Incidental Mutation 'R7857:Smc4'
| ID |
607268 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smc4
|
| Ensembl Gene |
ENSMUSG00000034349 |
| Gene Name |
structural maintenance of chromosomes 4 |
| Synonyms |
Smc4l1, 2500002A22Rik |
| MMRRC Submission |
045910-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.971)
|
| Stock # |
R7857 (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 C
at 68940552 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 1162
(V1162A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000047872
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000042901]
[ENSMUST00000107802]
[ENSMUST00000107803]
[ENSMUST00000136512]
[ENSMUST00000148385]
[ENSMUST00000195525]
|
| AlphaFold |
Q8CG47 |
| PDB Structure |
Crystal Structure of the Mouse Condensin Hinge Domain [X-RAY DIFFRACTION]
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000042901
AA Change: V1162A
PolyPhen 2
Score 0.612 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000047872
Gene: ENSMUSG00000034349
AA Change: V1162A
| 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 |
probably benign
Transcript: ENSMUST00000107802
|
| SMART Domains |
Protein: ENSMUSP00000103432
Gene: ENSMUSG00000034317
| Domain | Start | End | E-Value | Type |
|---|
|
RING
|
10 |
59 |
2.44e-8 |
SMART |
|
Pfam:zf-B_box
|
92 |
134 |
5.9e-10 |
PFAM |
|
transmembrane domain
|
329 |
348 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000107803
AA Change: V1137A
PolyPhen 2
Score 0.903 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000103433
Gene: ENSMUSG00000034349
AA Change: V1137A
| 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: ENSMUST00000136512
|
| SMART Domains |
Protein: ENSMUSP00000120270
Gene: ENSMUSG00000034317
| Domain | Start | End | E-Value | Type |
|---|
|
RING
|
10 |
59 |
2.44e-8 |
SMART |
|
Pfam:zf-B_box
|
92 |
134 |
8.4e-10 |
PFAM |
|
transmembrane domain
|
329 |
348 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000148385
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000195525
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.2%
|
| 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: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam6b |
A |
T |
12: 113,454,104 (GRCm39) |
N307I |
probably benign |
Het |
| Ahnak |
G |
A |
19: 8,984,832 (GRCm39) |
V2039M |
probably damaging |
Het |
| Arhgef40 |
T |
A |
14: 52,226,212 (GRCm39) |
H85Q |
probably damaging |
Het |
| Ash1l |
T |
A |
3: 88,891,616 (GRCm39) |
L1165* |
probably null |
Het |
| Cck |
A |
G |
9: 121,322,514 (GRCm39) |
W100R |
probably damaging |
Het |
| Cdon |
A |
G |
9: 35,367,908 (GRCm39) |
R268G |
possibly damaging |
Het |
| Cldn12 |
T |
C |
5: 5,558,209 (GRCm39) |
T73A |
probably benign |
Het |
| Cnot1 |
ACG |
A |
8: 96,472,275 (GRCm39) |
|
probably null |
Het |
| Ctnnd2 |
A |
T |
15: 30,620,076 (GRCm39) |
T143S |
probably benign |
Het |
| Cyp2b13 |
T |
A |
7: 25,788,153 (GRCm39) |
L427Q |
possibly damaging |
Het |
| Dnah3 |
A |
T |
7: 119,550,927 (GRCm39) |
Y152N |
probably damaging |
Het |
| Dsg1b |
A |
T |
18: 20,529,520 (GRCm39) |
M322L |
probably benign |
Het |
| Efhc1 |
T |
C |
1: 21,045,226 (GRCm39) |
M414T |
probably benign |
Het |
| Elp3 |
G |
A |
14: 65,800,759 (GRCm39) |
T302M |
probably benign |
Het |
| Entpd6 |
T |
C |
2: 150,607,473 (GRCm39) |
|
probably null |
Het |
| Epb41l4a |
G |
T |
18: 34,139,098 (GRCm39) |
C13* |
probably null |
Het |
| Ephb6 |
T |
C |
6: 41,590,331 (GRCm39) |
S28P |
probably benign |
Het |
| Fbxo21 |
T |
C |
5: 118,126,878 (GRCm39) |
S210P |
probably benign |
Het |
| Gapvd1 |
T |
A |
2: 34,619,079 (GRCm39) |
E98V |
probably benign |
Het |
| Gcdh |
A |
G |
8: 85,619,093 (GRCm39) |
V157A |
probably damaging |
Het |
| Gm10638 |
G |
T |
8: 87,472,891 (GRCm39) |
R188L |
unknown |
Het |
| Grk3 |
T |
C |
5: 113,109,427 (GRCm39) |
T177A |
unknown |
Het |
| Gsc |
T |
G |
12: 104,438,424 (GRCm39) |
E148A |
probably damaging |
Het |
| Hacd4 |
C |
T |
4: 88,355,702 (GRCm39) |
G61E |
probably damaging |
Het |
| Herc3 |
G |
A |
6: 58,820,637 (GRCm39) |
W7* |
probably null |
Het |
| Il1rl2 |
T |
C |
1: 40,366,642 (GRCm39) |
Y59H |
probably benign |
Het |
| Irag1 |
T |
A |
7: 110,522,742 (GRCm39) |
K234* |
probably null |
Het |
| Kif1c |
A |
G |
11: 70,619,103 (GRCm39) |
T913A |
probably benign |
Het |
| Lipg |
C |
T |
18: 75,078,891 (GRCm39) |
G454R |
probably damaging |
Het |
| Lrrc74a |
A |
G |
12: 86,788,485 (GRCm39) |
D155G |
probably benign |
Het |
| Ltf |
A |
T |
9: 110,851,444 (GRCm39) |
I137F |
probably benign |
Het |
| Med19 |
T |
A |
2: 84,515,969 (GRCm39) |
M166K |
probably damaging |
Het |
| Mei1 |
A |
T |
15: 81,976,918 (GRCm39) |
Y167F |
not run |
Het |
| Ncaph |
A |
C |
2: 126,946,165 (GRCm39) |
D724E |
probably damaging |
Het |
| Neb |
T |
A |
2: 52,112,996 (GRCm39) |
D4266V |
probably damaging |
Het |
| Npffr1 |
G |
T |
10: 61,449,765 (GRCm39) |
W13L |
probably benign |
Het |
| Or51b6 |
A |
T |
7: 103,555,817 (GRCm39) |
H54L |
|
Het |
| Pcdha12 |
A |
T |
18: 37,155,468 (GRCm39) |
D729V |
probably benign |
Het |
| Pcdha7 |
A |
T |
18: 37,108,892 (GRCm39) |
E639V |
probably damaging |
Het |
| Pcdhb18 |
A |
T |
18: 37,624,364 (GRCm39) |
M565L |
probably benign |
Het |
| Plcd3 |
A |
T |
11: 102,968,760 (GRCm39) |
D310E |
probably benign |
Het |
| Pmm2 |
C |
G |
16: 8,460,632 (GRCm39) |
Q29E |
probably benign |
Het |
| Poli |
T |
G |
18: 70,642,225 (GRCm39) |
E658D |
probably benign |
Het |
| Prss22 |
G |
A |
17: 24,212,853 (GRCm39) |
R295C |
probably damaging |
Het |
| Psg26 |
A |
G |
7: 18,212,215 (GRCm39) |
I380T |
possibly damaging |
Het |
| Reep5 |
A |
T |
18: 34,505,521 (GRCm39) |
V50E |
possibly damaging |
Het |
| Rfx7 |
A |
G |
9: 72,500,605 (GRCm39) |
T122A |
possibly damaging |
Het |
| Robo1 |
A |
G |
16: 72,767,099 (GRCm39) |
N424D |
probably damaging |
Het |
| Slc4a7 |
T |
C |
14: 14,772,624 (GRCm38) |
V711A |
probably benign |
Het |
| Snta1 |
A |
T |
2: 154,225,817 (GRCm39) |
L189H |
probably benign |
Het |
| Tmem121 |
C |
T |
12: 113,152,696 (GRCm39) |
R305C |
possibly damaging |
Het |
| Tmem68 |
A |
G |
4: 3,551,825 (GRCm39) |
V271A |
probably damaging |
Het |
| Tmx4 |
T |
G |
2: 134,481,582 (GRCm39) |
M114L |
probably benign |
Het |
| Trps1 |
T |
A |
15: 50,524,401 (GRCm39) |
R1176S |
probably damaging |
Het |
| Usp21 |
A |
G |
1: 171,114,335 (GRCm39) |
L63P |
probably benign |
Het |
| Vmn2r84 |
T |
A |
10: 130,226,738 (GRCm39) |
M367L |
probably benign |
Het |
| Wbp2nl |
A |
G |
15: 82,190,273 (GRCm39) |
N67S |
probably benign |
Het |
| Wdr35 |
T |
C |
12: 9,058,113 (GRCm39) |
|
probably null |
Het |
| Zfp236 |
G |
A |
18: 82,686,726 (GRCm39) |
Q271* |
probably null |
Het |
| Zfp831 |
T |
C |
2: 174,547,035 (GRCm39) |
V1406A |
probably benign |
Het |
| Zfp934 |
G |
A |
13: 62,665,361 (GRCm39) |
H459Y |
|
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 |
|
|
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 |
|
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'- GCCGAACTGGACAAAATTACTTC -3'
(R):5'- GGCATGCTGGGACTATAGATG -3'
Sequencing Primer
(F):5'- ACTGGACAAAATTACTTCTGAAAGAG -3'
(R):5'- GTTCCAACCTTCACACACT -3'
|
| Posted On |
2019-12-20 |
Incidental Mutation