benign |
|
|
R7630:Smc4
|
UTSW |
3 |
68,925,400 (GRCm39) |
critical splice acceptor site |
probably benign |
|
|
R7632:Smc4
|
UTSW |
3 |
68,925,400 (GRCm39) |
critical splice acceptor site |
probably benign |
|
|
R7633:Smc4
|
UTSW |
3 |
68,925,400 (GRCm39) |
critical splice acceptor site |
probably benign |
|
|
R7773:Smc4
|
UTSW |
3 |
68,923,496 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7857:Smc4
|
UTSW |
3 |
68,940,552 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
R8008:Smc4
|
UTSW |
3 |
68,914,645 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8398:Smc4
|
UTSW |
3 |
68,933,184 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8527:Smc4
|
UTSW |
3 |
68,940,224 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8936:Smc4
|
UTSW |
3 |
68,925,491 (GRCm39) |
missense |
probably benign |
0.21 |
|
R8998:Smc4
|
UTSW |
3 |
68,934,894 (GRCm39) |
utr 3 prime |
probably benign |
|
|
R9267:Smc4
|
UTSW |
3 |
68,941,786 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9440:Smc4
|
UTSW |
3 |
68,915,455 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9476:Smc4
|
UTSW |
3 |
68,914,662 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9510:Smc4
|
UTSW |
3 |
68,914,662 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9777:Smc4
|
UTSW |
3 |
68,929,655 (GRCm39) |
nonsense |
probably null |
|
|
X0063:Smc4
|
UTSW |
3 |
68,925,436 (GRCm39) |
missense |
possibly damaging |
0.47 |
|
| Predicted Primers |
PCR Primer
(F):5'- CCCCATGAGTTTAGGATATGTTTG -3'
(R):5'- GAGTCAGGACCGTTAGAACACTG -3'
Sequencing Primer
(F):5'- GCAGATGATAGACGTTCAAC -3'
(R):5'- GGACCGTTAGAACACTGAAATATC -3'
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| Posted On |
2018-07-23 |
Incidental Mutation