Incidental Mutation 'R0568:Smc4'
| ID |
46250 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smc4
|
| Ensembl Gene |
ENSMUSG00000034349 |
| Gene Name |
structural maintenance of chromosomes 4 |
| Synonyms |
Smc4l1, 2500002A22Rik |
| MMRRC Submission |
038759-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.972)
|
| Stock # |
R0568 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
68912071-68941956 bp(+) (GRCm39) |
| Type of Mutation |
critical splice donor site (2 bp from exon) |
| DNA Base Change (assembly) |
T to C
at 68929794 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000103433
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000042901]
[ENSMUST00000107803]
[ENSMUST00000136502]
[ENSMUST00000148385]
[ENSMUST00000195525]
|
| AlphaFold |
Q8CG47 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000042901
|
| SMART Domains |
Protein: ENSMUSP00000047872
Gene: ENSMUSG00000034349
| 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 null
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 |
noncoding transcript
Transcript: ENSMUST00000124983
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128134
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000136502
|
| SMART Domains |
Protein: ENSMUSP00000115033
Gene: ENSMUSG00000034349
| 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: ENSMUST00000148385
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000149174
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000194693
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000156354
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000195525
|
| Meta Mutation Damage Score |
0.9590 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.4%
- 10x: 96.5%
- 20x: 93.4%
|
| Validation Efficiency |
100% (38/38) |
| 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: 37 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acnat1 |
G |
A |
4: 49,451,003 (GRCm39) |
T36I |
possibly damaging |
Het |
| Adamts20 |
T |
C |
15: 94,189,594 (GRCm39) |
|
probably benign |
Het |
| Adamtsl1 |
T |
C |
4: 86,336,789 (GRCm39) |
L1558S |
probably damaging |
Het |
| Ap3b2 |
A |
G |
7: 81,114,377 (GRCm39) |
|
probably null |
Het |
| Bag2 |
T |
C |
1: 33,786,059 (GRCm39) |
M88V |
probably benign |
Het |
| Brms1l |
A |
G |
12: 55,908,173 (GRCm39) |
|
probably null |
Het |
| C8b |
A |
G |
4: 104,650,577 (GRCm39) |
I462V |
probably benign |
Het |
| Cfap410 |
C |
T |
10: 77,818,872 (GRCm39) |
T181I |
possibly damaging |
Het |
| Cfap410 |
A |
T |
10: 77,820,381 (GRCm39) |
*250C |
probably null |
Het |
| Cnpy4 |
A |
G |
5: 138,190,839 (GRCm39) |
E167G |
probably damaging |
Het |
| Copa |
T |
C |
1: 171,939,704 (GRCm39) |
V624A |
possibly damaging |
Het |
| Gm4553 |
G |
T |
7: 141,719,357 (GRCm39) |
P24T |
unknown |
Het |
| Gna12 |
A |
G |
5: 140,746,638 (GRCm39) |
V269A |
possibly damaging |
Het |
| Gtf2ird2 |
G |
T |
5: 134,240,083 (GRCm39) |
E302* |
probably null |
Het |
| Hmcn2 |
C |
A |
2: 31,305,248 (GRCm39) |
S3140R |
probably benign |
Het |
| Hspa4 |
A |
G |
11: 53,153,703 (GRCm39) |
|
probably benign |
Het |
| Hspbp1 |
A |
T |
7: 4,687,431 (GRCm39) |
L60* |
probably null |
Het |
| Lats1 |
A |
T |
10: 7,588,292 (GRCm39) |
I970F |
possibly damaging |
Het |
| Lipo3 |
T |
C |
19: 33,559,442 (GRCm39) |
|
probably benign |
Het |
| Lrrc3 |
T |
A |
10: 77,737,419 (GRCm39) |
R6W |
probably damaging |
Het |
| Lxn |
C |
T |
3: 67,368,335 (GRCm39) |
A143T |
probably damaging |
Het |
| Mga |
T |
C |
2: 119,765,903 (GRCm39) |
I1390T |
probably damaging |
Het |
| Ncapg2 |
T |
A |
12: 116,386,835 (GRCm39) |
I286N |
probably damaging |
Het |
| Or4c107 |
T |
A |
2: 88,789,387 (GRCm39) |
Y192* |
probably null |
Het |
| Pitpnm2 |
A |
G |
5: 124,278,580 (GRCm39) |
|
probably benign |
Het |
| Plxna2 |
T |
C |
1: 194,433,694 (GRCm39) |
V581A |
probably benign |
Het |
| Polr3d |
A |
T |
14: 70,676,959 (GRCm39) |
H378Q |
possibly damaging |
Het |
| Ptpn13 |
T |
C |
5: 103,637,631 (GRCm39) |
V173A |
probably damaging |
Het |
| Rbpms2 |
ACTGCTGCTGCTGCTGC |
ACTGCTGCTGCTGCTGCTGC |
9: 65,558,948 (GRCm39) |
|
probably benign |
Het |
| Snrnp40 |
C |
G |
4: 130,271,836 (GRCm39) |
|
probably null |
Het |
| Syngr3 |
C |
T |
17: 24,905,555 (GRCm39) |
A140T |
probably benign |
Het |
| Tent2 |
A |
G |
13: 93,291,500 (GRCm39) |
S381P |
probably benign |
Het |
| Tprn |
T |
C |
2: 25,154,333 (GRCm39) |
V545A |
probably damaging |
Het |
| Trim66 |
T |
C |
7: 109,059,902 (GRCm39) |
H828R |
probably benign |
Het |
| Ugt2b5 |
G |
A |
5: 87,285,224 (GRCm39) |
|
probably benign |
Het |
| Vps9d1 |
A |
G |
8: 123,973,487 (GRCm39) |
V432A |
probably damaging |
Het |
| Zswim9 |
A |
T |
7: 12,994,952 (GRCm39) |
D401E |
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 |
|
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 |
|
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'- TCAAAGATGGAAGTTGCTCAGTCAGAAC -3'
(R):5'- GGAGGTGGTGGGGATGTCTAACTAA -3'
Sequencing Primer
(F):5'- TCAGAACTTGATATCTATCTCAGTCG -3'
(R):5'- agccatctctccagccc -3'
|
| Posted On |
2013-06-11 |
Incidental Mutation