Incidental Mutation 'R8373:Phgdh'
| ID |
646533 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Phgdh
|
| Ensembl Gene |
ENSMUSG00000053398 |
| Gene Name |
3-phosphoglycerate dehydrogenase |
| Synonyms |
PGD, 3-PGDH, A10, PGAD, PGDH, SERA, 3PGDH |
| 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 |
98313170-98339990 bp(-) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 98321245 bp (GRCm38)
|
| 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 |
|---|
| 2210010C04Rik |
T |
G |
6: 41,031,688 (GRCm38) |
T231P |
possibly damaging |
Het |
| Adgrg6 |
T |
C |
10: 14,467,334 (GRCm38) |
T290A |
probably benign |
Het |
| Aff4 |
C |
T |
11: 53,400,267 (GRCm38) |
Q685* |
probably null |
Het |
| Ankmy1 |
A |
G |
1: 92,896,094 (GRCm38) |
M150T |
probably damaging |
Het |
| Armc1 |
T |
C |
3: 19,149,567 (GRCm38) |
Y65C |
probably damaging |
Het |
| Armc8 |
A |
G |
9: 99,527,099 (GRCm38) |
V222A |
probably benign |
Het |
| Bcar1 |
A |
T |
8: 111,715,738 (GRCm38) |
Y228* |
probably null |
Het |
| Cct2 |
T |
C |
10: 117,060,824 (GRCm38) |
D158G |
possibly damaging |
Het |
| Cul1 |
T |
A |
6: 47,515,063 (GRCm38) |
C426S |
possibly damaging |
Het |
| Deup1 |
G |
T |
9: 15,592,375 (GRCm38) |
L297M |
possibly damaging |
Het |
| Dpp10 |
A |
G |
1: 123,854,229 (GRCm38) |
S74P |
possibly damaging |
Het |
| Epha4 |
A |
G |
1: 77,507,079 (GRCm38) |
Y98H |
possibly damaging |
Het |
| Epn3 |
T |
G |
11: 94,492,936 (GRCm38) |
D296A |
probably damaging |
Het |
| Eri2 |
A |
C |
7: 119,772,597 (GRCm38) |
I252S |
probably benign |
Het |
| Gm14025 |
T |
A |
2: 129,038,171 (GRCm38) |
I612F |
|
Het |
| Gp9 |
C |
T |
6: 87,779,012 (GRCm38) |
T3I |
probably benign |
Het |
| H2-Q5 |
T |
A |
17: 35,394,456 (GRCm38) |
V55E |
|
Het |
| Kif3c |
G |
T |
12: 3,366,089 (GRCm38) |
V37L |
probably benign |
Het |
| Lct |
A |
T |
1: 128,303,840 (GRCm38) |
N757K |
probably damaging |
Het |
| Lhx8 |
A |
C |
3: 154,324,658 (GRCm38) |
N112K |
probably damaging |
Het |
| Loxl3 |
T |
A |
6: 83,048,891 (GRCm38) |
S373R |
possibly damaging |
Het |
| Mettl4 |
G |
A |
17: 94,733,649 (GRCm38) |
T359I |
probably damaging |
Het |
| Mpp7 |
A |
G |
18: 7,444,096 (GRCm38) |
S109P |
probably damaging |
Het |
| Nckap5 |
A |
G |
1: 126,026,295 (GRCm38) |
V840A |
probably benign |
Het |
| Ncoa4 |
T |
A |
14: 32,176,936 (GRCm38) |
L571Q |
probably damaging |
Het |
| Olfr453 |
T |
C |
6: 42,744,346 (GRCm38) |
F103S |
probably damaging |
Het |
| Olfr46 |
A |
T |
7: 140,610,295 (GRCm38) |
Y35F |
possibly damaging |
Het |
| Pla2g4d |
C |
T |
2: 120,277,499 (GRCm38) |
V310M |
probably null |
Het |
| Psmd12 |
C |
T |
11: 107,497,624 (GRCm38) |
P421L |
probably damaging |
Het |
| Ptch1 |
A |
G |
13: 63,541,168 (GRCm38) |
Y432H |
probably damaging |
Het |
| Rapgef1 |
G |
A |
2: 29,710,231 (GRCm38) |
G655S |
probably damaging |
Het |
| Rilpl2 |
C |
A |
5: 124,478,034 (GRCm38) |
A18S |
probably damaging |
Het |
| Srsf7 |
T |
C |
17: 80,205,386 (GRCm38) |
R88G |
probably benign |
Het |
| St6galnac1 |
T |
C |
11: 116,769,233 (GRCm38) |
K85E |
possibly damaging |
Het |
| Trip12 |
A |
T |
1: 84,795,767 (GRCm38) |
S49R |
probably damaging |
Het |
| Wdr48 |
A |
G |
9: 119,905,494 (GRCm38) |
T160A |
probably damaging |
Het |
| Zfp704 |
G |
A |
3: 9,609,442 (GRCm38) |
T93M |
unknown |
Het |
|
| Other mutations in Phgdh |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00429:Phgdh
|
APN |
3 |
98,328,315 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R0195:Phgdh
|
UTSW |
3 |
98,316,550 (GRCm38) |
unclassified |
probably benign |
|
|
R0636:Phgdh
|
UTSW |
3 |
98,333,291 (GRCm38) |
missense |
possibly damaging |
0.89 |
|
R0787:Phgdh
|
UTSW |
3 |
98,334,549 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R1626:Phgdh
|
UTSW |
3 |
98,316,409 (GRCm38) |
missense |
probably benign |
0.16 |
|
R1733:Phgdh
|
UTSW |
3 |
98,328,135 (GRCm38) |
missense |
probably benign |
0.00 |
|
R1782:Phgdh
|
UTSW |
3 |
98,320,747 (GRCm38) |
missense |
probably damaging |
0.97 |
|
R2173:Phgdh
|
UTSW |
3 |
98,315,111 (GRCm38) |
missense |
probably benign |
0.00 |
|
R2256:Phgdh
|
UTSW |
3 |
98,328,291 (GRCm38) |
missense |
probably benign |
0.30 |
|
R2367:Phgdh
|
UTSW |
3 |
98,314,296 (GRCm38) |
missense |
probably benign |
0.07 |
|
R2495:Phgdh
|
UTSW |
3 |
98,339,789 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4214:Phgdh
|
UTSW |
3 |
98,328,061 (GRCm38) |
missense |
possibly damaging |
0.79 |
|
R4410:Phgdh
|
UTSW |
3 |
98,314,275 (GRCm38) |
missense |
probably benign |
|
|
R5062:Phgdh
|
UTSW |
3 |
98,328,339 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5378:Phgdh
|
UTSW |
3 |
98,321,323 (GRCm38) |
splice site |
probably null |
|
|
R5528:Phgdh
|
UTSW |
3 |
98,328,339 (GRCm38) |
missense |
probably benign |
0.13 |
|
R7357:Phgdh
|
UTSW |
3 |
98,339,822 (GRCm38) |
missense |
probably benign |
0.00 |
|
R7436:Phgdh
|
UTSW |
3 |
98,339,729 (GRCm38) |
missense |
probably benign |
0.34 |
|
R7894:Phgdh
|
UTSW |
3 |
98,339,808 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R8467:Phgdh
|
UTSW |
3 |
98,321,311 (GRCm38) |
missense |
probably benign |
|
|
R8762:Phgdh
|
UTSW |
3 |
98,339,708 (GRCm38) |
missense |
possibly damaging |
0.51 |
|
R9547:Phgdh
|
UTSW |
3 |
98,334,634 (GRCm38) |
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