Incidental Mutation 'R0602:Smc4'
| ID |
55474 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smc4
|
| Ensembl Gene |
ENSMUSG00000034349 |
| Gene Name |
structural maintenance of chromosomes 4 |
| Synonyms |
Smc4l1, 2500002A22Rik |
| MMRRC Submission |
038791-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.972)
|
| Stock # |
R0602 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
68912071-68941956 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to C
at 68916871 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Proline
at position 187
(A187P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000115033
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000042901]
[ENSMUST00000107803]
[ENSMUST00000107812]
[ENSMUST00000136502]
[ENSMUST00000195525]
[ENSMUST00000148385]
[ENSMUST00000169064]
|
| AlphaFold |
Q8CG47 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000042901
AA Change: A187P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000047872
Gene: ENSMUSG00000034349
AA Change: A187P
| 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: A162P
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000103433
Gene: ENSMUSG00000034349
AA Change: A162P
| 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: A187P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000115033
Gene: ENSMUSG00000034349
AA Change: A187P
| 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 |
silent
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 |
|
| Meta Mutation Damage Score |
0.9685 |
| Coding Region Coverage |
- 1x: 99.6%
- 3x: 99.1%
- 10x: 97.5%
- 20x: 94.7%
|
| Validation Efficiency |
95% (58/61) |
| 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: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 9430038I01Rik |
T |
C |
7: 136,978,090 (GRCm39) |
|
probably benign |
Het |
| Arih1 |
A |
G |
9: 59,302,154 (GRCm39) |
|
probably benign |
Het |
| Bcl9 |
T |
C |
3: 97,113,102 (GRCm39) |
I1118V |
probably benign |
Het |
| Cap1 |
T |
C |
4: 122,766,202 (GRCm39) |
E12G |
probably damaging |
Het |
| Ccdc168 |
T |
A |
1: 44,099,127 (GRCm39) |
K657I |
possibly damaging |
Het |
| Ccr2 |
A |
G |
9: 123,906,658 (GRCm39) |
I313V |
probably benign |
Het |
| Cd1d2 |
T |
C |
3: 86,895,110 (GRCm39) |
S161P |
probably benign |
Het |
| Cd226 |
C |
T |
18: 89,287,135 (GRCm39) |
T311I |
probably benign |
Het |
| Col25a1 |
A |
G |
3: 130,369,063 (GRCm39) |
|
probably null |
Het |
| Cspg4 |
T |
C |
9: 56,795,301 (GRCm39) |
F1012S |
probably damaging |
Het |
| Dnah7b |
A |
G |
1: 46,364,002 (GRCm39) |
M3541V |
probably damaging |
Het |
| Erbb2 |
G |
A |
11: 98,325,097 (GRCm39) |
V852M |
probably damaging |
Het |
| Fer1l6 |
A |
C |
15: 58,449,794 (GRCm39) |
T667P |
probably damaging |
Het |
| Gal3st2c |
A |
G |
1: 93,936,901 (GRCm39) |
Y282C |
probably damaging |
Het |
| Glp1r |
T |
C |
17: 31,128,201 (GRCm39) |
L60P |
probably benign |
Het |
| Gtf2h2 |
A |
G |
13: 100,605,533 (GRCm39) |
V358A |
probably benign |
Het |
| H2ac18 |
T |
C |
3: 96,152,866 (GRCm39) |
|
probably benign |
Het |
| Hephl1 |
T |
A |
9: 15,000,347 (GRCm39) |
I302F |
probably damaging |
Het |
| Lgi2 |
T |
C |
5: 52,711,765 (GRCm39) |
D185G |
probably damaging |
Het |
| Lrtm1 |
T |
C |
14: 28,744,179 (GRCm39) |
|
probably benign |
Het |
| Megf10 |
T |
G |
18: 57,395,172 (GRCm39) |
D511E |
probably damaging |
Het |
| Myo5c |
A |
G |
9: 75,173,478 (GRCm39) |
|
probably null |
Het |
| Nrbf2 |
G |
A |
10: 67,103,605 (GRCm39) |
T166M |
probably damaging |
Het |
| Nrm |
C |
A |
17: 36,175,156 (GRCm39) |
Y61* |
probably null |
Het |
| Ola1 |
A |
G |
2: 72,924,056 (GRCm39) |
Y368H |
probably damaging |
Het |
| Or52s1 |
A |
C |
7: 102,861,787 (GRCm39) |
H229P |
possibly damaging |
Het |
| Or9i1b |
A |
G |
19: 13,897,145 (GRCm39) |
T254A |
probably benign |
Het |
| Or9q2 |
T |
C |
19: 13,772,026 (GRCm39) |
|
probably null |
Het |
| Panx1 |
A |
G |
9: 14,921,500 (GRCm39) |
L125P |
probably damaging |
Het |
| Pappa2 |
A |
G |
1: 158,590,625 (GRCm39) |
|
probably benign |
Het |
| Parp6 |
A |
G |
9: 59,556,648 (GRCm39) |
|
probably benign |
Het |
| Pomgnt2 |
A |
G |
9: 121,811,339 (GRCm39) |
Y481H |
probably benign |
Het |
| Ppp4c |
A |
G |
7: 126,388,254 (GRCm39) |
|
probably benign |
Het |
| Prl8a8 |
T |
A |
13: 27,692,533 (GRCm39) |
|
probably benign |
Het |
| Prpf40b |
C |
A |
15: 99,202,352 (GRCm39) |
A70E |
unknown |
Het |
| Ptgfr |
G |
A |
3: 151,540,839 (GRCm39) |
T223M |
probably damaging |
Het |
| Ptprc |
C |
T |
1: 138,017,223 (GRCm39) |
|
probably benign |
Het |
| Rgs22 |
T |
C |
15: 36,140,018 (GRCm39) |
|
probably benign |
Het |
| Rpgrip1 |
A |
G |
14: 52,371,313 (GRCm39) |
E344G |
possibly damaging |
Het |
| Sgca |
A |
T |
11: 94,854,061 (GRCm39) |
I383N |
possibly damaging |
Het |
| Sgms2 |
T |
A |
3: 131,118,756 (GRCm39) |
|
probably null |
Het |
| Slc9b1 |
C |
A |
3: 135,103,516 (GRCm39) |
Q549K |
probably benign |
Het |
| Smco1 |
A |
G |
16: 32,092,062 (GRCm39) |
S47G |
probably damaging |
Het |
| Sobp |
T |
A |
10: 42,898,385 (GRCm39) |
E400V |
probably damaging |
Het |
| Sp140l1 |
C |
G |
1: 85,077,226 (GRCm39) |
K113N |
probably benign |
Het |
| Stil |
T |
A |
4: 114,881,620 (GRCm39) |
|
probably benign |
Het |
| Sult3a2 |
A |
T |
10: 33,658,044 (GRCm39) |
M23K |
probably benign |
Het |
| Syne2 |
AGAGTGAG |
AGAGTGAGTGAG |
12: 76,144,734 (GRCm39) |
|
probably null |
Het |
| Tcam1 |
G |
A |
11: 106,174,904 (GRCm39) |
E120K |
probably benign |
Het |
| Tcof1 |
C |
A |
18: 60,966,605 (GRCm39) |
G329W |
probably damaging |
Het |
| Ttc13 |
A |
T |
8: 125,401,105 (GRCm39) |
S624T |
probably damaging |
Het |
| Vmn1r171 |
G |
T |
7: 23,332,602 (GRCm39) |
V276L |
probably benign |
Het |
| Vps13b |
T |
C |
15: 35,422,514 (GRCm39) |
L158P |
probably damaging |
Het |
| Vps54 |
A |
G |
11: 21,256,434 (GRCm39) |
I634M |
possibly damaging |
Het |
| Vwa8 |
T |
G |
14: 79,258,060 (GRCm39) |
S736R |
probably benign |
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 |
|
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 |
|
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'- TCATACACAATCTTTACTCGCAGACCCT -3'
(R):5'- ACACTCTTTCAAGCTTTAGTACAAGCCA -3'
Sequencing Primer
(F):5'- CAGTCACCAAGGTTATCTGAGTG -3'
(R):5'- TCAAGCTTTAGTACAAGCCAAAAATC -3'
|
| Posted On |
2013-07-11 |
Incidental Mutation