Incidental Mutation 'R4899:Smc4'
ID |
375990 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Smc4
|
Ensembl Gene |
ENSMUSG00000034349 |
Gene Name |
structural maintenance of chromosomes 4 |
Synonyms |
Smc4l1, 2500002A22Rik |
MMRRC Submission |
042503-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.971)
|
Stock # |
R4899 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
3 |
Chromosomal Location |
68912071-68941956 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 68939144 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Histidine to Glutamine
at position 978
(H978Q)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000103433
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000042901]
[ENSMUST00000107802]
[ENSMUST00000107803]
[ENSMUST00000148385]
[ENSMUST00000195525]
|
AlphaFold |
Q8CG47 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000042901
AA Change: H1003Q
PolyPhen 2
Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)
|
SMART Domains |
Protein: ENSMUSP00000047872 Gene: ENSMUSG00000034349 AA Change: H1003Q
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 |
probably damaging
Transcript: ENSMUST00000107803
AA Change: H978Q
PolyPhen 2
Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000103433 Gene: ENSMUSG00000034349 AA Change: H978Q
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: ENSMUST00000128118
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000148385
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000149174
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000195525
|
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.7%
- 20x: 93.7%
|
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: 75 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abhd18 |
C |
G |
3: 40,860,304 (GRCm39) |
|
probably null |
Het |
Adra2c |
A |
T |
5: 35,437,705 (GRCm39) |
Y159F |
probably damaging |
Het |
Alkal2 |
T |
A |
12: 30,934,972 (GRCm39) |
S64T |
probably benign |
Het |
Apbb1ip |
T |
C |
2: 22,713,361 (GRCm39) |
V72A |
unknown |
Het |
Atp13a5 |
A |
G |
16: 29,197,318 (GRCm39) |
L13P |
probably damaging |
Het |
Azin2 |
G |
A |
4: 128,828,446 (GRCm39) |
P254S |
probably benign |
Het |
Bmpr1b |
T |
C |
3: 141,546,444 (GRCm39) |
R481G |
probably damaging |
Het |
Cacna2d4 |
G |
A |
6: 119,245,157 (GRCm39) |
W288* |
probably null |
Het |
Cass4 |
A |
G |
2: 172,269,789 (GRCm39) |
T626A |
probably benign |
Het |
Cep112 |
T |
A |
11: 108,497,110 (GRCm39) |
D683E |
probably damaging |
Het |
Cfap300 |
A |
T |
9: 8,022,494 (GRCm39) |
S243T |
possibly damaging |
Het |
Chat |
G |
T |
14: 32,170,934 (GRCm39) |
S188R |
possibly damaging |
Het |
Cit |
A |
G |
5: 116,001,087 (GRCm39) |
Y162C |
possibly damaging |
Het |
Clca3a1 |
T |
A |
3: 144,443,722 (GRCm39) |
Y676F |
probably damaging |
Het |
Clec2h |
A |
G |
6: 128,652,787 (GRCm39) |
N185D |
probably benign |
Het |
Cnbd2 |
G |
T |
2: 156,181,141 (GRCm39) |
V192F |
probably benign |
Het |
Col6a3 |
C |
A |
1: 90,730,149 (GRCm39) |
G1112V |
probably damaging |
Het |
Csta2 |
A |
T |
16: 36,077,731 (GRCm39) |
Y96F |
possibly damaging |
Het |
Cyp3a25 |
A |
G |
5: 145,914,481 (GRCm39) |
F483S |
possibly damaging |
Het |
Dscam |
T |
C |
16: 96,485,018 (GRCm39) |
E1103G |
probably benign |
Het |
Dync2h1 |
G |
A |
9: 7,131,921 (GRCm39) |
Q1629* |
probably null |
Het |
Enpp6 |
A |
G |
8: 47,440,118 (GRCm39) |
Y38C |
probably damaging |
Het |
Epg5 |
T |
A |
18: 78,028,272 (GRCm39) |
L1271Q |
probably damaging |
Het |
Fam47e |
G |
A |
5: 92,722,528 (GRCm39) |
V75I |
probably benign |
Het |
Fat3 |
T |
C |
9: 15,881,095 (GRCm39) |
D3259G |
probably damaging |
Het |
Fbxw28 |
T |
C |
9: 109,159,921 (GRCm39) |
D211G |
probably damaging |
Het |
Flnc |
A |
G |
6: 29,446,842 (GRCm39) |
N990D |
probably benign |
Het |
Frat1 |
T |
G |
19: 41,818,761 (GRCm39) |
L52R |
probably damaging |
Het |
Ftmt |
C |
G |
18: 52,464,658 (GRCm39) |
|
probably benign |
Het |
H2-M1 |
C |
T |
17: 36,982,112 (GRCm39) |
G163D |
probably benign |
Het |
Hapln1 |
A |
G |
13: 89,749,769 (GRCm39) |
K105E |
possibly damaging |
Het |
Igkv17-127 |
G |
T |
6: 67,838,381 (GRCm39) |
A31S |
probably benign |
Het |
Il6st |
T |
C |
13: 112,637,695 (GRCm39) |
L628P |
probably damaging |
Het |
Kcnj6 |
A |
G |
16: 94,633,472 (GRCm39) |
I213T |
probably damaging |
Het |
Kidins220 |
T |
C |
12: 25,063,442 (GRCm39) |
|
probably null |
Het |
Lama2 |
TTTGCGCATT |
TTT |
10: 26,919,639 (GRCm39) |
|
probably null |
Het |
Llgl1 |
C |
T |
11: 60,600,394 (GRCm39) |
P581L |
probably benign |
Het |
Mertk |
C |
A |
2: 128,625,845 (GRCm39) |
P660Q |
probably damaging |
Het |
Mrtfa |
A |
G |
15: 80,902,587 (GRCm39) |
Y241H |
probably damaging |
Het |
Mtarc2 |
A |
T |
1: 184,577,821 (GRCm39) |
I65N |
probably damaging |
Het |
Napepld |
A |
G |
5: 21,888,438 (GRCm39) |
Y4H |
probably benign |
Het |
Ncam1 |
T |
A |
9: 49,456,551 (GRCm39) |
|
probably null |
Het |
Nuak2 |
A |
T |
1: 132,252,724 (GRCm39) |
K93* |
probably null |
Het |
Oat |
A |
T |
7: 132,165,951 (GRCm39) |
D211E |
probably benign |
Het |
Or1j19 |
A |
G |
2: 36,676,810 (GRCm39) |
Q91R |
probably benign |
Het |
Or2aj6 |
G |
A |
16: 19,442,950 (GRCm39) |
A300V |
probably benign |
Het |
Or4c109 |
A |
C |
2: 88,818,454 (GRCm39) |
L31V |
probably null |
Het |
Or51b17 |
A |
G |
7: 103,542,672 (GRCm39) |
I90T |
possibly damaging |
Het |
Or7a39 |
A |
T |
10: 78,715,041 (GRCm39) |
S12C |
probably benign |
Het |
Pde4dip |
C |
A |
3: 97,616,874 (GRCm39) |
K1789N |
probably damaging |
Het |
Piezo2 |
T |
C |
18: 63,211,862 (GRCm39) |
I1322V |
possibly damaging |
Het |
Pih1d1 |
A |
G |
7: 44,803,951 (GRCm39) |
|
probably benign |
Het |
Plekhd1 |
T |
C |
12: 80,769,101 (GRCm39) |
S454P |
probably damaging |
Het |
Polr2h |
G |
A |
16: 20,539,303 (GRCm39) |
V89M |
probably damaging |
Het |
Pptc7 |
G |
A |
5: 122,422,780 (GRCm39) |
G17S |
possibly damaging |
Het |
Pramel55 |
T |
C |
5: 95,949,586 (GRCm39) |
V111A |
probably benign |
Het |
Ptpra |
T |
C |
2: 130,386,356 (GRCm39) |
V602A |
probably damaging |
Het |
Rnf123 |
C |
T |
9: 107,940,879 (GRCm39) |
R654H |
probably damaging |
Het |
Rufy4 |
T |
C |
1: 74,186,822 (GRCm39) |
C537R |
probably damaging |
Het |
Samsn1 |
A |
G |
16: 75,675,991 (GRCm39) |
S135P |
probably damaging |
Het |
Sgsm3 |
A |
G |
15: 80,890,980 (GRCm39) |
N147S |
probably benign |
Het |
Shoc1 |
T |
C |
4: 59,062,640 (GRCm39) |
Y872C |
probably damaging |
Het |
Slc22a29 |
T |
C |
19: 8,138,933 (GRCm39) |
T510A |
probably benign |
Het |
Sox7 |
G |
A |
14: 64,185,927 (GRCm39) |
R321H |
probably damaging |
Het |
Spred3 |
T |
C |
7: 28,861,258 (GRCm39) |
D307G |
probably damaging |
Het |
Syne2 |
T |
A |
12: 75,900,875 (GRCm39) |
D11E |
probably benign |
Het |
Tob1 |
ACAGCAGCAGCAGCAGCAGCAGCAGCA |
ACAGCAGCAGCAGCAGCAGCAGCA |
11: 94,105,278 (GRCm39) |
|
probably benign |
Het |
Top2b |
A |
T |
14: 16,387,313 (GRCm38) |
I134F |
probably damaging |
Het |
Tspan1 |
T |
A |
4: 116,020,563 (GRCm39) |
R206* |
probably null |
Het |
Ttc3 |
A |
T |
16: 94,230,314 (GRCm39) |
N837I |
probably damaging |
Het |
Vmn1r36 |
T |
C |
6: 66,693,549 (GRCm39) |
T72A |
possibly damaging |
Het |
Vmn2r10 |
A |
G |
5: 109,151,324 (GRCm39) |
S97P |
probably damaging |
Het |
Zfp2 |
T |
A |
11: 50,790,841 (GRCm39) |
I401F |
probably damaging |
Het |
Zfp629 |
T |
C |
7: 127,210,190 (GRCm39) |
T540A |
possibly damaging |
Het |
Zfr |
G |
A |
15: 12,166,231 (GRCm39) |
V834I |
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 |
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 |
|
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'- TGGTTCTACATTACAGGGTAGATG -3'
(R):5'- CCATGCATGATGTATAGTCACTAC -3'
Sequencing Primer
(F):5'- AACTATGACCTTAAACTTTCGGTG -3'
(R):5'- GGTACTAGATTCCCTGGAGCTAC -3'
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Posted On |
2016-03-17 |