Incidental Mutation 'R5633:Smc4'
| ID |
439965 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smc4
|
| Ensembl Gene |
ENSMUSG00000034349 |
| Gene Name |
structural maintenance of chromosomes 4 |
| Synonyms |
Smc4l1, 2500002A22Rik |
| MMRRC Submission |
043284-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.971)
|
| Stock # |
R5633 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
68912071-68941956 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 68915443 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Lysine
at position 165
(I165K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000115033
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000042901]
[ENSMUST00000107803]
[ENSMUST00000107812]
[ENSMUST00000136502]
[ENSMUST00000169064]
[ENSMUST00000195525]
[ENSMUST00000154741]
[ENSMUST00000148385]
[ENSMUST00000148031]
|
| AlphaFold |
Q8CG47 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000042901
AA Change: I165K
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000047872
Gene: ENSMUSG00000034349
AA Change: I165K
| 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 damaging
Transcript: ENSMUST00000107803
AA Change: I140K
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000103433
Gene: ENSMUSG00000034349
AA Change: I140K
| 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 |
probably damaging
Transcript: ENSMUST00000136502
AA Change: I165K
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000115033
Gene: ENSMUSG00000034349
AA Change: I165K
| 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 |
noncoding transcript
Transcript: ENSMUST00000176135
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000192467
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000152502
|
| 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 |
probably benign
Transcript: ENSMUST00000195525
|
| 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 |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000148385
|
| 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 |
|
| Meta Mutation Damage Score |
0.6760 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.8%
- 10x: 97.6%
- 20x: 96.0%
|
| Validation Efficiency |
98% (55/56) |
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aadacl4 |
T |
A |
4: 144,344,598 (GRCm39) |
C125S |
probably benign |
Het |
| Abcb8 |
T |
C |
5: 24,608,107 (GRCm39) |
L382P |
probably damaging |
Het |
| Acot3 |
A |
G |
12: 84,105,724 (GRCm39) |
|
probably null |
Het |
| Acsl6 |
A |
T |
11: 54,228,015 (GRCm39) |
Q345L |
probably benign |
Het |
| Adcy8 |
A |
G |
15: 64,571,134 (GRCm39) |
S1170P |
probably damaging |
Het |
| Ankrd28 |
T |
G |
14: 31,457,022 (GRCm39) |
D182A |
probably damaging |
Het |
| B3galt5 |
A |
T |
16: 96,116,709 (GRCm39) |
H114L |
probably benign |
Het |
| Bcas2 |
T |
A |
3: 103,085,740 (GRCm39) |
Y207* |
probably null |
Het |
| Best1 |
A |
G |
19: 9,969,467 (GRCm39) |
L197P |
probably benign |
Het |
| Chil6 |
C |
A |
3: 106,296,068 (GRCm39) |
C389F |
probably damaging |
Het |
| Chrna4 |
T |
C |
2: 180,671,253 (GRCm39) |
T168A |
probably damaging |
Het |
| Ckmt1 |
C |
G |
2: 121,194,110 (GRCm39) |
|
probably benign |
Het |
| Dhcr7 |
T |
C |
7: 143,401,160 (GRCm39) |
L441P |
probably damaging |
Het |
| Dmtn |
T |
C |
14: 70,842,419 (GRCm39) |
M365V |
probably benign |
Het |
| Dmxl1 |
T |
A |
18: 50,010,764 (GRCm39) |
S974T |
probably damaging |
Het |
| Dnajb13 |
T |
C |
7: 100,156,626 (GRCm39) |
D150G |
probably benign |
Het |
| Eef2k |
C |
A |
7: 120,472,513 (GRCm39) |
|
probably benign |
Het |
| Elp2 |
T |
A |
18: 24,748,267 (GRCm39) |
V213E |
probably damaging |
Het |
| Fbxo43 |
A |
T |
15: 36,162,241 (GRCm39) |
|
probably null |
Het |
| Gm11559 |
C |
A |
11: 99,755,412 (GRCm39) |
C20* |
probably null |
Het |
| Gnb2 |
T |
C |
5: 137,527,454 (GRCm39) |
I213V |
probably benign |
Het |
| Gnb5 |
C |
T |
9: 75,251,796 (GRCm39) |
T306I |
probably damaging |
Het |
| Ica1 |
A |
T |
6: 8,667,257 (GRCm39) |
I303N |
possibly damaging |
Het |
| Idh1 |
A |
G |
1: 65,204,295 (GRCm39) |
Y272H |
probably damaging |
Het |
| Ikzf2 |
G |
A |
1: 69,578,256 (GRCm39) |
Q273* |
probably null |
Het |
| Itpkb |
A |
T |
1: 180,154,790 (GRCm39) |
⇒1 |
probably benign |
Het |
| Kntc1 |
C |
T |
5: 123,957,120 (GRCm39) |
T2143I |
probably damaging |
Het |
| Lin9 |
T |
A |
1: 180,496,763 (GRCm39) |
L351I |
probably benign |
Het |
| Lmbrd1 |
C |
A |
1: 24,787,943 (GRCm39) |
D464E |
possibly damaging |
Het |
| Med13 |
A |
G |
11: 86,169,757 (GRCm39) |
|
probably benign |
Het |
| Mn1 |
T |
C |
5: 111,568,192 (GRCm39) |
F721L |
possibly damaging |
Het |
| Myo9a |
T |
A |
9: 59,775,467 (GRCm39) |
L1026Q |
possibly damaging |
Het |
| Or6c204 |
A |
T |
10: 129,022,718 (GRCm39) |
F191I |
probably benign |
Het |
| P4htm |
A |
C |
9: 108,456,922 (GRCm39) |
D428E |
probably damaging |
Het |
| Parp8 |
C |
T |
13: 117,013,116 (GRCm39) |
R602H |
probably damaging |
Het |
| Pkd2 |
T |
A |
5: 104,646,372 (GRCm39) |
S726R |
probably damaging |
Het |
| Pla2g6 |
A |
T |
15: 79,183,342 (GRCm39) |
I495N |
possibly damaging |
Het |
| Psmd5 |
A |
G |
2: 34,746,500 (GRCm39) |
I359T |
probably benign |
Het |
| Rassf6 |
T |
C |
5: 90,751,977 (GRCm39) |
H292R |
possibly damaging |
Het |
| Rnf145 |
T |
C |
11: 44,450,915 (GRCm39) |
I413T |
probably damaging |
Het |
| Rpn2 |
T |
A |
2: 157,125,516 (GRCm39) |
V9D |
possibly damaging |
Het |
| Rpp30 |
T |
C |
19: 36,064,390 (GRCm39) |
L57P |
probably damaging |
Het |
| Slc41a1 |
A |
G |
1: 131,774,325 (GRCm39) |
H464R |
possibly damaging |
Het |
| Slc47a1 |
G |
T |
11: 61,260,087 (GRCm39) |
P163Q |
probably damaging |
Het |
| Stra6l |
T |
A |
4: 45,881,455 (GRCm39) |
I439K |
probably benign |
Het |
| Syt9 |
C |
T |
7: 107,024,503 (GRCm39) |
T132I |
probably damaging |
Het |
| Timd6 |
C |
T |
11: 46,465,433 (GRCm39) |
S9L |
unknown |
Het |
| Trpm2 |
T |
C |
10: 77,774,187 (GRCm39) |
I471V |
possibly damaging |
Het |
| Uap1l1 |
A |
G |
2: 25,253,361 (GRCm39) |
M358T |
probably benign |
Het |
| Vmn1r91 |
A |
T |
7: 19,835,870 (GRCm39) |
H263L |
possibly damaging |
Het |
| Zfp407 |
T |
C |
18: 84,579,169 (GRCm39) |
D648G |
probably benign |
Het |
| Zpbp2 |
T |
C |
11: 98,445,584 (GRCm39) |
I150T |
probably 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 |
|
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 |
|
|
R6682:Smc4
|
UTSW |
3 |
68,914,574 (GRCm39) |
missense |
probably damaging |
0.98 |
|
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'- TGTATTATTGGACCAAATGGCAGTG -3'
(R):5'- GCCCATATTTATAGTGAGTGAATGCTG -3'
Sequencing Primer
(F):5'- CCAAATGGCAGTGGAAAATCC -3'
(R):5'- TGAATTAGCACTTAGGGCCC -3'
|
| Posted On |
2016-11-08 |
Incidental Mutation