Incidental Mutation 'R0970:Smc5'
ID |
84045 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Smc5
|
Ensembl Gene |
ENSMUSG00000024943 |
Gene Name |
structural maintenance of chromosomes 5 |
Synonyms |
Smc5l1 |
MMRRC Submission |
039099-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R0970 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
19 |
Chromosomal Location |
23183815-23251261 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 23216362 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Isoleucine to Phenylalanine
at position 489
(I489F)
|
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: I489F
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000084837 Gene: ENSMUSG00000024943 AA Change: I489F
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: I489F
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000226111
AA Change: I413F
PolyPhen 2
Score 0.824 (Sensitivity: 0.84; Specificity: 0.93)
|
Meta Mutation Damage Score |
0.3377 |
Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.8%
- 10x: 97.3%
- 20x: 95.2%
|
Validation Efficiency |
98% (40/41) |
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: 39 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
A3galt2 |
T |
C |
4: 128,661,364 (GRCm39) |
S307P |
probably damaging |
Het |
Amdhd2 |
C |
T |
17: 24,375,544 (GRCm39) |
|
probably null |
Het |
Ano1 |
A |
T |
7: 144,149,308 (GRCm39) |
M851K |
probably benign |
Het |
Arid3b |
A |
T |
9: 57,740,834 (GRCm39) |
|
probably benign |
Het |
Arpp21 |
A |
G |
9: 111,965,516 (GRCm39) |
|
probably benign |
Het |
Atxn7l3 |
C |
G |
11: 102,183,261 (GRCm39) |
|
probably benign |
Het |
C87436 |
G |
A |
6: 86,424,310 (GRCm39) |
V281M |
probably damaging |
Het |
Cep70 |
A |
G |
9: 99,157,652 (GRCm39) |
K184E |
possibly damaging |
Het |
Clcn7 |
T |
C |
17: 25,370,208 (GRCm39) |
|
probably null |
Het |
Col1a2 |
G |
A |
6: 4,518,822 (GRCm39) |
|
probably benign |
Het |
Col4a2 |
A |
G |
8: 11,465,438 (GRCm39) |
T383A |
probably benign |
Het |
Commd5 |
A |
T |
15: 76,784,885 (GRCm39) |
|
probably null |
Het |
Cyp4b1 |
G |
A |
4: 115,492,833 (GRCm39) |
A292V |
probably benign |
Het |
Dthd1 |
T |
C |
5: 63,045,324 (GRCm39) |
L696P |
probably damaging |
Het |
Dync1h1 |
G |
A |
12: 110,602,943 (GRCm39) |
E2195K |
probably benign |
Het |
Eepd1 |
A |
G |
9: 25,514,722 (GRCm39) |
R510G |
probably damaging |
Het |
Eno3 |
T |
C |
11: 70,551,628 (GRCm39) |
I196T |
probably damaging |
Het |
Eva1a |
A |
G |
6: 82,069,084 (GRCm39) |
E137G |
probably damaging |
Het |
Gapvd1 |
T |
A |
2: 34,620,625 (GRCm39) |
|
probably null |
Het |
Ggnbp2 |
T |
C |
11: 84,753,138 (GRCm39) |
M34V |
possibly damaging |
Het |
Gpihbp1 |
G |
A |
15: 75,469,795 (GRCm39) |
S170N |
probably benign |
Het |
Kdm3b |
T |
C |
18: 34,942,092 (GRCm39) |
S528P |
probably damaging |
Het |
Lrrk2 |
A |
T |
15: 91,613,372 (GRCm39) |
Q832L |
probably benign |
Het |
Nav2 |
C |
A |
7: 49,233,901 (GRCm39) |
P1861Q |
probably damaging |
Het |
Or52n5 |
A |
C |
7: 104,588,284 (GRCm39) |
M184L |
probably benign |
Het |
Piezo1 |
A |
T |
8: 123,213,549 (GRCm39) |
I1782N |
possibly damaging |
Het |
Pikfyve |
T |
A |
1: 65,304,983 (GRCm39) |
S1757T |
probably damaging |
Het |
Plxnb1 |
G |
T |
9: 108,932,331 (GRCm39) |
W523C |
probably damaging |
Het |
Pmm2 |
G |
T |
16: 8,460,640 (GRCm39) |
L31F |
probably damaging |
Het |
Ppm1f |
T |
C |
16: 16,721,457 (GRCm39) |
|
probably null |
Het |
Prss16 |
T |
C |
13: 22,189,287 (GRCm39) |
Y34C |
probably damaging |
Het |
Slc10a2 |
C |
G |
8: 5,155,115 (GRCm39) |
E23D |
probably benign |
Het |
Snx2 |
T |
C |
18: 53,343,762 (GRCm39) |
|
probably benign |
Het |
Stradb |
C |
T |
1: 59,016,219 (GRCm39) |
L3F |
possibly damaging |
Het |
Tnxb |
C |
G |
17: 34,917,917 (GRCm39) |
P2277A |
possibly damaging |
Het |
Tpm2 |
T |
A |
4: 43,515,968 (GRCm39) |
I270F |
probably benign |
Het |
Ugt2b38 |
T |
G |
5: 87,560,232 (GRCm39) |
N361H |
probably damaging |
Het |
Urb1 |
A |
T |
16: 90,566,335 (GRCm39) |
L1484Q |
possibly damaging |
Het |
Xylt1 |
G |
A |
7: 117,233,963 (GRCm39) |
V497I |
probably damaging |
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 |
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 |
|
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'- GAAACTGCAACCCCATGAAGGAGAA -3'
(R):5'- TGAGTCCCAGTGAGATGCTTGGAAAT -3'
Sequencing Primer
(F):5'- CCCCATGAAGGAGAAAAGCAG -3'
(R):5'- gcacacgtctttaatcccag -3'
|
Posted On |
2013-11-08 |