Incidental Mutation 'R1368:Smc5'
ID |
155907 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Smc5
|
Ensembl Gene |
ENSMUSG00000024943 |
Gene Name |
structural maintenance of chromosomes 5 |
Synonyms |
Smc5l1 |
MMRRC Submission |
039433-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R1368 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
19 |
Chromosomal Location |
23183815-23251261 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 23187807 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Alanine
at position 1003
(V1003A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000153364
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000087556]
[ENSMUST00000223934]
[ENSMUST00000226111]
|
AlphaFold |
Q8CG46 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000087556
AA Change: V1017A
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
SMART Domains |
Protein: ENSMUSP00000084837 Gene: ENSMUSG00000024943 AA Change: V1017A
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 |
probably damaging
Transcript: ENSMUST00000223934
AA Change: V1003A
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224008
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224441
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000226111
AA Change: V927A
PolyPhen 2
Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
|
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 95.1%
|
Validation Efficiency |
98% (55/56) |
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: 53 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca13 |
A |
G |
11: 9,241,836 (GRCm39) |
D1233G |
probably benign |
Het |
Abcc8 |
G |
A |
7: 45,772,284 (GRCm39) |
R832W |
probably damaging |
Het |
Atp10b |
A |
G |
11: 43,092,981 (GRCm39) |
T439A |
probably damaging |
Het |
Brd10 |
C |
A |
19: 29,693,796 (GRCm39) |
S1966I |
probably damaging |
Het |
C130073F10Rik |
T |
A |
4: 101,747,953 (GRCm39) |
N74Y |
possibly damaging |
Het |
Cct8 |
G |
A |
16: 87,288,200 (GRCm39) |
S124L |
probably damaging |
Het |
Cdh9 |
T |
A |
15: 16,848,568 (GRCm39) |
|
probably benign |
Het |
Cep290 |
C |
T |
10: 100,330,828 (GRCm39) |
|
probably benign |
Het |
Chrng |
T |
A |
1: 87,133,575 (GRCm39) |
L10H |
probably damaging |
Het |
Cnn3 |
T |
C |
3: 121,250,786 (GRCm39) |
L189S |
probably benign |
Het |
Cog4 |
A |
G |
8: 111,585,157 (GRCm39) |
|
probably benign |
Het |
Cxcl12 |
A |
G |
6: 117,153,111 (GRCm39) |
|
probably benign |
Het |
Eif2b2 |
G |
A |
12: 85,270,230 (GRCm39) |
A257T |
probably damaging |
Het |
Entrep2 |
A |
T |
7: 64,469,625 (GRCm39) |
V41E |
probably damaging |
Het |
Fanca |
G |
A |
8: 124,031,020 (GRCm39) |
|
probably benign |
Het |
Fcgbpl1 |
A |
G |
7: 27,858,903 (GRCm39) |
Q2341R |
possibly damaging |
Het |
Fktn |
G |
A |
4: 53,734,880 (GRCm39) |
G173R |
probably damaging |
Het |
Gabbr2 |
T |
C |
4: 46,674,464 (GRCm39) |
N841S |
probably benign |
Het |
Gm5622 |
T |
A |
14: 51,899,647 (GRCm39) |
V167E |
possibly damaging |
Het |
Gnaq |
T |
C |
19: 16,355,651 (GRCm39) |
V289A |
probably benign |
Het |
Gpatch2l |
T |
G |
12: 86,307,439 (GRCm39) |
D272E |
possibly damaging |
Het |
Gzmg |
G |
A |
14: 56,395,263 (GRCm39) |
T74I |
probably benign |
Het |
Ikzf2 |
G |
A |
1: 69,578,474 (GRCm39) |
A271V |
possibly damaging |
Het |
Lig4 |
T |
C |
8: 10,021,176 (GRCm39) |
D868G |
possibly damaging |
Het |
Mfsd6 |
T |
C |
1: 52,747,764 (GRCm39) |
E367G |
possibly damaging |
Het |
Mpz |
T |
C |
1: 170,987,533 (GRCm39) |
L223P |
probably damaging |
Het |
Muc17 |
T |
C |
5: 137,175,674 (GRCm39) |
|
probably benign |
Het |
Or2f1b |
C |
A |
6: 42,739,613 (GRCm39) |
T209K |
possibly damaging |
Het |
Pdcd2 |
G |
T |
17: 15,746,846 (GRCm39) |
N104K |
probably damaging |
Het |
Pigg |
G |
T |
5: 108,465,154 (GRCm39) |
G129V |
probably damaging |
Het |
Ppp3cc |
T |
C |
14: 70,483,311 (GRCm39) |
Y254C |
probably damaging |
Het |
Prl3b1 |
G |
A |
13: 27,427,848 (GRCm39) |
A53T |
probably benign |
Het |
Psg23 |
A |
G |
7: 18,348,645 (GRCm39) |
V54A |
probably benign |
Het |
Psmd3 |
A |
G |
11: 98,573,746 (GRCm39) |
D64G |
probably damaging |
Het |
Psmg2 |
CTTCAGTT |
CTTCAGTTCAGTT |
18: 67,779,095 (GRCm39) |
|
probably null |
Het |
Ptgdr |
T |
A |
14: 45,090,799 (GRCm39) |
I320F |
probably damaging |
Het |
Rad50 |
T |
A |
11: 53,574,072 (GRCm39) |
K722* |
probably null |
Het |
Rasl10b |
G |
A |
11: 83,308,665 (GRCm39) |
|
probably null |
Het |
Rgs9 |
G |
A |
11: 109,138,977 (GRCm39) |
S255L |
probably benign |
Het |
Ror1 |
C |
T |
4: 100,298,334 (GRCm39) |
P569L |
possibly damaging |
Het |
Rsad2 |
T |
C |
12: 26,497,147 (GRCm39) |
|
probably null |
Het |
Scn8a |
A |
G |
15: 100,933,422 (GRCm39) |
D1501G |
probably damaging |
Het |
Sema3c |
A |
G |
5: 17,883,330 (GRCm39) |
T313A |
possibly damaging |
Het |
Serpinc1 |
T |
A |
1: 160,821,094 (GRCm39) |
F59L |
probably damaging |
Het |
Sike1 |
A |
G |
3: 102,903,500 (GRCm39) |
D63G |
possibly damaging |
Het |
Slc25a11 |
T |
A |
11: 70,536,352 (GRCm39) |
|
probably null |
Het |
Slc32a1 |
A |
G |
2: 158,453,240 (GRCm39) |
M27V |
probably benign |
Het |
Tll2 |
G |
A |
19: 41,108,667 (GRCm39) |
R328C |
probably damaging |
Het |
Topaz1 |
A |
G |
9: 122,577,315 (GRCm39) |
E75G |
possibly damaging |
Het |
Tspan3 |
A |
T |
9: 56,054,783 (GRCm39) |
V48E |
probably benign |
Het |
Ugt1a6b |
T |
C |
1: 88,035,358 (GRCm39) |
I232T |
probably benign |
Het |
Unc79 |
A |
G |
12: 103,122,772 (GRCm39) |
K2290E |
probably damaging |
Het |
Vmn1r19 |
T |
C |
6: 57,381,656 (GRCm39) |
F70L |
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 |
|
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 |
|
R5754:Smc5
|
UTSW |
19 |
23,221,467 (GRCm39) |
missense |
possibly damaging |
0.92 |
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'- GCACGAAGTCTAAGCTCTGGAACAG -3'
(R):5'- AGTAGAATTGCCACAGAGACAGCAC -3'
Sequencing Primer
(F):5'- CGCTTCCTTAGATGACAGATGAC -3'
(R):5'- ACAGAGACAGCACTCATTTTTC -3'
|
Posted On |
2014-02-11 |