Incidental Mutation 'R2367:Phgdh'
| ID |
246367 |
| 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 |
040348-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R2367 (G1)
|
| Quality Score |
168 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
98220487-98247285 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to G
at 98221612 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glycine to Alanine
at position 440
(G440A)
|
| 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: G440A
PolyPhen 2
Score 0.070 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000064755
Gene: ENSMUSG00000053398
AA Change: G440A
| 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 |
|
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.3%
- 20x: 95.2%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the 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: 33 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adipoq |
T |
C |
16: 22,974,069 (GRCm39) |
V32A |
probably benign |
Het |
| Ceacam3 |
T |
C |
7: 16,885,813 (GRCm39) |
|
probably null |
Het |
| Cep250 |
G |
A |
2: 155,834,552 (GRCm39) |
R2159K |
probably damaging |
Het |
| Cfap46 |
C |
A |
7: 139,233,414 (GRCm39) |
V296F |
probably damaging |
Het |
| Ctdspl2 |
T |
C |
2: 121,817,499 (GRCm39) |
V182A |
probably benign |
Het |
| Cyp2c69 |
T |
C |
19: 39,866,038 (GRCm39) |
N185S |
probably benign |
Het |
| Daxx |
C |
T |
17: 34,130,821 (GRCm39) |
R279W |
probably benign |
Het |
| Dnajc28 |
G |
A |
16: 91,413,755 (GRCm39) |
T187M |
probably damaging |
Het |
| Fat3 |
G |
A |
9: 15,909,567 (GRCm39) |
S2145F |
probably damaging |
Het |
| Galnt13 |
A |
T |
2: 55,002,956 (GRCm39) |
M552L |
probably benign |
Het |
| Gstt2 |
C |
T |
10: 75,668,524 (GRCm39) |
G108S |
probably benign |
Het |
| Heatr1 |
T |
A |
13: 12,448,605 (GRCm39) |
L422Q |
probably damaging |
Het |
| Kntc1 |
C |
T |
5: 123,919,255 (GRCm39) |
L845F |
probably damaging |
Het |
| Krtap26-1 |
C |
A |
16: 88,444,213 (GRCm39) |
R136L |
probably benign |
Het |
| Mrgprb5 |
C |
T |
7: 47,818,347 (GRCm39) |
W129* |
probably null |
Het |
| Ms4a3 |
G |
A |
19: 11,607,108 (GRCm39) |
P186S |
probably benign |
Het |
| Myo15a |
T |
A |
11: 60,408,064 (GRCm39) |
M3184K |
probably damaging |
Het |
| Olig2 |
G |
A |
16: 91,023,454 (GRCm39) |
R56Q |
possibly damaging |
Het |
| Or8u9 |
T |
C |
2: 86,001,981 (GRCm39) |
Y60C |
probably damaging |
Het |
| Pgap3 |
C |
T |
11: 98,281,985 (GRCm39) |
|
probably null |
Het |
| Scn1a |
T |
C |
2: 66,158,023 (GRCm39) |
Q450R |
probably damaging |
Het |
| Sema4d |
CGGGG |
CGGGGGGG |
13: 51,857,176 (GRCm39) |
|
probably benign |
Het |
| Sik1 |
C |
T |
17: 32,065,271 (GRCm39) |
V776I |
possibly damaging |
Het |
| Slc25a39 |
T |
A |
11: 102,294,477 (GRCm39) |
T316S |
possibly damaging |
Het |
| Slc38a10 |
C |
T |
11: 120,001,087 (GRCm39) |
E578K |
probably benign |
Het |
| Slc44a5 |
T |
A |
3: 153,953,446 (GRCm39) |
I276K |
possibly damaging |
Het |
| Smarcc2 |
A |
G |
10: 128,318,036 (GRCm39) |
T610A |
possibly damaging |
Het |
| Spag9 |
G |
A |
11: 94,007,583 (GRCm39) |
S1090N |
probably damaging |
Het |
| Tpr |
T |
C |
1: 150,309,479 (GRCm39) |
V277A |
probably damaging |
Het |
| Traf3ip1 |
T |
G |
1: 91,435,242 (GRCm39) |
S314A |
possibly damaging |
Het |
| Tril |
T |
A |
6: 53,796,151 (GRCm39) |
D357V |
probably damaging |
Het |
| Tube1 |
T |
C |
10: 39,020,915 (GRCm39) |
L267P |
probably damaging |
Het |
| Vmn1r11 |
A |
G |
6: 57,114,416 (GRCm39) |
I27V |
probably benign |
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 |
|
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 |
|
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'- TACTTCAGAAGCCTGGCCAG -3'
(R):5'- ACTAGTGAGCCAGGACTGAAC -3'
Sequencing Primer
(F):5'- GCCTCCCTGACAAAAAGCCTTC -3'
(R):5'- TGGGCCAGGCTAGATCTCTCTC -3'
|
| Posted On |
2014-10-30 |
Incidental Mutation