Incidental Mutation 'R5242:Shmt2'
| ID |
400936 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Shmt2
|
| Ensembl Gene |
ENSMUSG00000025403 |
| Gene Name |
serine hydroxymethyltransferase 2 (mitochondrial) |
| Synonyms |
2700043D08Rik |
| MMRRC Submission |
042813-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5242 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
10 |
| Chromosomal Location |
127352992-127358313 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 127354789 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Isoleucine
at position 299
(V299I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000026470
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000026470]
[ENSMUST00000035735]
[ENSMUST00000219239]
|
| AlphaFold |
Q9CZN7 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000026470
AA Change: V299I
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
| SMART Domains |
Protein: ENSMUSP00000026470
Gene: ENSMUSG00000025403
AA Change: V299I
| 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 |
probably benign
Transcript: ENSMUST00000219239
AA Change: V296I
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000220356
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000218492
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.2%
|
| Validation Efficiency |
|
| 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: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgrl1 |
T |
C |
8: 84,657,711 (GRCm39) |
V439A |
possibly damaging |
Het |
| Aldh6a1 |
A |
G |
12: 84,483,157 (GRCm39) |
V390A |
probably damaging |
Het |
| Alox5 |
T |
C |
6: 116,437,927 (GRCm39) |
D20G |
probably damaging |
Het |
| Atp2a2 |
A |
T |
5: 122,600,009 (GRCm39) |
F487I |
probably damaging |
Het |
| BC048679 |
G |
A |
7: 81,145,091 (GRCm39) |
T84M |
probably damaging |
Het |
| C2cd3 |
T |
C |
7: 100,039,373 (GRCm39) |
S191P |
probably benign |
Het |
| Cdh6 |
A |
G |
15: 13,064,497 (GRCm39) |
V131A |
probably benign |
Het |
| Chrna9 |
A |
G |
5: 66,134,423 (GRCm39) |
T425A |
probably benign |
Het |
| Cplane2 |
T |
C |
4: 140,947,158 (GRCm39) |
Y180H |
probably damaging |
Het |
| Ddx39a |
A |
G |
8: 84,448,440 (GRCm39) |
S231G |
probably benign |
Het |
| Diaph1 |
C |
T |
18: 37,984,688 (GRCm39) |
G1176R |
probably damaging |
Het |
| Dnah10 |
G |
T |
5: 124,864,484 (GRCm39) |
V2230L |
probably benign |
Het |
| Foxo1 |
T |
C |
3: 52,176,676 (GRCm39) |
S152P |
probably damaging |
Het |
| Fras1 |
T |
A |
5: 96,805,109 (GRCm39) |
D1250E |
probably benign |
Het |
| G6pd2 |
A |
G |
5: 61,966,785 (GRCm39) |
I187V |
probably benign |
Het |
| Gm10113 |
T |
C |
13: 46,330,992 (GRCm39) |
|
noncoding transcript |
Het |
| Hoxd1 |
A |
G |
2: 74,593,792 (GRCm39) |
D116G |
probably damaging |
Het |
| Igkv13-85 |
A |
T |
6: 68,907,544 (GRCm39) |
I19K |
probably benign |
Het |
| Jag2 |
C |
T |
12: 112,880,486 (GRCm39) |
V288M |
probably damaging |
Het |
| Ndrg2 |
A |
G |
14: 52,148,541 (GRCm39) |
|
probably null |
Het |
| Neurl3 |
G |
A |
1: 36,308,501 (GRCm39) |
Q104* |
probably null |
Het |
| Nudt16l1 |
C |
T |
16: 4,757,485 (GRCm39) |
R133W |
probably damaging |
Het |
| Oasl2 |
A |
T |
5: 115,043,122 (GRCm39) |
Q298L |
possibly damaging |
Het |
| Or3a10 |
A |
T |
11: 73,935,848 (GRCm39) |
M84K |
possibly damaging |
Het |
| Or51a25 |
C |
T |
7: 102,373,483 (GRCm39) |
M71I |
probably benign |
Het |
| Pnma2 |
C |
A |
14: 67,153,746 (GRCm39) |
Q57K |
probably benign |
Het |
| Pramel22 |
A |
T |
4: 143,382,181 (GRCm39) |
L172I |
probably benign |
Het |
| Rps7 |
T |
A |
12: 28,681,136 (GRCm39) |
E188D |
probably benign |
Het |
| Rrp1b |
T |
C |
17: 32,270,677 (GRCm39) |
V212A |
possibly damaging |
Het |
| Serpina9 |
C |
A |
12: 103,974,644 (GRCm39) |
A170S |
probably benign |
Het |
| Siae |
C |
T |
9: 37,556,148 (GRCm39) |
P435S |
probably damaging |
Het |
| Smarcal1 |
T |
C |
1: 72,630,242 (GRCm39) |
S99P |
probably benign |
Het |
| Sntb1 |
C |
G |
15: 55,506,191 (GRCm39) |
G461R |
probably damaging |
Het |
| Stimate |
T |
A |
14: 30,547,793 (GRCm39) |
F36I |
probably damaging |
Het |
| Tas2r124 |
T |
C |
6: 132,732,503 (GRCm39) |
Y271H |
possibly damaging |
Het |
| Thsd7a |
A |
T |
6: 12,327,582 (GRCm39) |
I1430K |
probably damaging |
Het |
| Trmt9b |
A |
G |
8: 36,979,084 (GRCm39) |
K229R |
probably benign |
Het |
| Tsc22d2 |
T |
A |
3: 58,323,360 (GRCm39) |
V84E |
possibly damaging |
Het |
| Ube2s |
C |
T |
7: 4,813,434 (GRCm39) |
R110Q |
possibly damaging |
Het |
| Usp3 |
C |
T |
9: 66,434,432 (GRCm39) |
C283Y |
probably damaging |
Het |
| Vmn2r81 |
T |
A |
10: 79,129,309 (GRCm39) |
Y733* |
probably null |
Het |
| Wdr75 |
T |
A |
1: 45,856,487 (GRCm39) |
C503* |
probably null |
Het |
| Zfp764 |
T |
C |
7: 127,004,541 (GRCm39) |
M197V |
probably benign |
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 |
|
R2342:Shmt2
|
UTSW |
10 |
127,354,680 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
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 |
|
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'- GCCTCGGCTTTAGGTACAAG -3'
(R):5'- TGGGGTTAAACCTTCTTCCC -3'
Sequencing Primer
(F):5'- GCAAAACCTCTGGCCCAGTG -3'
(R):5'- GAGCCTGACTATGCATCT -3'
|
| Posted On |
2016-07-06 |
Incidental Mutation