Incidental Mutation 'R6618:Shmt1'
| ID |
526316 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Shmt1
|
| Ensembl Gene |
ENSMUSG00000020534 |
| Gene Name |
serine hydroxymethyltransferase 1 (soluble) |
| Synonyms |
mshmt, mshmt2, mshmt1, Shmt |
| MMRRC Submission |
044741-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R6618 (G1)
|
| Quality Score |
185.009 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
60678933-60702091 bp(-) (GRCm39) |
| Type of Mutation |
splice site (3 bp from exon) |
| DNA Base Change (assembly) |
T to C
at 60683772 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000018744]
[ENSMUST00000056907]
|
| AlphaFold |
P50431 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000018744
|
| SMART Domains |
Protein: ENSMUSP00000018744
Gene: ENSMUSG00000020534
| 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 |
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 |
probably null
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 |
|
| Predicted Effect |
probably null
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 |
|
| Meta Mutation Damage Score |
0.9756 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 97.8%
- 20x: 93.4%
|
| Validation Efficiency |
100% (37/37) |
| 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: 37 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Atp1b2 |
T |
C |
11: 69,494,289 (GRCm39) |
D68G |
probably damaging |
Het |
| Barx2 |
G |
A |
9: 31,758,168 (GRCm39) |
L257F |
probably benign |
Het |
| Bbx |
C |
G |
16: 50,086,626 (GRCm39) |
W90S |
probably damaging |
Het |
| Bmp1 |
T |
A |
14: 70,728,808 (GRCm39) |
D588V |
probably damaging |
Het |
| Caskin2 |
C |
T |
11: 115,690,855 (GRCm39) |
M1188I |
possibly damaging |
Het |
| Ccdc180 |
T |
A |
4: 45,950,708 (GRCm39) |
I1651N |
probably damaging |
Het |
| Cimip2a |
C |
A |
2: 25,110,635 (GRCm39) |
L148M |
probably benign |
Het |
| Cr2 |
T |
C |
1: 194,839,687 (GRCm39) |
D580G |
probably damaging |
Het |
| Crebbp |
C |
T |
16: 3,937,670 (GRCm39) |
A698T |
possibly damaging |
Het |
| Fam204a |
T |
C |
19: 60,209,069 (GRCm39) |
|
probably null |
Het |
| Fam83h |
T |
C |
15: 75,875,360 (GRCm39) |
D659G |
probably damaging |
Het |
| Garin3 |
A |
G |
11: 46,298,126 (GRCm39) |
T477A |
probably damaging |
Het |
| Hells |
G |
T |
19: 38,945,528 (GRCm39) |
R589L |
probably benign |
Het |
| Helz |
A |
G |
11: 107,489,976 (GRCm39) |
T144A |
probably benign |
Het |
| Il1r1 |
T |
A |
1: 40,339,971 (GRCm39) |
V258D |
probably damaging |
Het |
| Isoc2a |
A |
T |
7: 4,898,325 (GRCm39) |
I183F |
probably benign |
Het |
| Kat2a |
G |
T |
11: 100,603,196 (GRCm39) |
|
probably benign |
Het |
| Klf9 |
A |
G |
19: 23,142,235 (GRCm39) |
M232V |
probably benign |
Het |
| Lars1 |
G |
T |
18: 42,377,973 (GRCm39) |
S147R |
possibly damaging |
Het |
| Mkrn3 |
A |
G |
7: 62,068,781 (GRCm39) |
F337L |
probably benign |
Het |
| Mrc2 |
A |
T |
11: 105,240,708 (GRCm39) |
N1466I |
probably damaging |
Het |
| Myo5c |
G |
A |
9: 75,182,919 (GRCm39) |
|
probably null |
Het |
| Pigs |
T |
C |
11: 78,232,056 (GRCm39) |
L396P |
probably damaging |
Het |
| Prkcb |
G |
A |
7: 122,226,886 (GRCm39) |
R624Q |
probably benign |
Het |
| R3hdm1 |
T |
C |
1: 128,121,302 (GRCm39) |
S269P |
probably benign |
Het |
| Racgap1 |
A |
T |
15: 99,521,875 (GRCm39) |
I505K |
probably damaging |
Het |
| Ralgds |
T |
A |
2: 28,440,523 (GRCm39) |
D777E |
probably benign |
Het |
| Rdh14 |
A |
G |
12: 10,445,123 (GRCm39) |
I325V |
probably benign |
Het |
| Rpn2 |
T |
A |
2: 157,163,781 (GRCm39) |
H624Q |
probably benign |
Het |
| Scarb1 |
C |
T |
5: 125,381,394 (GRCm39) |
S50N |
probably damaging |
Het |
| Slc49a3 |
G |
T |
5: 108,590,964 (GRCm39) |
T400K |
probably benign |
Het |
| Smim24 |
A |
G |
10: 81,229,966 (GRCm39) |
N27S |
possibly damaging |
Het |
| Snx13 |
A |
G |
12: 35,162,444 (GRCm39) |
D550G |
probably damaging |
Het |
| Tnfsf18 |
T |
A |
1: 161,322,349 (GRCm39) |
L23* |
probably null |
Het |
| Trpc3 |
T |
A |
3: 36,694,844 (GRCm39) |
K703N |
possibly damaging |
Het |
| Ugt1a1 |
CAGAGAGAGAGAGA |
CAGAGAGAGAGA |
1: 88,139,706 (GRCm39) |
|
probably benign |
Het |
| Zfy2 |
A |
G |
Y: 2,121,477 (GRCm39) |
S139P |
probably benign |
Homo |
|
| 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 |
|
|
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 |
|
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'- ATCTCTCATGTGAACCTCAGCTG -3'
(R):5'- TGCTCCTGAGTCACAACTTG -3'
Sequencing Primer
(F):5'- TCAGCTGTTCCCAGAATATGCAG -3'
(R):5'- CCTGAGTCACAACTTGTTTTTAAAGC -3'
|
| Posted On |
2018-06-22 |
Incidental Mutation