Incidental Mutation 'R6667:Pcmt1'
| ID |
527028 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcmt1
|
| Ensembl Gene |
ENSMUSG00000019795 |
| Gene Name |
protein-L-isoaspartate (D-aspartate) O-methyltransferase 1 |
| Synonyms |
protein carboxyl methyltransferase, PIMT |
| MMRRC Submission |
044787-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.170)
|
| Stock # |
R6667 (G1)
|
| Quality Score |
224.009 |
|
Status
|
Validated
|
| Chromosome |
10 |
| Chromosomal Location |
7505137-7556900 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 7538913 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Proline
at position 38
(L38P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000125144
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000040135]
[ENSMUST00000159917]
[ENSMUST00000159977]
[ENSMUST00000161123]
[ENSMUST00000162606]
[ENSMUST00000163085]
[ENSMUST00000162682]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000040135
|
| SMART Domains |
Protein: ENSMUSP00000046732
Gene: ENSMUSG00000040034
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:WD40
|
1 |
48 |
1e-15 |
BLAST |
|
WD40
|
64 |
101 |
3.57e0 |
SMART |
|
WD40
|
124 |
157 |
2.45e2 |
SMART |
|
WD40
|
160 |
199 |
9.55e0 |
SMART |
|
WD40
|
206 |
246 |
2.15e-4 |
SMART |
|
WD40
|
250 |
290 |
2.19e-5 |
SMART |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000159917
AA Change: L52P
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000124932
Gene: ENSMUSG00000019795
AA Change: L52P
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
7 |
25 |
N/A |
INTRINSIC |
|
Pfam:PCMT
|
66 |
279 |
1.1e-88 |
PFAM |
|
Pfam:Ubie_methyltran
|
126 |
258 |
3.4e-7 |
PFAM |
|
Pfam:Methyltransf_31
|
134 |
284 |
1.1e-8 |
PFAM |
|
Pfam:Methyltransf_18
|
136 |
241 |
3e-9 |
PFAM |
|
Pfam:Methyltransf_11
|
141 |
239 |
1.5e-6 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000159977
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160250
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160517
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000161123
AA Change: L39P
PolyPhen 2
Score 0.076 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000124100
Gene: ENSMUSG00000019795
AA Change: L39P
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
15 |
37 |
N/A |
INTRINSIC |
|
Pfam:PCMT
|
53 |
108 |
4.2e-14 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162346
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000162606
AA Change: L52P
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000123866
Gene: ENSMUSG00000019795
AA Change: L52P
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
7 |
25 |
N/A |
INTRINSIC |
|
Pfam:PCMT
|
66 |
279 |
2e-88 |
PFAM |
|
Pfam:Ubie_methyltran
|
126 |
259 |
1e-6 |
PFAM |
|
Pfam:Methyltransf_31
|
134 |
283 |
3.5e-8 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000163085
AA Change: L38P
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000125144
Gene: ENSMUSG00000019795
AA Change: L38P
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
15 |
37 |
N/A |
INTRINSIC |
|
Pfam:PCMT
|
52 |
265 |
9.1e-89 |
PFAM |
|
Pfam:Ubie_methyltran
|
112 |
244 |
3.1e-7 |
PFAM |
|
Pfam:Methyltransf_31
|
120 |
270 |
9.8e-9 |
PFAM |
|
Pfam:Methyltransf_18
|
122 |
227 |
2.7e-9 |
PFAM |
|
Pfam:Methyltransf_11
|
127 |
225 |
1.4e-6 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000162682
|
| SMART Domains |
Protein: ENSMUSP00000124246
Gene: ENSMUSG00000019795
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:PCMT
|
1 |
66 |
7.5e-26 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162527
|
| Meta Mutation Damage Score |
0.2191 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.1%
- 20x: 94.6%
|
| Validation Efficiency |
98% (41/42) |
| MGI Phenotype |
PHENOTYPE: Homozygous disruption of this gene causes accumulation of modified proteins, growth retardation and fatal epileptic seizures. Homozygotes for one null allele also show a small spleen, altered lipid, hormone, mineral and enzyme profiles, kyphosis, enlarged brain and abnormal dendritic arborizations. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 44 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 3100002H09Rik |
G |
T |
4: 124,504,435 (GRCm39) |
A39E |
probably damaging |
Het |
| Agtr1b |
T |
A |
3: 20,369,913 (GRCm39) |
N231I |
possibly damaging |
Het |
| Alpk2 |
T |
C |
18: 65,440,811 (GRCm39) |
E661G |
probably damaging |
Het |
| Ankrd26 |
C |
T |
6: 118,484,749 (GRCm39) |
S1496N |
probably benign |
Het |
| Asah2 |
T |
C |
19: 31,972,758 (GRCm39) |
N659S |
probably benign |
Het |
| Atp12a |
T |
C |
14: 56,621,645 (GRCm39) |
V760A |
possibly damaging |
Het |
| Casp2 |
T |
C |
6: 42,256,770 (GRCm39) |
C343R |
probably damaging |
Het |
| Cblb |
T |
A |
16: 51,973,007 (GRCm39) |
M446K |
possibly damaging |
Het |
| Cipc |
T |
C |
12: 87,008,864 (GRCm39) |
V241A |
probably benign |
Het |
| Ddit4l |
A |
G |
3: 137,331,882 (GRCm39) |
K83E |
probably benign |
Het |
| Eif1ad10 |
A |
T |
12: 88,216,475 (GRCm39) |
D132E |
unknown |
Het |
| Epc2 |
A |
G |
2: 49,412,681 (GRCm39) |
T220A |
probably damaging |
Het |
| Epha5 |
T |
C |
5: 84,219,050 (GRCm39) |
D741G |
probably damaging |
Het |
| Flg2 |
A |
T |
3: 93,109,068 (GRCm39) |
R365S |
possibly damaging |
Het |
| Ggn |
A |
T |
7: 28,872,093 (GRCm39) |
H491L |
possibly damaging |
Het |
| Gpat2 |
G |
C |
2: 127,273,838 (GRCm39) |
G294R |
possibly damaging |
Het |
| Ighv6-4 |
A |
G |
12: 114,370,152 (GRCm39) |
V100A |
probably benign |
Het |
| Invs |
A |
T |
4: 48,402,870 (GRCm39) |
Y501F |
possibly damaging |
Het |
| Iqcm |
G |
T |
8: 76,479,980 (GRCm39) |
G313W |
probably damaging |
Het |
| Jph2 |
A |
G |
2: 163,218,206 (GRCm39) |
S157P |
probably damaging |
Het |
| Mast4 |
T |
C |
13: 102,874,004 (GRCm39) |
E1596G |
probably damaging |
Het |
| Mllt6 |
T |
A |
11: 97,567,760 (GRCm39) |
L759Q |
probably damaging |
Het |
| Nalcn |
A |
G |
14: 123,558,735 (GRCm39) |
L837P |
probably damaging |
Het |
| Neb |
G |
A |
2: 52,037,201 (GRCm39) |
T6836I |
probably damaging |
Het |
| Nol12 |
T |
A |
15: 78,824,280 (GRCm39) |
D133E |
probably benign |
Het |
| Or5w13 |
A |
G |
2: 87,523,914 (GRCm39) |
V104A |
probably benign |
Het |
| Oxtr |
C |
A |
6: 112,454,060 (GRCm39) |
|
probably benign |
Het |
| Pik3r2 |
T |
C |
8: 71,221,817 (GRCm39) |
Y617C |
probably damaging |
Het |
| Potefam3b |
T |
C |
8: 21,161,955 (GRCm39) |
S267P |
probably benign |
Het |
| Prl7a2 |
T |
C |
13: 27,845,024 (GRCm39) |
N121D |
probably benign |
Het |
| Pvr |
G |
T |
7: 19,639,727 (GRCm39) |
Q380K |
probably benign |
Het |
| Rtn2 |
A |
G |
7: 19,021,184 (GRCm39) |
E188G |
probably benign |
Het |
| Setd4 |
C |
A |
16: 93,386,918 (GRCm39) |
R260L |
probably benign |
Het |
| Six5 |
A |
G |
7: 18,830,494 (GRCm39) |
N374D |
probably benign |
Het |
| Slc9b1 |
T |
C |
3: 135,077,726 (GRCm39) |
I140T |
probably damaging |
Het |
| Supt16 |
A |
G |
14: 52,409,520 (GRCm39) |
F797L |
probably damaging |
Het |
| Tbata |
T |
C |
10: 61,021,142 (GRCm39) |
L262P |
probably damaging |
Het |
| Tti1 |
A |
T |
2: 157,850,347 (GRCm39) |
C297* |
probably null |
Het |
| Ush1c |
C |
A |
7: 45,875,048 (GRCm39) |
G139C |
probably damaging |
Het |
| Vmn1r1 |
C |
T |
1: 181,985,342 (GRCm39) |
V108I |
probably benign |
Het |
| Vmn2r116 |
C |
T |
17: 23,620,066 (GRCm39) |
T600I |
probably damaging |
Het |
| Zfp764l1 |
A |
G |
7: 126,992,595 (GRCm39) |
M5T |
probably benign |
Het |
| Zfp873 |
A |
G |
10: 81,896,423 (GRCm39) |
T422A |
probably benign |
Het |
| Zfp943 |
G |
A |
17: 22,211,889 (GRCm39) |
C325Y |
probably damaging |
Het |
|
| Other mutations in Pcmt1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02934:Pcmt1
|
APN |
10 |
7,516,491 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1968:Pcmt1
|
UTSW |
10 |
7,516,474 (GRCm39) |
nonsense |
probably null |
|
|
R3889:Pcmt1
|
UTSW |
10 |
7,524,814 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5454:Pcmt1
|
UTSW |
10 |
7,516,509 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5630:Pcmt1
|
UTSW |
10 |
7,524,857 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5705:Pcmt1
|
UTSW |
10 |
7,513,954 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R7163:Pcmt1
|
UTSW |
10 |
7,513,922 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7168:Pcmt1
|
UTSW |
10 |
7,513,946 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7531:Pcmt1
|
UTSW |
10 |
7,556,369 (GRCm39) |
splice site |
probably null |
|
|
R8012:Pcmt1
|
UTSW |
10 |
7,516,527 (GRCm39) |
missense |
probably benign |
0.26 |
|
R8435:Pcmt1
|
UTSW |
10 |
7,515,825 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R9134:Pcmt1
|
UTSW |
10 |
7,520,207 (GRCm39) |
splice site |
probably benign |
|
|
R9140:Pcmt1
|
UTSW |
10 |
7,514,678 (GRCm39) |
makesense |
probably null |
|
|
R9595:Pcmt1
|
UTSW |
10 |
7,524,817 (GRCm39) |
missense |
possibly damaging |
0.52 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGCTAGTCCAGTCACCAGAAAC -3'
(R):5'- AACTGAGCAGCGTTCGTTTG -3'
Sequencing Primer
(F):5'- TCCACATCGCCGAGTGACAG -3'
(R):5'- ACCGAGCACTGGTTATCGC -3'
|
| Posted On |
2018-07-23 |
Incidental Mutation