Incidental Mutation 'R4410:Phgdh'
| ID |
327848 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Phgdh
|
| Ensembl Gene |
ENSMUSG00000053398 |
| Gene Name |
3-phosphoglycerate dehydrogenase |
| Synonyms |
3PGDH, 3-PGDH, A10, PGAD, PGD, PGDH, SERA |
| MMRRC Submission |
041692-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4410 (G1)
|
| Quality Score |
173 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
98220487-98247285 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 98221591 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Threonine
at position 447
(M447T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000064755
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000065793]
[ENSMUST00000090746]
[ENSMUST00000120541]
|
| AlphaFold |
Q61753 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000065793
AA Change: M447T
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000064755
Gene: ENSMUSG00000053398
AA Change: M447T
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:2-Hacid_dh
|
9 |
317 |
2.1e-42 |
PFAM |
|
Pfam:2-Hacid_dh_C
|
111 |
285 |
3.5e-60 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000090746
|
| SMART Domains |
Protein: ENSMUSP00000088249
Gene: ENSMUSG00000027875
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:HMG_CoA_synt_N
|
50 |
223 |
2.9e-111 |
PFAM |
|
Pfam:HMG_CoA_synt_C
|
224 |
506 |
6.6e-131 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000120541
|
| SMART Domains |
Protein: ENSMUSP00000113296
Gene: ENSMUSG00000027875
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:HMG_CoA_synt_N
|
50 |
223 |
7.2e-108 |
PFAM |
|
Pfam:HMG_CoA_synt_C
|
224 |
506 |
1.8e-131 |
PFAM |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.0%
|
| Validation Efficiency |
96% (46/48) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the enzyme which is involved in the early steps of L-serine synthesis in animal cells. L-serine is required for D-serine and other amino acid synthesis. The enzyme requires NAD/NADH as a cofactor and forms homotetramers for activity. Mutations in this gene have been found in a family with congenital microcephaly, psychomotor retardation and other symptoms. Multiple alternatively spliced transcript variants have been found, however the full-length nature of most are not known. [provided by RefSeq, Aug 2011]
PHENOTYPE: Mice homozygous for a null allele die by E13.5 and exhibit abnormal neural development. [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 |
|---|
| Arhgap39 |
A |
T |
15: 76,609,712 (GRCm39) |
|
probably benign |
Het |
| Arrb1 |
G |
T |
7: 99,247,503 (GRCm39) |
|
probably benign |
Het |
| Cadps |
A |
G |
14: 12,822,323 (GRCm38) |
M139T |
probably damaging |
Het |
| Casr |
A |
G |
16: 36,320,703 (GRCm39) |
C482R |
probably benign |
Het |
| Cdca4 |
A |
T |
12: 112,785,499 (GRCm39) |
H76Q |
probably benign |
Het |
| Ddias |
A |
G |
7: 92,507,287 (GRCm39) |
L876P |
probably benign |
Het |
| Dnah9 |
T |
C |
11: 65,976,303 (GRCm39) |
S1249G |
possibly damaging |
Het |
| Dnttip1 |
A |
G |
2: 164,609,739 (GRCm39) |
|
probably benign |
Het |
| Eme2 |
A |
G |
17: 25,112,598 (GRCm39) |
S160P |
probably benign |
Het |
| Fbxw24 |
A |
T |
9: 109,437,256 (GRCm39) |
D210E |
probably damaging |
Het |
| Folr2 |
T |
C |
7: 101,489,881 (GRCm39) |
E129G |
probably damaging |
Het |
| Herc6 |
T |
A |
6: 57,636,664 (GRCm39) |
N793K |
possibly damaging |
Het |
| Iqcg |
T |
G |
16: 32,851,186 (GRCm39) |
K262Q |
possibly damaging |
Het |
| Lhfpl3 |
A |
G |
5: 22,980,690 (GRCm39) |
|
probably benign |
Het |
| Lmod2 |
A |
C |
6: 24,604,629 (GRCm39) |
S535R |
probably damaging |
Het |
| Lrp1b |
T |
A |
2: 40,555,094 (GRCm39) |
S342C |
possibly damaging |
Het |
| Lrrn3 |
T |
A |
12: 41,502,583 (GRCm39) |
Y578F |
possibly damaging |
Het |
| Map3k4 |
T |
A |
17: 12,467,885 (GRCm39) |
R1050W |
probably damaging |
Het |
| Muc6 |
T |
A |
7: 141,217,576 (GRCm39) |
T2301S |
possibly damaging |
Het |
| Mycbp2 |
T |
C |
14: 103,372,702 (GRCm39) |
E4048G |
probably damaging |
Het |
| Myh3 |
G |
C |
11: 66,975,858 (GRCm39) |
E297Q |
possibly damaging |
Het |
| Nkain3 |
A |
G |
4: 20,778,284 (GRCm39) |
V11A |
probably benign |
Het |
| Or4c102 |
G |
A |
2: 88,422,765 (GRCm39) |
V206I |
probably benign |
Het |
| P3h2 |
G |
C |
16: 25,924,040 (GRCm39) |
R132G |
possibly damaging |
Het |
| Pals2 |
C |
T |
6: 50,175,248 (GRCm39) |
Q520* |
probably null |
Het |
| Pmfbp1 |
G |
A |
8: 110,258,695 (GRCm39) |
A667T |
probably benign |
Het |
| Pramel41 |
A |
T |
5: 94,593,720 (GRCm39) |
Q15L |
probably benign |
Het |
| Psmd2 |
T |
G |
16: 20,473,776 (GRCm39) |
C230G |
probably damaging |
Het |
| Rin2 |
C |
T |
2: 145,702,366 (GRCm39) |
T354I |
probably benign |
Het |
| Slc37a3 |
T |
A |
6: 39,315,747 (GRCm39) |
Y443F |
probably benign |
Het |
| Sorl1 |
C |
A |
9: 41,915,288 (GRCm39) |
G1314* |
probably null |
Het |
| Spag7 |
T |
C |
11: 70,555,688 (GRCm39) |
D83G |
probably damaging |
Het |
| St7 |
C |
T |
6: 17,854,932 (GRCm39) |
R267* |
probably null |
Het |
| Syne2 |
C |
T |
12: 76,141,167 (GRCm39) |
S99L |
probably damaging |
Het |
| Tacc2 |
T |
G |
7: 130,343,941 (GRCm39) |
S2533R |
possibly damaging |
Het |
| Tmem59l |
A |
G |
8: 70,939,951 (GRCm39) |
L6S |
unknown |
Het |
| Uaca |
T |
G |
9: 60,777,173 (GRCm39) |
V518G |
probably damaging |
Het |
| Usp43 |
T |
C |
11: 67,746,716 (GRCm39) |
E992G |
probably benign |
Het |
| Vmn1r55 |
A |
G |
7: 5,150,075 (GRCm39) |
V116A |
probably benign |
Het |
| Wdr3 |
G |
A |
3: 100,047,543 (GRCm39) |
T844M |
probably benign |
Het |
| Wdr7 |
T |
A |
18: 63,911,320 (GRCm39) |
M904K |
probably damaging |
Het |
| Zbtb39 |
A |
G |
10: 127,578,696 (GRCm39) |
I423M |
possibly damaging |
Het |
| Zmym1 |
A |
T |
4: 126,941,897 (GRCm39) |
C830* |
probably null |
Het |
|
| Other mutations in Phgdh |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00429:Phgdh
|
APN |
3 |
98,235,631 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0195:Phgdh
|
UTSW |
3 |
98,223,866 (GRCm39) |
unclassified |
probably benign |
|
|
R0636:Phgdh
|
UTSW |
3 |
98,240,607 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R0787:Phgdh
|
UTSW |
3 |
98,241,865 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1626:Phgdh
|
UTSW |
3 |
98,223,725 (GRCm39) |
missense |
probably benign |
0.16 |
|
R1733:Phgdh
|
UTSW |
3 |
98,235,451 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1782:Phgdh
|
UTSW |
3 |
98,228,063 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R2173:Phgdh
|
UTSW |
3 |
98,222,427 (GRCm39) |
missense |
probably benign |
0.00 |
|
R2256:Phgdh
|
UTSW |
3 |
98,235,607 (GRCm39) |
missense |
probably benign |
0.30 |
|
R2367:Phgdh
|
UTSW |
3 |
98,221,612 (GRCm39) |
missense |
probably benign |
0.07 |
|
R2495:Phgdh
|
UTSW |
3 |
98,247,105 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4214:Phgdh
|
UTSW |
3 |
98,235,377 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
R5062:Phgdh
|
UTSW |
3 |
98,235,655 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5378:Phgdh
|
UTSW |
3 |
98,228,639 (GRCm39) |
splice site |
probably null |
|
|
R5528:Phgdh
|
UTSW |
3 |
98,235,655 (GRCm39) |
missense |
probably benign |
0.13 |
|
R7357:Phgdh
|
UTSW |
3 |
98,247,138 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7436:Phgdh
|
UTSW |
3 |
98,247,045 (GRCm39) |
missense |
probably benign |
0.34 |
|
R7894:Phgdh
|
UTSW |
3 |
98,247,124 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8373:Phgdh
|
UTSW |
3 |
98,228,561 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8467:Phgdh
|
UTSW |
3 |
98,228,627 (GRCm39) |
missense |
probably benign |
|
|
R8762:Phgdh
|
UTSW |
3 |
98,247,024 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
R9547:Phgdh
|
UTSW |
3 |
98,241,950 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GGGACATATAGACATGCCTGAG -3'
(R):5'- ACATGGGTAATTAGGCTGTGTC -3'
Sequencing Primer
(F):5'- AGGGCCCAATTCTAGGGATTC -3'
(R):5'- AATTAGGCTGTGTCTCTGTCTTC -3'
|
| Posted On |
2015-07-07 |
Incidental Mutation