Incidental Mutation 'R8373:Phgdh'
| ID |
646533 |
| 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 |
067741-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R8373 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
98220487-98247285 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 98228561 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Isoleucine
at position 204
(T204I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000064755
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000065793]
|
| AlphaFold |
Q61753 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000065793
AA Change: T204I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000064755
Gene: ENSMUSG00000053398
AA Change: T204I
| 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: ENSMUST00000148488
|
| SMART Domains |
Protein: ENSMUSP00000117525
Gene: ENSMUSG00000053398
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 98.8%
|
| 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: 37 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgrg6 |
T |
C |
10: 14,343,078 (GRCm39) |
T290A |
probably benign |
Het |
| Aff4 |
C |
T |
11: 53,291,094 (GRCm39) |
Q685* |
probably null |
Het |
| Ankmy1 |
A |
G |
1: 92,823,816 (GRCm39) |
M150T |
probably damaging |
Het |
| Armc1 |
T |
C |
3: 19,203,731 (GRCm39) |
Y65C |
probably damaging |
Het |
| Armc8 |
A |
G |
9: 99,409,152 (GRCm39) |
V222A |
probably benign |
Het |
| Bcar1 |
A |
T |
8: 112,442,370 (GRCm39) |
Y228* |
probably null |
Het |
| Cct2 |
T |
C |
10: 116,896,729 (GRCm39) |
D158G |
possibly damaging |
Het |
| Cul1 |
T |
A |
6: 47,491,997 (GRCm39) |
C426S |
possibly damaging |
Het |
| Deup1 |
G |
T |
9: 15,503,671 (GRCm39) |
L297M |
possibly damaging |
Het |
| Dpp10 |
A |
G |
1: 123,781,958 (GRCm39) |
S74P |
possibly damaging |
Het |
| Epha4 |
A |
G |
1: 77,483,716 (GRCm39) |
Y98H |
possibly damaging |
Het |
| Epn3 |
T |
G |
11: 94,383,762 (GRCm39) |
D296A |
probably damaging |
Het |
| Eri2 |
A |
C |
7: 119,371,820 (GRCm39) |
I252S |
probably benign |
Het |
| Gp9 |
C |
T |
6: 87,755,994 (GRCm39) |
T3I |
probably benign |
Het |
| H2-Q5 |
T |
A |
17: 35,613,432 (GRCm39) |
V55E |
|
Het |
| Kif3c |
G |
T |
12: 3,416,089 (GRCm39) |
V37L |
probably benign |
Het |
| Lct |
A |
T |
1: 128,231,577 (GRCm39) |
N757K |
probably damaging |
Het |
| Lhx8 |
A |
C |
3: 154,030,295 (GRCm39) |
N112K |
probably damaging |
Het |
| Loxl3 |
T |
A |
6: 83,025,872 (GRCm39) |
S373R |
possibly damaging |
Het |
| Mettl4 |
G |
A |
17: 95,041,077 (GRCm39) |
T359I |
probably damaging |
Het |
| Mpp7 |
A |
G |
18: 7,444,096 (GRCm39) |
S109P |
probably damaging |
Het |
| Nckap5 |
A |
G |
1: 125,954,032 (GRCm39) |
V840A |
probably benign |
Het |
| Ncoa4 |
T |
A |
14: 31,898,893 (GRCm39) |
L571Q |
probably damaging |
Het |
| Or13a18 |
A |
T |
7: 140,190,208 (GRCm39) |
Y35F |
possibly damaging |
Het |
| Or2f1 |
T |
C |
6: 42,721,280 (GRCm39) |
F103S |
probably damaging |
Het |
| Pla2g4d |
C |
T |
2: 120,107,980 (GRCm39) |
V310M |
probably null |
Het |
| Prss3b |
T |
G |
6: 41,008,622 (GRCm39) |
T231P |
possibly damaging |
Het |
| Psmd12 |
C |
T |
11: 107,388,450 (GRCm39) |
P421L |
probably damaging |
Het |
| Ptch1 |
A |
G |
13: 63,688,982 (GRCm39) |
Y432H |
probably damaging |
Het |
| Rapgef1 |
G |
A |
2: 29,600,243 (GRCm39) |
G655S |
probably damaging |
Het |
| Rilpl2 |
C |
A |
5: 124,616,097 (GRCm39) |
A18S |
probably damaging |
Het |
| Srsf7 |
T |
C |
17: 80,512,815 (GRCm39) |
R88G |
probably benign |
Het |
| St6galnac1 |
T |
C |
11: 116,660,059 (GRCm39) |
K85E |
possibly damaging |
Het |
| Trip12 |
A |
T |
1: 84,773,488 (GRCm39) |
S49R |
probably damaging |
Het |
| Vinac1 |
T |
A |
2: 128,880,091 (GRCm39) |
I612F |
|
Het |
| Wdr48 |
A |
G |
9: 119,734,560 (GRCm39) |
T160A |
probably damaging |
Het |
| Zfp704 |
G |
A |
3: 9,674,502 (GRCm39) |
T93M |
unknown |
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 |
|
|
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 |
|
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'- CGGGATGCCAGTTGTACTAC -3'
(R):5'- CGTGTGGCACCAGTTACTGATG -3'
Sequencing Primer
(F):5'- GGATGCCAGTTGTACTACCTCAG -3'
(R):5'- CACCAGTTACTGATGGTGCAGTTAC -3'
|
| Posted On |
2020-09-02 |
Incidental Mutation