Incidental Mutation 'R5101:Pms2'
| ID |
392352 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pms2
|
| Ensembl Gene |
ENSMUSG00000079109 |
| Gene Name |
PMS1 homolog2, mismatch repair system component |
| Synonyms |
mismatch repair, DNA mismatch repair |
| MMRRC Submission |
042852-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.226)
|
| Stock # |
R5101 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
143846782-143870786 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 143865006 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 696
(D696G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000119875
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000110709]
[ENSMUST00000148011]
[ENSMUST00000166847]
[ENSMUST00000164999]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000031618
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000110707
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000110709
AA Change: D298G
PolyPhen 2
Score 0.025 (Sensitivity: 0.95; Specificity: 0.81)
|
| SMART Domains |
Protein: ENSMUSP00000106337
Gene: ENSMUSG00000079109
AA Change: D298G
| Domain | Start | End | E-Value | Type |
|---|
|
HATPase_c
|
30 |
165 |
3.77e-1 |
SMART |
|
MutL_C
|
277 |
421 |
1.59e-36 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000110710
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000126331
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141942
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000148011
AA Change: D696G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000119875
Gene: ENSMUSG00000079109
AA Change: D696G
| Domain | Start | End | E-Value | Type |
|---|
|
HATPase_c
|
30 |
165 |
3.77e-1 |
SMART |
|
DNA_mis_repair
|
227 |
364 |
4.76e-41 |
SMART |
|
MutL_C
|
675 |
819 |
1.59e-36 |
SMART |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000172367
AA Change: T5A
|
| SMART Domains |
Protein: ENSMUSP00000132104
Gene: ENSMUSG00000104633
AA Change: T5A
| Domain | Start | End | E-Value | Type |
|---|
|
MutL_C
|
5 |
139 |
1.78e-1 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000167009
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170083
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000166847
|
| SMART Domains |
Protein: ENSMUSP00000132687
Gene: ENSMUSG00000075569
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
3 |
14 |
N/A |
INTRINSIC |
|
low complexity region
|
39 |
50 |
N/A |
INTRINSIC |
|
low complexity region
|
63 |
75 |
N/A |
INTRINSIC |
|
MORN
|
107 |
128 |
5.9e-7 |
SMART |
|
MORN
|
130 |
151 |
9.35e-1 |
SMART |
|
MORN
|
153 |
174 |
1.23e0 |
SMART |
|
MORN
|
177 |
198 |
1.84e0 |
SMART |
|
MORN
|
202 |
223 |
3.21e1 |
SMART |
|
MORN
|
225 |
246 |
1.67e-6 |
SMART |
|
MORN
|
249 |
270 |
1.85e1 |
SMART |
|
MORN
|
282 |
303 |
2.71e-6 |
SMART |
|
MORN
|
305 |
326 |
3.53e-5 |
SMART |
|
low complexity region
|
409 |
420 |
N/A |
INTRINSIC |
|
low complexity region
|
629 |
649 |
N/A |
INTRINSIC |
|
coiled coil region
|
787 |
841 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000164999
|
| SMART Domains |
Protein: ENSMUSP00000133062
Gene: ENSMUSG00000079109
| Domain | Start | End | E-Value | Type |
|---|
|
DNA_mis_repair
|
1 |
70 |
4.47e-2 |
SMART |
|
| Meta Mutation Damage Score |
0.9744 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.4%
- 20x: 93.0%
|
| Validation Efficiency |
100% (57/57) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a key component of the mismatch repair system that functions to correct DNA mismatches and small insertions and deletions that can occur during DNA replication and homologous recombination. This protein forms heterodimers with the gene product of the mutL homolog 1 (MLH1) gene to form the MutL-alpha heterodimer. The MutL-alpha heterodimer possesses an endonucleolytic activity that is activated following recognition of mismatches and insertion/deletion loops by the MutS-alpha and MutS-beta heterodimers, and is necessary for removal of the mismatched DNA. There is a DQHA(X)2E(X)4E motif found at the C-terminus of the protein encoded by this gene that forms part of the active site of the nuclease. Mutations in this gene have been associated with hereditary nonpolyposis colorectal cancer (HNPCC; also known as Lynch syndrome) and Turcot syndrome. [provided by RefSeq, Apr 2016]
PHENOTYPE: Homozygotes for targeted null mutations exhibit microsatellite instability and develop a high incidence of lymphomas with some sarcomas after 6 months of age. Mutant males are sterile, with impaired synapsis and only abnormal spermatozoa. [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 |
|---|
| Adam17 |
T |
C |
12: 21,423,406 (GRCm39) |
T10A |
possibly damaging |
Het |
| Adgrg3 |
T |
C |
8: 95,763,563 (GRCm39) |
F288S |
probably benign |
Het |
| Ago2 |
A |
G |
15: 72,991,339 (GRCm39) |
V533A |
probably damaging |
Het |
| Akap9 |
T |
G |
5: 4,051,748 (GRCm39) |
V1505G |
probably damaging |
Het |
| Apob |
T |
C |
12: 8,061,934 (GRCm39) |
I3439T |
probably benign |
Het |
| C1qtnf7 |
T |
A |
5: 43,773,314 (GRCm39) |
Y204* |
probably null |
Het |
| Cdc42bpb |
T |
C |
12: 111,265,549 (GRCm39) |
E1461G |
probably damaging |
Het |
| Cdh3 |
C |
T |
8: 107,268,024 (GRCm39) |
A353V |
possibly damaging |
Het |
| Clec4d |
A |
G |
6: 123,244,071 (GRCm39) |
Y60C |
probably damaging |
Het |
| Cmya5 |
T |
A |
13: 93,228,111 (GRCm39) |
T2326S |
possibly damaging |
Het |
| Cnot1 |
G |
A |
8: 96,486,815 (GRCm39) |
L631F |
possibly damaging |
Het |
| Cntnap5a |
C |
T |
1: 116,370,026 (GRCm39) |
T881I |
probably benign |
Het |
| Col6a1 |
T |
A |
10: 76,545,740 (GRCm39) |
T911S |
unknown |
Het |
| Ctsw |
A |
G |
19: 5,515,703 (GRCm39) |
V287A |
probably benign |
Het |
| Cyp2c23 |
T |
C |
19: 44,017,622 (GRCm39) |
E2G |
unknown |
Het |
| Cytip |
A |
T |
2: 58,037,911 (GRCm39) |
I151N |
probably damaging |
Het |
| Dnah10 |
A |
G |
5: 124,909,577 (GRCm39) |
T4399A |
possibly damaging |
Het |
| Dock3 |
A |
T |
9: 106,846,980 (GRCm39) |
I883N |
probably damaging |
Het |
| Entpd3 |
A |
G |
9: 120,395,608 (GRCm39) |
*530W |
probably null |
Het |
| Gm4787 |
G |
C |
12: 81,424,604 (GRCm39) |
T518S |
probably benign |
Het |
| Gp1ba |
G |
A |
11: 70,532,225 (GRCm39) |
V664M |
probably benign |
Het |
| Gpd2 |
T |
A |
2: 57,245,913 (GRCm39) |
I481N |
probably damaging |
Het |
| Gvin-ps5 |
T |
C |
7: 105,929,096 (GRCm39) |
|
noncoding transcript |
Het |
| Ildr2 |
A |
G |
1: 166,135,331 (GRCm39) |
D342G |
probably damaging |
Het |
| Krt87 |
A |
G |
15: 101,385,391 (GRCm39) |
I327T |
probably benign |
Het |
| Lats1 |
T |
A |
10: 7,588,348 (GRCm39) |
C988* |
probably null |
Het |
| Lpin2 |
G |
A |
17: 71,550,965 (GRCm39) |
W708* |
probably null |
Het |
| Mast4 |
T |
C |
13: 102,872,864 (GRCm39) |
D2168G |
probably benign |
Het |
| Myo6 |
G |
T |
9: 80,177,321 (GRCm39) |
E606* |
probably null |
Het |
| Nek7 |
A |
G |
1: 138,443,431 (GRCm39) |
V174A |
probably benign |
Het |
| Nid1 |
T |
A |
13: 13,658,339 (GRCm39) |
C695S |
probably damaging |
Het |
| Nme8 |
A |
G |
13: 19,875,017 (GRCm39) |
|
probably null |
Het |
| Nr2c2 |
T |
C |
6: 92,131,497 (GRCm39) |
|
probably null |
Het |
| Or1e16 |
AGCGGTCGTAGGC |
AGC |
11: 73,286,480 (GRCm39) |
|
probably null |
Het |
| Or2ag18 |
A |
T |
7: 106,405,420 (GRCm39) |
I83K |
possibly damaging |
Het |
| Or4x11 |
A |
G |
2: 89,867,391 (GRCm39) |
M43V |
probably benign |
Het |
| Or51ab3 |
G |
A |
7: 103,201,150 (GRCm39) |
E53K |
probably damaging |
Het |
| Or9g19 |
A |
G |
2: 85,600,268 (GRCm39) |
N41S |
probably damaging |
Het |
| Psapl1 |
T |
A |
5: 36,361,494 (GRCm39) |
C29S |
probably damaging |
Het |
| Scn3a |
A |
T |
2: 65,291,850 (GRCm39) |
V1632D |
probably damaging |
Het |
| Slc22a1 |
C |
T |
17: 12,886,129 (GRCm39) |
G168D |
probably damaging |
Het |
| Smad4 |
A |
G |
18: 73,808,931 (GRCm39) |
V112A |
probably benign |
Het |
| Smc4 |
T |
C |
3: 68,935,845 (GRCm39) |
V796A |
probably benign |
Het |
| Smco4 |
A |
G |
9: 15,455,968 (GRCm39) |
E18G |
unknown |
Het |
| Spata31e2 |
T |
C |
1: 26,722,417 (GRCm39) |
E921G |
possibly damaging |
Het |
| Sugp2 |
A |
G |
8: 70,713,139 (GRCm39) |
E1035G |
probably damaging |
Het |
| Syde2 |
T |
C |
3: 145,721,393 (GRCm39) |
S820P |
probably damaging |
Het |
| Syn2 |
T |
C |
6: 115,240,860 (GRCm39) |
L410P |
probably damaging |
Het |
| Tmem131l |
T |
C |
3: 83,844,811 (GRCm39) |
N466S |
probably damaging |
Het |
| Uba1y |
T |
G |
Y: 821,447 (GRCm39) |
|
probably null |
Het |
| Unc79 |
T |
C |
12: 103,078,769 (GRCm39) |
S1645P |
probably damaging |
Het |
| Vmn2r17 |
A |
T |
5: 109,576,217 (GRCm39) |
S363C |
probably damaging |
Het |
| Vmn2r78 |
T |
C |
7: 86,571,563 (GRCm39) |
Y458H |
probably damaging |
Het |
|
| Other mutations in Pms2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01893:Pms2
|
APN |
5 |
143,860,337 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02009:Pms2
|
APN |
5 |
143,862,582 (GRCm39) |
missense |
probably benign |
0.42 |
|
IGL02801:Pms2
|
APN |
5 |
143,862,653 (GRCm39) |
missense |
probably benign |
0.06 |
|
P0047:Pms2
|
UTSW |
5 |
143,856,416 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1367:Pms2
|
UTSW |
5 |
143,862,731 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1422:Pms2
|
UTSW |
5 |
143,850,523 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1854:Pms2
|
UTSW |
5 |
143,862,714 (GRCm39) |
missense |
probably benign |
0.08 |
|
R1997:Pms2
|
UTSW |
5 |
143,850,518 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2248:Pms2
|
UTSW |
5 |
143,853,324 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2873:Pms2
|
UTSW |
5 |
143,848,732 (GRCm39) |
splice site |
probably benign |
|
|
R4072:Pms2
|
UTSW |
5 |
143,865,819 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4082:Pms2
|
UTSW |
5 |
143,867,837 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4358:Pms2
|
UTSW |
5 |
143,862,744 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5100:Pms2
|
UTSW |
5 |
143,865,006 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5228:Pms2
|
UTSW |
5 |
143,860,415 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5484:Pms2
|
UTSW |
5 |
143,864,943 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6310:Pms2
|
UTSW |
5 |
143,860,401 (GRCm39) |
missense |
probably benign |
0.06 |
|
R6331:Pms2
|
UTSW |
5 |
143,851,451 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R6567:Pms2
|
UTSW |
5 |
143,865,786 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6718:Pms2
|
UTSW |
5 |
143,860,307 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6747:Pms2
|
UTSW |
5 |
143,862,237 (GRCm39) |
missense |
probably benign |
0.02 |
|
R6980:Pms2
|
UTSW |
5 |
143,848,842 (GRCm39) |
missense |
probably benign |
0.21 |
|
R7207:Pms2
|
UTSW |
5 |
143,850,452 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7349:Pms2
|
UTSW |
5 |
143,862,654 (GRCm39) |
missense |
probably benign |
0.11 |
|
R7657:Pms2
|
UTSW |
5 |
143,856,357 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R7820:Pms2
|
UTSW |
5 |
143,851,451 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
R7980:Pms2
|
UTSW |
5 |
143,867,909 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8213:Pms2
|
UTSW |
5 |
143,851,589 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8534:Pms2
|
UTSW |
5 |
143,860,445 (GRCm39) |
missense |
probably benign |
0.16 |
|
R9021:Pms2
|
UTSW |
5 |
143,862,744 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9218:Pms2
|
UTSW |
5 |
143,867,945 (GRCm39) |
missense |
probably benign |
|
|
R9494:Pms2
|
UTSW |
5 |
143,853,214 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9614:Pms2
|
UTSW |
5 |
143,854,420 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9712:Pms2
|
UTSW |
5 |
143,851,614 (GRCm39) |
missense |
probably damaging |
0.99 |
|
X0064:Pms2
|
UTSW |
5 |
143,853,284 (GRCm39) |
nonsense |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GAGCACTGATTATGTGGATAACTGAG -3'
(R):5'- ACATGTACGTGTCTGTGCGC -3'
Sequencing Primer
(F):5'- CAAGACAGGGTTTCTCTGTATAGCC -3'
(R):5'- GCACAGCTGCTGGCATACATAAC -3'
|
| Posted On |
2016-06-15 |
Incidental Mutation