Incidental Mutation 'R2342:Shmt2'
| ID |
246790 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Shmt2
|
| Ensembl Gene |
ENSMUSG00000025403 |
| Gene Name |
serine hydroxymethyltransferase 2 (mitochondrial) |
| Synonyms |
2700043D08Rik |
| MMRRC Submission |
040328-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R2342 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
10 |
| Chromosomal Location |
127352992-127358313 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 127354680 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 335
(V335A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000026470
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000026470]
[ENSMUST00000035735]
[ENSMUST00000219239]
|
| AlphaFold |
Q9CZN7 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000026470
AA Change: V335A
PolyPhen 2
Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000026470
Gene: ENSMUSG00000025403
AA Change: V335A
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SHMT
|
49 |
448 |
5.4e-211 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000035735
|
| SMART Domains |
Protein: ENSMUSP00000042185
Gene: ENSMUSG00000040280
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:B12D
|
16 |
84 |
2.5e-32 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000217682
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000218035
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000218258
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000218302
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000218313
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000219239
AA Change: V332A
PolyPhen 2
Score 0.877 (Sensitivity: 0.83; Specificity: 0.94)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000220356
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000218492
|
| Meta Mutation Damage Score |
0.0885 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.2%
|
| Validation Efficiency |
100% (39/39) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is primarily responsible for glycine synthesis. The activity of the encoded protein has been suggested to be the primary source of intracellular glycine. The gene which encodes the cytosolic form of this enzyme is located on chromosome 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit lethlity after E13.5, decreased size, anemia and reduced MEF cellular respiration and proliferation. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 35 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Arhgef28 |
C |
T |
13: 98,130,537 (GRCm39) |
E434K |
probably benign |
Het |
| Babam1 |
T |
A |
8: 71,855,515 (GRCm39) |
M236K |
probably benign |
Het |
| Camk1 |
T |
C |
6: 113,318,942 (GRCm39) |
|
probably benign |
Het |
| Chd8 |
A |
C |
14: 52,442,674 (GRCm39) |
N625K |
probably benign |
Het |
| Dcaf8 |
A |
G |
1: 172,013,928 (GRCm39) |
H373R |
possibly damaging |
Het |
| Dscam |
G |
A |
16: 96,420,702 (GRCm39) |
T1728M |
probably damaging |
Het |
| Elf1 |
T |
C |
14: 79,802,896 (GRCm39) |
|
probably benign |
Het |
| Epha2 |
C |
T |
4: 141,050,842 (GRCm39) |
A866V |
probably benign |
Het |
| Frmd6 |
C |
A |
12: 70,930,592 (GRCm39) |
Y237* |
probably null |
Het |
| Glg1 |
A |
T |
8: 111,914,439 (GRCm39) |
C448* |
probably null |
Het |
| Gm4787 |
G |
T |
12: 81,425,532 (GRCm39) |
R209S |
possibly damaging |
Het |
| Hhipl1 |
T |
C |
12: 108,284,721 (GRCm39) |
L358P |
probably damaging |
Het |
| Hmgxb3 |
G |
A |
18: 61,296,063 (GRCm39) |
T315I |
possibly damaging |
Het |
| Irak2 |
C |
A |
6: 113,670,632 (GRCm39) |
T539K |
probably benign |
Het |
| Lrp1b |
C |
A |
2: 40,809,208 (GRCm39) |
G2568C |
possibly damaging |
Het |
| Meis1 |
C |
T |
11: 18,831,647 (GRCm39) |
A464T |
probably damaging |
Het |
| Or10g1b |
C |
A |
14: 52,627,322 (GRCm39) |
A303S |
possibly damaging |
Het |
| Or6a2 |
T |
C |
7: 106,600,116 (GRCm39) |
D317G |
probably benign |
Het |
| Orc4 |
A |
G |
2: 48,817,152 (GRCm39) |
S179P |
probably damaging |
Het |
| Plxna2 |
C |
T |
1: 194,431,625 (GRCm39) |
S538F |
probably damaging |
Het |
| Pnliprp1 |
A |
G |
19: 58,729,691 (GRCm39) |
|
probably benign |
Het |
| Prpf40b |
T |
A |
15: 99,204,049 (GRCm39) |
V174D |
probably damaging |
Het |
| Rnf169 |
T |
C |
7: 99,574,652 (GRCm39) |
K648E |
possibly damaging |
Het |
| Rtf1 |
A |
G |
2: 119,542,598 (GRCm39) |
T301A |
probably benign |
Het |
| Sdccag8 |
T |
C |
1: 176,747,207 (GRCm39) |
V528A |
probably benign |
Het |
| Sgsh |
A |
G |
11: 119,238,540 (GRCm39) |
V308A |
probably benign |
Het |
| Skint6 |
T |
A |
4: 113,034,180 (GRCm39) |
T316S |
probably benign |
Het |
| Tbl2 |
G |
A |
5: 135,187,607 (GRCm39) |
R288Q |
possibly damaging |
Het |
| Ttc3 |
C |
T |
16: 94,232,857 (GRCm39) |
P1003L |
probably damaging |
Het |
| Usp34 |
A |
G |
11: 23,353,599 (GRCm39) |
K1469E |
possibly damaging |
Het |
| Virma |
T |
C |
4: 11,501,316 (GRCm39) |
Y92H |
probably damaging |
Het |
| Vmn2r112 |
T |
A |
17: 22,822,096 (GRCm39) |
V258E |
probably damaging |
Het |
| Wnt16 |
A |
G |
6: 22,288,923 (GRCm39) |
E80G |
probably damaging |
Het |
| Zbtb10 |
C |
T |
3: 9,330,255 (GRCm39) |
P538S |
possibly damaging |
Het |
| Zup1 |
G |
A |
10: 33,804,113 (GRCm39) |
H454Y |
probably damaging |
Het |
|
| Other mutations in Shmt2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02862:Shmt2
|
APN |
10 |
127,354,743 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0057:Shmt2
|
UTSW |
10 |
127,356,917 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R0057:Shmt2
|
UTSW |
10 |
127,356,917 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R0504:Shmt2
|
UTSW |
10 |
127,355,941 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1493:Shmt2
|
UTSW |
10 |
127,354,812 (GRCm39) |
splice site |
probably null |
|
|
R2006:Shmt2
|
UTSW |
10 |
127,355,029 (GRCm39) |
missense |
probably benign |
0.22 |
|
R2358:Shmt2
|
UTSW |
10 |
127,353,897 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4352:Shmt2
|
UTSW |
10 |
127,354,686 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R4998:Shmt2
|
UTSW |
10 |
127,354,139 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5242:Shmt2
|
UTSW |
10 |
127,354,789 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5568:Shmt2
|
UTSW |
10 |
127,356,250 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5654:Shmt2
|
UTSW |
10 |
127,353,668 (GRCm39) |
missense |
probably benign |
0.05 |
|
R6167:Shmt2
|
UTSW |
10 |
127,353,731 (GRCm39) |
missense |
probably benign |
|
|
R8465:Shmt2
|
UTSW |
10 |
127,355,945 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8503:Shmt2
|
UTSW |
10 |
127,354,789 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8776:Shmt2
|
UTSW |
10 |
127,356,785 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8776-TAIL:Shmt2
|
UTSW |
10 |
127,356,785 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9099:Shmt2
|
UTSW |
10 |
127,355,962 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R9124:Shmt2
|
UTSW |
10 |
127,355,561 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
Z1176:Shmt2
|
UTSW |
10 |
127,355,347 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
Z1177:Shmt2
|
UTSW |
10 |
127,356,804 (GRCm39) |
nonsense |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TGTACTGAACAAGGAGGACTCC -3'
(R):5'- ACCTATGCCAGTCATCCGTC -3'
Sequencing Primer
(F):5'- CATGACCCCGGCTTTGCTG -3'
(R):5'- TCCTTTTAGAGCCTGACTATGC -3'
|
| Posted On |
2014-10-30 |
Incidental Mutation