Incidental Mutation 'R0470:Shmt1'
| ID |
41808 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Shmt1
|
| Ensembl Gene |
ENSMUSG00000020534 |
| Gene Name |
serine hydroxymethyltransferase 1 (soluble) |
| Synonyms |
mshmt, mshmt2, mshmt1, Shmt |
| MMRRC Submission |
038670-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R0470 (G1)
|
| Quality Score |
218 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
60678933-60702091 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 60683789 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 341
(Y341C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000018744
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000018744]
[ENSMUST00000056907]
|
| AlphaFold |
P50431 |
| PDB Structure |
RECOMBINANT SERINE HYDROXYMETHYLTRANSFERASE (MOUSE) [X-RAY DIFFRACTION]
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000018744
AA Change: Y341C
PolyPhen 2
Score 0.910 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000018744
Gene: ENSMUSG00000020534
AA Change: Y341C
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SHMT
|
20 |
419 |
1.3e-211 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000056907
|
| SMART Domains |
Protein: ENSMUSP00000055926
Gene: ENSMUSG00000049323
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
13 |
30 |
N/A |
INTRINSIC |
|
Pfam:Folliculin
|
78 |
262 |
5e-12 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000124227
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000135081
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172804
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173260
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174093
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000174214
AA Change: Y340C
|
| SMART Domains |
Protein: ENSMUSP00000134269
Gene: ENSMUSG00000020534
AA Change: Y340C
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SHMT
|
20 |
408 |
4.6e-196 |
PFAM |
|
Pfam:Aminotran_1_2
|
153 |
409 |
3.1e-6 |
PFAM |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000174719
AA Change: Y301C
|
| SMART Domains |
Protein: ENSMUSP00000134318
Gene: ENSMUSG00000020534
AA Change: Y301C
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SHMT
|
20 |
268 |
6.4e-137 |
PFAM |
|
Pfam:SHMT
|
265 |
380 |
3.9e-51 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000174174
|
| SMART Domains |
Protein: ENSMUSP00000134703
Gene: ENSMUSG00000020534
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SHMT
|
20 |
79 |
7.1e-26 |
PFAM |
|
| Meta Mutation Damage Score |
0.8262 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.3%
- 20x: 93.0%
|
| Validation Efficiency |
98% (55/56) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the cytosolic form of serine hydroxymethyltransferase, a pyridoxal phosphate-containing enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. This reaction provides one-carbon units for synthesis of methionine, thymidylate, and purines in the cytoplasm. This gene is located within the Smith-Magenis syndrome region on chromosome 17. A pseudogene of this gene is located on the short arm of chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
PHENOTYPE: Mice with deficiencies in this gene display abnormalities in hepatic partioning of methylenetetrahydrofolate but are otherwise healthy and fertile. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ahnak |
T |
G |
19: 8,986,331 (GRCm39) |
D2538E |
probably benign |
Het |
| Akr1c13 |
T |
A |
13: 4,248,500 (GRCm39) |
L235H |
probably damaging |
Het |
| Ank |
G |
A |
15: 27,571,721 (GRCm39) |
C331Y |
probably damaging |
Het |
| Ankrd12 |
T |
C |
17: 66,293,129 (GRCm39) |
E768G |
probably benign |
Het |
| Atm |
A |
T |
9: 53,372,266 (GRCm39) |
V2172E |
probably damaging |
Het |
| Atp10b |
T |
A |
11: 43,093,866 (GRCm39) |
L470Q |
possibly damaging |
Het |
| Bcl2 |
G |
A |
1: 106,640,292 (GRCm39) |
R107C |
probably damaging |
Het |
| Ccn4 |
A |
G |
15: 66,789,227 (GRCm39) |
I238V |
probably benign |
Het |
| Cdadc1 |
A |
T |
14: 59,811,290 (GRCm39) |
|
probably benign |
Het |
| Cfhr2 |
A |
T |
1: 139,749,517 (GRCm39) |
V155E |
probably damaging |
Het |
| Chp1 |
C |
T |
2: 119,391,244 (GRCm39) |
R34C |
probably damaging |
Het |
| Cilp2 |
A |
T |
8: 70,338,055 (GRCm39) |
V192E |
possibly damaging |
Het |
| Cyth1 |
T |
C |
11: 118,023,074 (GRCm39) |
|
probably benign |
Het |
| Dnah8 |
T |
A |
17: 30,927,514 (GRCm39) |
|
probably benign |
Het |
| Gja3 |
T |
C |
14: 57,273,884 (GRCm39) |
T163A |
probably damaging |
Het |
| Gsdmcl1 |
C |
T |
15: 63,722,280 (GRCm39) |
|
noncoding transcript |
Het |
| Herc6 |
C |
T |
6: 57,596,437 (GRCm39) |
T459M |
probably damaging |
Het |
| Hexb |
A |
G |
13: 97,314,507 (GRCm39) |
L412P |
probably damaging |
Het |
| Il17ra |
T |
G |
6: 120,458,767 (GRCm39) |
D639E |
probably benign |
Het |
| Kcnh5 |
G |
A |
12: 75,161,188 (GRCm39) |
T240I |
probably benign |
Het |
| Lef1 |
T |
C |
3: 130,906,475 (GRCm39) |
|
probably benign |
Het |
| Lilrb4a |
T |
A |
10: 51,370,923 (GRCm39) |
N282K |
possibly damaging |
Het |
| Mbnl2 |
A |
T |
14: 120,642,062 (GRCm39) |
H342L |
probably damaging |
Het |
| Minar2 |
C |
T |
18: 59,208,711 (GRCm39) |
R120C |
probably damaging |
Het |
| Nipal3 |
A |
G |
4: 135,174,683 (GRCm39) |
V356A |
probably damaging |
Het |
| Or2a54 |
C |
G |
6: 43,093,558 (GRCm39) |
A294G |
probably null |
Het |
| Or51i1 |
A |
T |
7: 103,670,877 (GRCm39) |
I216N |
probably damaging |
Het |
| Plekha6 |
G |
A |
1: 133,200,045 (GRCm39) |
R208Q |
probably benign |
Het |
| Prkar1b |
A |
G |
5: 139,036,504 (GRCm39) |
I82T |
probably damaging |
Het |
| Prrc1 |
C |
T |
18: 57,496,469 (GRCm39) |
T140M |
probably damaging |
Het |
| Psg22 |
A |
C |
7: 18,453,589 (GRCm39) |
S95R |
probably damaging |
Het |
| Ptk6 |
T |
C |
2: 180,837,732 (GRCm39) |
T396A |
probably benign |
Het |
| Ptov1 |
A |
G |
7: 44,514,235 (GRCm39) |
S9P |
probably damaging |
Het |
| Scin |
A |
C |
12: 40,123,291 (GRCm39) |
|
probably benign |
Het |
| Sec13 |
T |
C |
6: 113,717,593 (GRCm39) |
|
probably benign |
Het |
| Setd1a |
G |
A |
7: 127,384,229 (GRCm39) |
|
probably benign |
Het |
| Sf3a2 |
G |
A |
10: 80,640,388 (GRCm39) |
|
probably benign |
Het |
| Slc27a4 |
T |
A |
2: 29,694,197 (GRCm39) |
L7Q |
probably benign |
Het |
| Slc41a2 |
T |
C |
10: 83,152,086 (GRCm39) |
M130V |
possibly damaging |
Het |
| Sorcs3 |
T |
C |
19: 48,785,956 (GRCm39) |
|
probably null |
Het |
| Tex24 |
C |
T |
8: 27,834,936 (GRCm39) |
R155* |
probably null |
Het |
| Tgfb1 |
T |
A |
7: 25,387,355 (GRCm39) |
|
probably benign |
Het |
| Tmc5 |
A |
G |
7: 118,239,154 (GRCm39) |
D349G |
possibly damaging |
Het |
| Trappc13 |
C |
T |
13: 104,297,512 (GRCm39) |
V131I |
possibly damaging |
Het |
| Trim66 |
A |
G |
7: 109,056,749 (GRCm39) |
|
probably benign |
Het |
| Tspoap1 |
T |
C |
11: 87,666,988 (GRCm39) |
S1027P |
probably damaging |
Het |
| Usp34 |
C |
T |
11: 23,386,001 (GRCm39) |
H2143Y |
possibly damaging |
Het |
| Vmn1r179 |
A |
C |
7: 23,627,818 (GRCm39) |
Y3S |
probably benign |
Het |
| Vmn1r231 |
G |
A |
17: 21,110,265 (GRCm39) |
Q217* |
probably null |
Het |
| Vmn1r62 |
T |
A |
7: 5,679,066 (GRCm39) |
L249* |
probably null |
Het |
| Vmn1r71 |
G |
C |
7: 10,482,019 (GRCm39) |
S223C |
possibly damaging |
Het |
| Vmn2r109 |
T |
C |
17: 20,773,148 (GRCm39) |
Q491R |
probably benign |
Het |
| Vwf |
G |
A |
6: 125,605,391 (GRCm39) |
V925M |
possibly damaging |
Het |
| Zbtb6 |
A |
C |
2: 37,319,505 (GRCm39) |
L141W |
probably damaging |
Het |
| Zranb1 |
G |
T |
7: 132,584,500 (GRCm39) |
L615F |
probably damaging |
Het |
|
| Other mutations in Shmt1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02088:Shmt1
|
APN |
11 |
60,680,479 (GRCm39) |
missense |
probably damaging |
1.00 |
|
PIT4514001:Shmt1
|
UTSW |
11 |
60,695,173 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0787:Shmt1
|
UTSW |
11 |
60,683,802 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1768:Shmt1
|
UTSW |
11 |
60,683,790 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2179:Shmt1
|
UTSW |
11 |
60,697,825 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R3715:Shmt1
|
UTSW |
11 |
60,688,402 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4647:Shmt1
|
UTSW |
11 |
60,692,291 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5024:Shmt1
|
UTSW |
11 |
60,688,305 (GRCm39) |
intron |
probably benign |
|
|
R5183:Shmt1
|
UTSW |
11 |
60,688,308 (GRCm39) |
intron |
probably benign |
|
|
R5461:Shmt1
|
UTSW |
11 |
60,685,725 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R6014:Shmt1
|
UTSW |
11 |
60,688,383 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6618:Shmt1
|
UTSW |
11 |
60,683,772 (GRCm39) |
splice site |
probably null |
|
|
R6969:Shmt1
|
UTSW |
11 |
60,695,153 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7108:Shmt1
|
UTSW |
11 |
60,689,470 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7158:Shmt1
|
UTSW |
11 |
60,681,068 (GRCm39) |
missense |
probably benign |
0.03 |
|
R7215:Shmt1
|
UTSW |
11 |
60,692,361 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7514:Shmt1
|
UTSW |
11 |
60,692,812 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8717:Shmt1
|
UTSW |
11 |
60,685,763 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9673:Shmt1
|
UTSW |
11 |
60,692,769 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9781:Shmt1
|
UTSW |
11 |
60,692,329 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCCATGTTGGGTGTCAAATGGAAGC -3'
(R):5'- GTGGTAATCGGATAACCACTGGGC -3'
Sequencing Primer
(F):5'- GGTGTCAAATGGAAGCTACTTG -3'
(R):5'- gggtggcagggtagttaag -3'
|
| Posted On |
2013-05-23 |
Incidental Mutation