Incidental Mutation 'R5461:Shmt1'
| ID |
433036 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Shmt1
|
| Ensembl Gene |
ENSMUSG00000020534 |
| Gene Name |
serine hydroxymethyltransferase 1 (soluble) |
| Synonyms |
mshmt, mshmt2, mshmt1, Shmt |
| MMRRC Submission |
043023-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5461 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
60678933-60702091 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 60685725 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 284
(S284P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000018744
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000018744]
|
| AlphaFold |
P50431 |
| PDB Structure |
RECOMBINANT SERINE HYDROXYMETHYLTRANSFERASE (MOUSE) [X-RAY DIFFRACTION]
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000018744
AA Change: S284P
PolyPhen 2
Score 0.943 (Sensitivity: 0.80; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000018744
Gene: ENSMUSG00000020534
AA Change: S284P
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SHMT
|
20 |
419 |
1.3e-211 |
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: ENSMUST00000173698
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174093
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000174214
AA Change: S283P
|
| SMART Domains |
Protein: ENSMUSP00000134269
Gene: ENSMUSG00000020534
AA Change: S283P
| 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 |
probably benign
Transcript: ENSMUST00000174719
|
| SMART Domains |
Protein: ENSMUSP00000134318
Gene: ENSMUSG00000020534
| 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 |
0.0870 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 94.9%
|
| Validation Efficiency |
100% (57/57) |
| 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: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930522L14Rik |
A |
T |
5: 109,884,643 (GRCm39) |
I405K |
possibly damaging |
Het |
| 4930562C15Rik |
G |
A |
16: 4,682,227 (GRCm39) |
G180E |
probably damaging |
Het |
| Adgrg6 |
A |
T |
10: 14,296,248 (GRCm39) |
W1079R |
probably damaging |
Het |
| Arsa |
T |
C |
15: 89,357,478 (GRCm39) |
H495R |
probably benign |
Het |
| Bptf |
T |
C |
11: 106,952,590 (GRCm39) |
T2088A |
probably damaging |
Het |
| Brsk2 |
T |
C |
7: 141,541,643 (GRCm39) |
L152P |
probably damaging |
Het |
| C8a |
T |
C |
4: 104,673,042 (GRCm39) |
|
probably benign |
Het |
| Ccdc177 |
G |
A |
12: 80,804,816 (GRCm39) |
A486V |
unknown |
Het |
| Cpa2 |
A |
G |
6: 30,544,180 (GRCm39) |
T38A |
probably benign |
Het |
| Crim1 |
T |
G |
17: 78,545,236 (GRCm39) |
C133G |
probably damaging |
Het |
| Dnah2 |
C |
T |
11: 69,364,177 (GRCm39) |
|
probably null |
Het |
| Ep400 |
G |
A |
5: 110,824,550 (GRCm39) |
Q2392* |
probably null |
Het |
| Exoc2 |
C |
T |
13: 31,109,738 (GRCm39) |
S210N |
possibly damaging |
Het |
| Gm7003 |
A |
G |
12: 113,766,847 (GRCm39) |
|
probably benign |
Het |
| Hydin |
A |
G |
8: 111,245,863 (GRCm39) |
K2192R |
probably damaging |
Het |
| Ica1l |
T |
C |
1: 60,053,010 (GRCm39) |
D176G |
probably damaging |
Het |
| Ints10 |
G |
A |
8: 69,246,693 (GRCm39) |
E8K |
possibly damaging |
Het |
| Itgb8 |
T |
C |
12: 119,131,740 (GRCm39) |
E635G |
probably benign |
Het |
| Kmt2d |
G |
A |
15: 98,749,990 (GRCm39) |
|
probably benign |
Het |
| Kng1 |
A |
G |
16: 22,897,887 (GRCm39) |
H429R |
probably benign |
Het |
| Mcm3 |
T |
C |
1: 20,884,661 (GRCm39) |
I281V |
probably benign |
Het |
| Msi1 |
T |
C |
5: 115,579,450 (GRCm39) |
S200P |
possibly damaging |
Het |
| Nat3 |
T |
C |
8: 68,000,514 (GRCm39) |
L131P |
probably damaging |
Het |
| Ncor2 |
T |
C |
5: 125,104,177 (GRCm39) |
E1752G |
probably damaging |
Het |
| Nnt |
C |
T |
13: 119,505,131 (GRCm39) |
A414T |
possibly damaging |
Het |
| Nrp2 |
C |
T |
1: 62,786,370 (GRCm39) |
Q292* |
probably null |
Het |
| Or51ah3 |
T |
A |
7: 103,209,780 (GRCm39) |
L32Q |
probably damaging |
Het |
| Or52k2 |
G |
A |
7: 102,253,615 (GRCm39) |
G18D |
probably damaging |
Het |
| Otop1 |
A |
T |
5: 38,457,059 (GRCm39) |
I273F |
probably damaging |
Het |
| Phactr3 |
T |
A |
2: 177,920,694 (GRCm39) |
N177K |
probably benign |
Het |
| Pik3c2b |
C |
T |
1: 133,027,440 (GRCm39) |
T1313I |
possibly damaging |
Het |
| Pikfyve |
C |
A |
1: 65,274,192 (GRCm39) |
D677E |
probably damaging |
Het |
| Poc1a |
T |
C |
9: 106,165,209 (GRCm39) |
F157L |
probably damaging |
Het |
| Prodh2 |
G |
T |
7: 30,193,948 (GRCm39) |
R185L |
possibly damaging |
Het |
| Rcc1 |
T |
C |
4: 132,061,497 (GRCm39) |
I350M |
probably benign |
Het |
| Rhd |
G |
A |
4: 134,611,928 (GRCm39) |
A249T |
probably damaging |
Het |
| Rtf2 |
A |
G |
2: 172,287,252 (GRCm39) |
Y57C |
probably damaging |
Het |
| Shpk |
T |
C |
11: 73,090,361 (GRCm39) |
V6A |
probably benign |
Het |
| Slc4a5 |
T |
C |
6: 83,262,836 (GRCm39) |
V661A |
probably benign |
Het |
| Spesp1 |
A |
T |
9: 62,180,014 (GRCm39) |
L298Q |
probably damaging |
Het |
| Tas1r2 |
C |
A |
4: 139,387,320 (GRCm39) |
Q231K |
probably benign |
Het |
| Tcp11l1 |
T |
C |
2: 104,518,856 (GRCm39) |
Y280C |
probably benign |
Het |
| Tnip1 |
T |
C |
11: 54,801,625 (GRCm39) |
|
probably benign |
Het |
| Topbp1 |
T |
A |
9: 103,192,395 (GRCm39) |
D295E |
probably benign |
Het |
| Unc79 |
C |
T |
12: 103,078,397 (GRCm39) |
L1521F |
probably damaging |
Het |
| Usp10 |
T |
C |
8: 120,683,406 (GRCm39) |
I759T |
probably benign |
Het |
| Vmn1r30 |
A |
T |
6: 58,412,759 (GRCm39) |
C24* |
probably null |
Het |
| Vmn2r104 |
T |
A |
17: 20,250,343 (GRCm39) |
I643F |
probably damaging |
Het |
| Wwc1 |
T |
A |
11: 35,758,199 (GRCm39) |
T716S |
probably damaging |
Het |
| Zfp949 |
C |
T |
9: 88,451,537 (GRCm39) |
T369M |
probably benign |
Het |
| Zhx3 |
A |
G |
2: 160,621,938 (GRCm39) |
V743A |
probably benign |
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 |
|
R0470:Shmt1
|
UTSW |
11 |
60,683,789 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
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 |
|
|
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'- TGTCTCCTACACAGACACTGC -3'
(R):5'- GTCTAGCATTGCAAACACCTTTC -3'
Sequencing Primer
(F):5'- CCTAAGCTCATTCTCTAGCATGGAAG -3'
(R):5'- TTTCCTCGGAACCAGTCAGG -3'
|
| Posted On |
2016-10-06 |
Incidental Mutation