Incidental Mutation 'R5754:Smc5'
ID |
444979 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Smc5
|
Ensembl Gene |
ENSMUSG00000024943 |
Gene Name |
structural maintenance of chromosomes 5 |
Synonyms |
Smc5l1 |
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R5754 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
19 |
Chromosomal Location |
23183815-23251261 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 23221467 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Glutamic Acid to Glycine
at position 354
(E354G)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000153364
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000087556]
[ENSMUST00000223934]
[ENSMUST00000226111]
|
AlphaFold |
Q8CG46 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000087556
AA Change: E354G
PolyPhen 2
Score 0.915 (Sensitivity: 0.81; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000084837 Gene: ENSMUSG00000024943 AA Change: E354G
Domain | Start | End | E-Value | Type |
Pfam:SMC_N
|
52 |
1057 |
9.2e-19 |
PFAM |
Pfam:AAA_23
|
55 |
456 |
1.2e-9 |
PFAM |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000223934
AA Change: E354G
PolyPhen 2
Score 0.915 (Sensitivity: 0.81; Specificity: 0.94)
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000226111
AA Change: E278G
PolyPhen 2
Score 0.228 (Sensitivity: 0.91; Specificity: 0.88)
|
Meta Mutation Damage Score |
0.1585 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.8%
|
Validation Efficiency |
98% (61/62) |
MGI Phenotype |
PHENOTYPE: Homozygous knockout in embryonic stem cells causes abnormal mitosis, increased apoptosis and a shift from pluripotency to differentiation. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 57 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abcb4 |
T |
A |
5: 8,984,320 (GRCm39) |
N683K |
probably benign |
Het |
Atad2b |
T |
A |
12: 5,060,351 (GRCm39) |
H915Q |
probably benign |
Het |
Bltp2 |
T |
C |
11: 78,160,367 (GRCm39) |
S609P |
probably damaging |
Het |
Camk1d |
G |
T |
2: 5,449,908 (GRCm39) |
P91Q |
probably benign |
Het |
Camk1d |
G |
C |
2: 5,449,910 (GRCm39) |
S90R |
probably damaging |
Het |
Card11 |
T |
C |
5: 140,885,524 (GRCm39) |
E345G |
probably damaging |
Het |
Ccpg1 |
G |
T |
9: 72,920,526 (GRCm39) |
V714L |
possibly damaging |
Het |
Chst9 |
T |
C |
18: 15,586,254 (GRCm39) |
E103G |
possibly damaging |
Het |
Cnga1 |
C |
T |
5: 72,762,615 (GRCm39) |
V300I |
probably benign |
Het |
Crb1 |
T |
C |
1: 139,159,337 (GRCm39) |
Y1295C |
probably damaging |
Het |
Dnah5 |
A |
G |
15: 28,402,014 (GRCm39) |
T3392A |
probably benign |
Het |
Elp3 |
C |
A |
14: 65,785,439 (GRCm39) |
R473L |
probably damaging |
Het |
Epgn |
T |
A |
5: 91,181,807 (GRCm39) |
I145N |
probably benign |
Het |
Fam107b |
G |
A |
2: 3,779,457 (GRCm39) |
G220D |
probably damaging |
Het |
Fbn2 |
A |
G |
18: 58,257,383 (GRCm39) |
V328A |
probably benign |
Het |
Fn1 |
A |
T |
1: 71,639,481 (GRCm39) |
I1770N |
probably damaging |
Het |
Fndc1 |
T |
A |
17: 7,988,585 (GRCm39) |
Y1159F |
unknown |
Het |
Frem2 |
A |
G |
3: 53,444,679 (GRCm39) |
L2484P |
probably damaging |
Het |
Grk2 |
C |
T |
19: 4,340,496 (GRCm39) |
R295H |
probably damaging |
Het |
Gtf3c1 |
A |
T |
7: 125,243,237 (GRCm39) |
V1789D |
possibly damaging |
Het |
Hmgcl |
T |
C |
4: 135,677,898 (GRCm39) |
V33A |
probably damaging |
Het |
Ighv7-1 |
A |
G |
12: 113,860,239 (GRCm39) |
F51S |
probably damaging |
Het |
Kcna6 |
A |
G |
6: 126,716,688 (GRCm39) |
L67P |
probably damaging |
Het |
Lamc1 |
A |
T |
1: 153,123,030 (GRCm39) |
V720E |
probably benign |
Het |
Lrch1 |
T |
C |
14: 75,054,558 (GRCm39) |
D312G |
probably damaging |
Het |
Mix23 |
A |
G |
16: 35,905,427 (GRCm39) |
N63S |
probably benign |
Het |
Nav2 |
A |
G |
7: 49,206,794 (GRCm39) |
T1540A |
probably damaging |
Het |
Nisch |
A |
T |
14: 30,913,373 (GRCm39) |
|
probably benign |
Het |
Nos1ap |
T |
A |
1: 170,176,968 (GRCm39) |
K145M |
probably damaging |
Het |
Npc1l1 |
A |
G |
11: 6,177,839 (GRCm39) |
Y524H |
probably damaging |
Het |
Nrap |
T |
C |
19: 56,377,916 (GRCm39) |
T25A |
possibly damaging |
Het |
Nusap1 |
A |
G |
2: 119,477,580 (GRCm39) |
K363R |
probably damaging |
Het |
Or5ar1 |
T |
C |
2: 85,671,656 (GRCm39) |
T160A |
probably damaging |
Het |
Or5b124 |
A |
G |
19: 13,611,357 (GRCm39) |
E294G |
probably damaging |
Het |
Or7e177 |
T |
A |
9: 20,212,390 (GRCm39) |
L298Q |
probably damaging |
Het |
Pde4d |
T |
C |
13: 110,074,547 (GRCm39) |
I384T |
probably damaging |
Het |
Pkhd1 |
T |
A |
1: 20,593,875 (GRCm39) |
R1413* |
probably null |
Het |
Plcd3 |
T |
A |
11: 102,964,592 (GRCm39) |
Y593F |
possibly damaging |
Het |
Plxna1 |
A |
T |
6: 89,310,087 (GRCm39) |
I1026N |
possibly damaging |
Het |
Podxl |
T |
A |
6: 31,501,329 (GRCm39) |
I409F |
probably damaging |
Het |
Polq |
A |
C |
16: 36,837,625 (GRCm39) |
Q179P |
probably benign |
Het |
Pomt1 |
T |
C |
2: 32,137,602 (GRCm39) |
V401A |
probably damaging |
Het |
Qdpr |
C |
T |
5: 45,596,727 (GRCm39) |
G146S |
probably damaging |
Het |
Shc4 |
T |
A |
2: 125,512,218 (GRCm39) |
Q2L |
probably damaging |
Het |
Skint8 |
T |
A |
4: 111,807,387 (GRCm39) |
C358S |
probably benign |
Het |
Snx30 |
T |
C |
4: 59,868,275 (GRCm39) |
V129A |
probably damaging |
Het |
Sp110 |
G |
C |
1: 85,504,923 (GRCm39) |
|
probably benign |
Het |
Spag6 |
T |
A |
2: 18,703,613 (GRCm39) |
|
probably benign |
Het |
Trim28 |
T |
A |
7: 12,763,036 (GRCm39) |
Y450N |
probably benign |
Het |
Trip11 |
C |
T |
12: 101,851,924 (GRCm39) |
W428* |
probably null |
Het |
Umodl1 |
T |
A |
17: 31,213,761 (GRCm39) |
V966E |
probably damaging |
Het |
Utf1 |
A |
G |
7: 139,524,704 (GRCm39) |
|
probably benign |
Het |
Vmn1r72 |
T |
C |
7: 11,403,776 (GRCm39) |
Y224C |
probably damaging |
Het |
Whrn |
A |
G |
4: 63,334,825 (GRCm39) |
S748P |
probably damaging |
Het |
Zbtb41 |
T |
A |
1: 139,359,816 (GRCm39) |
|
probably null |
Het |
Zfhx3 |
T |
C |
8: 109,526,964 (GRCm39) |
F954L |
probably damaging |
Het |
Zfp456 |
A |
T |
13: 67,514,359 (GRCm39) |
I449K |
probably benign |
Het |
|
Other mutations in Smc5 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00569:Smc5
|
APN |
19 |
23,213,329 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01070:Smc5
|
APN |
19 |
23,208,965 (GRCm39) |
missense |
possibly damaging |
0.86 |
IGL01315:Smc5
|
APN |
19 |
23,208,968 (GRCm39) |
missense |
probably benign |
|
IGL01879:Smc5
|
APN |
19 |
23,205,548 (GRCm39) |
missense |
probably damaging |
0.97 |
IGL01902:Smc5
|
APN |
19 |
23,237,132 (GRCm39) |
missense |
possibly damaging |
0.85 |
IGL02016:Smc5
|
APN |
19 |
23,251,076 (GRCm39) |
missense |
probably benign |
0.00 |
IGL02186:Smc5
|
APN |
19 |
23,209,223 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL02383:Smc5
|
APN |
19 |
23,191,996 (GRCm39) |
splice site |
probably benign |
|
IGL02447:Smc5
|
APN |
19 |
23,234,856 (GRCm39) |
missense |
probably benign |
0.01 |
IGL02534:Smc5
|
APN |
19 |
23,205,536 (GRCm39) |
critical splice donor site |
probably null |
|
IGL02834:Smc5
|
APN |
19 |
23,234,968 (GRCm39) |
missense |
probably benign |
0.30 |
IGL03290:Smc5
|
APN |
19 |
23,251,022 (GRCm39) |
missense |
probably benign |
0.19 |
R0722:Smc5
|
UTSW |
19 |
23,186,291 (GRCm39) |
missense |
probably damaging |
0.99 |
R0893:Smc5
|
UTSW |
19 |
23,241,017 (GRCm39) |
missense |
possibly damaging |
0.67 |
R0970:Smc5
|
UTSW |
19 |
23,216,362 (GRCm39) |
missense |
probably damaging |
1.00 |
R1281:Smc5
|
UTSW |
19 |
23,213,247 (GRCm39) |
missense |
probably benign |
|
R1368:Smc5
|
UTSW |
19 |
23,187,807 (GRCm39) |
missense |
probably damaging |
1.00 |
R2092:Smc5
|
UTSW |
19 |
23,216,263 (GRCm39) |
missense |
probably benign |
|
R3721:Smc5
|
UTSW |
19 |
23,187,856 (GRCm39) |
missense |
probably benign |
0.21 |
R4382:Smc5
|
UTSW |
19 |
23,246,210 (GRCm39) |
missense |
probably benign |
0.39 |
R4735:Smc5
|
UTSW |
19 |
23,220,069 (GRCm39) |
missense |
probably benign |
|
R4936:Smc5
|
UTSW |
19 |
23,211,367 (GRCm39) |
missense |
probably damaging |
1.00 |
R5306:Smc5
|
UTSW |
19 |
23,237,009 (GRCm39) |
critical splice donor site |
probably null |
|
R6175:Smc5
|
UTSW |
19 |
23,191,534 (GRCm39) |
missense |
possibly damaging |
0.60 |
R6313:Smc5
|
UTSW |
19 |
23,186,312 (GRCm39) |
nonsense |
probably null |
|
R6527:Smc5
|
UTSW |
19 |
23,205,554 (GRCm39) |
missense |
probably benign |
0.00 |
R6611:Smc5
|
UTSW |
19 |
23,206,283 (GRCm39) |
missense |
probably benign |
0.13 |
R6750:Smc5
|
UTSW |
19 |
23,220,004 (GRCm39) |
missense |
probably damaging |
1.00 |
R6801:Smc5
|
UTSW |
19 |
23,192,010 (GRCm39) |
missense |
probably benign |
0.34 |
R6821:Smc5
|
UTSW |
19 |
23,220,151 (GRCm39) |
missense |
probably benign |
0.20 |
R7002:Smc5
|
UTSW |
19 |
23,209,247 (GRCm39) |
missense |
probably benign |
0.00 |
R7198:Smc5
|
UTSW |
19 |
23,237,064 (GRCm39) |
nonsense |
probably null |
|
R7386:Smc5
|
UTSW |
19 |
23,192,539 (GRCm39) |
missense |
possibly damaging |
0.59 |
R7439:Smc5
|
UTSW |
19 |
23,220,064 (GRCm39) |
missense |
probably damaging |
0.97 |
R7596:Smc5
|
UTSW |
19 |
23,191,533 (GRCm39) |
missense |
probably damaging |
0.99 |
R7666:Smc5
|
UTSW |
19 |
23,206,381 (GRCm39) |
missense |
probably benign |
0.15 |
R7760:Smc5
|
UTSW |
19 |
23,213,254 (GRCm39) |
missense |
probably benign |
0.01 |
R7990:Smc5
|
UTSW |
19 |
23,213,246 (GRCm39) |
missense |
probably benign |
0.01 |
R8255:Smc5
|
UTSW |
19 |
23,186,290 (GRCm39) |
missense |
|
|
R8359:Smc5
|
UTSW |
19 |
23,211,443 (GRCm39) |
missense |
possibly damaging |
0.49 |
R8473:Smc5
|
UTSW |
19 |
23,221,446 (GRCm39) |
missense |
probably benign |
0.02 |
R8711:Smc5
|
UTSW |
19 |
23,243,058 (GRCm39) |
missense |
probably damaging |
0.98 |
R8815:Smc5
|
UTSW |
19 |
23,221,422 (GRCm39) |
missense |
probably damaging |
1.00 |
R8885:Smc5
|
UTSW |
19 |
23,191,234 (GRCm39) |
missense |
probably damaging |
0.99 |
R8940:Smc5
|
UTSW |
19 |
23,237,126 (GRCm39) |
missense |
probably benign |
0.00 |
R9642:Smc5
|
UTSW |
19 |
23,238,752 (GRCm39) |
missense |
probably damaging |
0.99 |
|
Predicted Primers |
PCR Primer
(F):5'- GCACACGCCTCAGATCATTT -3'
(R):5'- TTAGACCCAGCCCCAGGTT -3'
Sequencing Primer
(F):5'- ACGCCTCAGATCATTTGTGACG -3'
(R):5'- TCCAATAGCTGACTGTGAGC -3'
|
Posted On |
2016-11-21 |