Incidental Mutation 'R5528:Phgdh'
| ID |
433515 |
| 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 |
043086-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5528 (G1)
|
| Quality Score |
122 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
98220487-98247285 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 98235655 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 121
(I121V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000064755
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000065793]
|
| AlphaFold |
Q61753 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000065793
AA Change: I121V
PolyPhen 2
Score 0.130 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000064755
Gene: ENSMUSG00000053398
AA Change: I121V
| 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 |
unknown
Transcript: ENSMUST00000148488
AA Change: I92V
|
| SMART Domains |
Protein: ENSMUSP00000117525
Gene: ENSMUSG00000053398
AA Change: I92V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:2-Hacid_dh
|
7 |
145 |
1.1e-27 |
PFAM |
|
Pfam:2-Hacid_dh_C
|
83 |
149 |
1.3e-21 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000152106
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153694
|
| Coding Region Coverage |
- 1x: 98.6%
- 3x: 97.4%
- 10x: 95.4%
- 20x: 91.4%
|
| Validation Efficiency |
|
| 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: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1110002E22Rik |
T |
C |
3: 137,772,260 (GRCm39) |
L483P |
probably benign |
Het |
| 4930519G04Rik |
T |
G |
5: 115,012,415 (GRCm39) |
|
probably null |
Het |
| Ablim2 |
C |
T |
5: 36,013,510 (GRCm39) |
Q148* |
probably null |
Het |
| Ap3s2 |
A |
T |
7: 79,530,234 (GRCm39) |
*194R |
probably null |
Het |
| Arpp21 |
C |
T |
9: 111,978,421 (GRCm39) |
A235T |
probably benign |
Het |
| C9orf72 |
T |
C |
4: 35,213,556 (GRCm39) |
D198G |
probably benign |
Het |
| Ccdc33 |
T |
C |
9: 57,936,078 (GRCm39) |
D939G |
probably benign |
Het |
| Celsr2 |
A |
T |
3: 108,320,610 (GRCm39) |
I734N |
probably damaging |
Het |
| Clcn1 |
C |
A |
6: 42,277,275 (GRCm39) |
N455K |
probably benign |
Het |
| Cpne8 |
C |
T |
15: 90,503,893 (GRCm39) |
V91I |
possibly damaging |
Het |
| Cstdc7 |
A |
G |
18: 42,306,727 (GRCm39) |
|
probably null |
Het |
| Ddx1 |
A |
G |
12: 13,279,295 (GRCm39) |
V448A |
probably damaging |
Het |
| Dnhd1 |
G |
A |
7: 105,352,416 (GRCm39) |
R2523Q |
probably damaging |
Het |
| Eeig1 |
G |
A |
2: 32,456,339 (GRCm39) |
A334T |
probably damaging |
Het |
| Eif2a |
G |
T |
3: 58,455,933 (GRCm39) |
D311Y |
probably damaging |
Het |
| Eif2ak4 |
G |
A |
2: 118,258,419 (GRCm39) |
E512K |
probably damaging |
Het |
| Esp15 |
A |
T |
17: 39,955,640 (GRCm39) |
Y69F |
probably benign |
Het |
| Gucy1a1 |
A |
T |
3: 82,016,380 (GRCm39) |
Y203N |
probably damaging |
Het |
| Hook3 |
T |
C |
8: 26,562,321 (GRCm39) |
Q248R |
probably damaging |
Het |
| Ifit2 |
T |
A |
19: 34,550,937 (GRCm39) |
V159E |
possibly damaging |
Het |
| Il17rd |
T |
C |
14: 26,810,024 (GRCm39) |
V20A |
possibly damaging |
Het |
| Kcnq3 |
T |
A |
15: 65,897,027 (GRCm39) |
D291V |
probably damaging |
Het |
| Klf11 |
A |
T |
12: 24,704,929 (GRCm39) |
M111L |
probably benign |
Het |
| Lama5 |
T |
A |
2: 179,836,356 (GRCm39) |
H1165L |
probably benign |
Het |
| Lmo7 |
A |
G |
14: 102,139,522 (GRCm39) |
N702S |
probably damaging |
Het |
| Lta4h |
T |
C |
10: 93,307,736 (GRCm39) |
V323A |
probably damaging |
Het |
| Mkrn3 |
T |
C |
7: 62,068,735 (GRCm39) |
E352G |
possibly damaging |
Het |
| Ms4a19 |
T |
C |
19: 11,118,999 (GRCm39) |
S37G |
possibly damaging |
Het |
| Mtf2 |
T |
A |
5: 108,242,023 (GRCm39) |
L277Q |
probably damaging |
Het |
| Myo9b |
A |
G |
8: 71,775,918 (GRCm39) |
N370D |
probably benign |
Het |
| Nlrp4e |
A |
C |
7: 23,036,316 (GRCm39) |
K723T |
probably benign |
Het |
| Nsun3 |
A |
G |
16: 62,555,689 (GRCm39) |
V279A |
possibly damaging |
Het |
| Pde6b |
A |
G |
5: 108,571,424 (GRCm39) |
D459G |
probably benign |
Het |
| Pik3r5 |
T |
C |
11: 68,386,803 (GRCm39) |
C811R |
probably damaging |
Het |
| Spaca6 |
A |
C |
17: 18,051,344 (GRCm39) |
I27L |
probably benign |
Het |
| Trmt1l |
G |
A |
1: 151,330,746 (GRCm39) |
V588I |
probably benign |
Het |
| Tshr |
A |
G |
12: 91,503,967 (GRCm39) |
N302D |
probably damaging |
Het |
| Vmn2r23 |
A |
G |
6: 123,689,961 (GRCm39) |
D279G |
probably damaging |
Het |
| Wnt3a |
T |
C |
11: 59,166,106 (GRCm39) |
N58S |
probably damaging |
Het |
| Zkscan8 |
A |
G |
13: 21,704,895 (GRCm39) |
V276A |
probably damaging |
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 |
|
R4410:Phgdh
|
UTSW |
3 |
98,221,591 (GRCm39) |
missense |
probably benign |
|
|
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 |
|
|
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'- TCAGTTCTGTCCCCATGAACTG -3'
(R):5'- ACCAATGTTCTCACTGTCCCAG -3'
Sequencing Primer
(F):5'- TCTGTCCCCATGAACTGCAACC -3'
(R):5'- AGCCTTCCCTTATACACAGTGG -3'
|
| Posted On |
2016-10-06 |
Incidental Mutation