Incidental Mutation 'IGL02088:Shmt1'
| ID |
279322 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Shmt1
|
| Ensembl Gene |
ENSMUSG00000020534 |
| Gene Name |
serine hydroxymethyltransferase 1 (soluble) |
| Synonyms |
mshmt, mshmt2, mshmt1, Shmt |
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
IGL02088
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
11 |
| Chromosomal Location |
60678933-60702091 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 60680479 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 403
(T403A)
|
| 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 |
probably damaging
Transcript: ENSMUST00000018744
AA Change: T403A
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000018744
Gene: ENSMUSG00000020534
AA Change: T403A
| 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: ENSMUST00000174093
|
| 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 |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000174719
AA Change: T363A
|
| SMART Domains |
Protein: ENSMUSP00000134318
Gene: ENSMUSG00000020534
AA Change: T363A
| 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: ENSMUST00000174214
|
| SMART Domains |
Protein: ENSMUSP00000134269
Gene: ENSMUSG00000020534
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SHMT
|
20 |
408 |
4.6e-196 |
PFAM |
|
Pfam:Aminotran_1_2
|
153 |
409 |
3.1e-6 |
PFAM |
|
| Coding Region Coverage |
|
| Validation Efficiency |
|
| 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: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ackr4 |
T |
C |
9: 103,976,080 (GRCm39) |
E289G |
probably damaging |
Het |
| Aldh1l1 |
A |
T |
6: 90,557,572 (GRCm39) |
|
probably benign |
Het |
| Ampd3 |
T |
A |
7: 110,392,893 (GRCm39) |
D220E |
probably benign |
Het |
| Ank3 |
T |
C |
10: 69,835,203 (GRCm39) |
V136A |
probably damaging |
Het |
| Atg14 |
T |
C |
14: 47,780,316 (GRCm39) |
K486R |
probably benign |
Het |
| Axin1 |
A |
G |
17: 26,407,669 (GRCm39) |
I637V |
probably benign |
Het |
| Axin2 |
T |
A |
11: 108,814,442 (GRCm39) |
F110Y |
probably damaging |
Het |
| Cdh12 |
A |
T |
15: 21,480,425 (GRCm39) |
K214* |
probably null |
Het |
| Cfap44 |
A |
C |
16: 44,271,991 (GRCm39) |
E1248A |
possibly damaging |
Het |
| Cryba4 |
A |
G |
5: 112,398,875 (GRCm39) |
|
probably benign |
Het |
| Cyp2c68 |
A |
G |
19: 39,691,965 (GRCm39) |
|
probably benign |
Het |
| Dnah5 |
G |
T |
15: 28,459,264 (GRCm39) |
|
probably null |
Het |
| Dok3 |
A |
T |
13: 55,672,183 (GRCm39) |
V165E |
probably damaging |
Het |
| Etl4 |
A |
T |
2: 20,811,359 (GRCm39) |
R1147S |
probably damaging |
Het |
| Fbxl6 |
G |
T |
15: 76,420,106 (GRCm39) |
C502* |
probably null |
Het |
| Gp2 |
A |
T |
7: 119,053,692 (GRCm39) |
Y90N |
probably damaging |
Het |
| H1f7 |
G |
T |
15: 98,155,059 (GRCm39) |
T30K |
probably damaging |
Het |
| Inka1 |
A |
G |
9: 107,861,656 (GRCm39) |
F220S |
probably damaging |
Het |
| Itfg2 |
A |
G |
6: 128,388,569 (GRCm39) |
V306A |
probably benign |
Het |
| Lrig2 |
T |
C |
3: 104,374,424 (GRCm39) |
Y219C |
probably damaging |
Het |
| Mccc1 |
A |
T |
3: 36,028,351 (GRCm39) |
I485N |
probably damaging |
Het |
| Mettl25 |
A |
G |
10: 105,659,111 (GRCm39) |
F391L |
probably damaging |
Het |
| Muc19 |
C |
T |
15: 91,775,362 (GRCm39) |
|
noncoding transcript |
Het |
| Muc2 |
T |
C |
7: 141,305,241 (GRCm39) |
C182R |
probably damaging |
Het |
| Nlrp4g |
T |
C |
9: 124,350,453 (GRCm38) |
|
noncoding transcript |
Het |
| Nms |
A |
G |
1: 38,978,358 (GRCm39) |
|
probably benign |
Het |
| Nr3c1 |
T |
C |
18: 39,557,444 (GRCm39) |
N503S |
probably damaging |
Het |
| Or10q12 |
T |
C |
19: 13,746,030 (GRCm39) |
F108S |
probably damaging |
Het |
| Or5h18 |
A |
G |
16: 58,847,415 (GRCm39) |
L285P |
probably damaging |
Het |
| Or7g16 |
C |
T |
9: 18,727,219 (GRCm39) |
V124I |
probably benign |
Het |
| Pcdhb5 |
G |
A |
18: 37,455,012 (GRCm39) |
S464N |
probably benign |
Het |
| Pcgf6 |
T |
C |
19: 47,039,243 (GRCm39) |
T6A |
unknown |
Het |
| Rdx |
A |
G |
9: 51,972,183 (GRCm39) |
|
probably benign |
Het |
| Slc35d1 |
A |
G |
4: 103,068,522 (GRCm39) |
F148L |
probably benign |
Het |
| Tk1 |
A |
G |
11: 117,715,491 (GRCm39) |
|
probably benign |
Het |
| Tnks |
T |
A |
8: 35,307,148 (GRCm39) |
I1134F |
possibly damaging |
Het |
| Ttn |
A |
G |
2: 76,557,035 (GRCm39) |
V29990A |
probably damaging |
Het |
| Tut4 |
A |
G |
4: 108,369,415 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Shmt1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
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 |
|
|
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 |
|
| Posted On |
2015-04-16 |
Incidental Mutation