Incidental Mutation 'R4214:Phgdh'
ID 319335
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 041041-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4214 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 98220487-98247285 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 98235377 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 166 (S166T)
Ref Sequence ENSEMBL: ENSMUSP00000064755 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000065793]
AlphaFold Q61753
Predicted Effect possibly damaging
Transcript: ENSMUST00000065793
AA Change: S166T

PolyPhen 2 Score 0.790 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000064755
Gene: ENSMUSG00000053398
AA Change: S166T

DomainStartEndE-ValueType
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: S137T
SMART Domains Protein: ENSMUSP00000117525
Gene: ENSMUSG00000053398
AA Change: S137T

DomainStartEndE-ValueType
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
Meta Mutation Damage Score 0.3118 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.2%
  • 20x: 95.5%
Validation Efficiency 98% (64/65)
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A730013G03Rik C T 1: 192,515,845 (GRCm39) noncoding transcript Het
Abca12 T A 1: 71,327,856 (GRCm39) D1408V probably damaging Het
Abca13 A T 11: 9,243,877 (GRCm39) L1913F probably damaging Het
Acad9 A G 3: 36,127,752 (GRCm39) E118G probably damaging Het
Adamts5 G A 16: 85,665,531 (GRCm39) A590V probably damaging Het
Ano6 A C 15: 95,863,790 (GRCm39) Y791S probably benign Het
Aox1 T C 1: 58,346,603 (GRCm39) probably null Het
Aox4 T A 1: 58,261,051 (GRCm39) I128N probably damaging Het
Atp2b3 A G X: 72,613,921 (GRCm39) M1142V probably benign Het
AU041133 A G 10: 81,987,223 (GRCm39) H292R probably damaging Het
Bco2 A G 9: 50,456,666 (GRCm39) M158T probably benign Het
Bpnt1 T A 1: 185,077,626 (GRCm39) probably benign Het
Cadm1 A G 9: 47,708,741 (GRCm39) D157G probably damaging Het
Catsperg1 T C 7: 28,895,357 (GRCm39) R499G possibly damaging Het
Ccr7 T C 11: 99,035,872 (GRCm39) E350G probably damaging Het
Ceacam5 T A 7: 17,486,076 (GRCm39) S524R probably benign Het
Cep78 T C 19: 15,936,943 (GRCm39) T588A probably benign Het
Cfap65 T A 1: 74,966,840 (GRCm39) E282D possibly damaging Het
Drd2 A G 9: 49,316,221 (GRCm39) K327R probably benign Het
Erich5 C T 15: 34,471,557 (GRCm39) P262L possibly damaging Het
Ezh2 A C 6: 47,510,748 (GRCm39) D578E probably damaging Het
Fez1 A G 9: 36,781,784 (GRCm39) N20S probably damaging Het
Folr2 T G 7: 101,492,906 (GRCm39) K39T probably damaging Het
Gm10549 G T 18: 33,597,530 (GRCm39) probably null Het
Gm14393 C T 2: 174,903,640 (GRCm39) C89Y probably benign Het
Gm5329 T G 7: 31,671,828 (GRCm39) noncoding transcript Het
Gm7367 A G 7: 59,805,517 (GRCm39) noncoding transcript Het
Gpr162 A T 6: 124,837,031 (GRCm39) W338R probably damaging Het
Ift80 A T 3: 68,898,141 (GRCm39) F65I possibly damaging Het
Klra6 T G 6: 129,995,885 (GRCm39) I158L probably benign Het
Lpp T A 16: 24,580,804 (GRCm39) Y173* probably null Het
Lrp12 A G 15: 39,735,976 (GRCm39) V671A probably benign Het
Lrrc27 C T 7: 138,803,609 (GRCm39) R178C probably damaging Het
Lrrc49 G A 9: 60,573,609 (GRCm39) T225M probably benign Het
Megf8 T A 7: 25,054,793 (GRCm39) S1915T probably benign Het
Mmadhc T C 2: 50,181,344 (GRCm39) T109A probably benign Het
Mon2 T C 10: 122,852,397 (GRCm39) E992G probably benign Het
Msl3 A G X: 167,450,059 (GRCm39) I267T probably damaging Het
Msl3 A T X: 167,445,430 (GRCm39) N430K probably damaging Het
Nab2 G T 10: 127,500,917 (GRCm39) Y25* probably null Het
Notch3 T C 17: 32,351,181 (GRCm39) E1938G possibly damaging Het
Or5ae2 C T 7: 84,506,497 (GRCm39) H307Y probably benign Het
Osgepl1 A G 1: 53,354,167 (GRCm39) T44A probably damaging Het
Pdpr A G 8: 111,856,212 (GRCm39) probably benign Het
Pfkp A G 13: 6,669,261 (GRCm39) S241P probably damaging Het
Plcl1 C T 1: 55,790,494 (GRCm39) Q1055* probably null Het
Plscr2 A G 9: 92,169,790 (GRCm39) N80S probably benign Het
Polr3k A T 2: 181,510,035 (GRCm39) M80L probably benign Het
Prex2 A G 1: 11,171,383 (GRCm39) D304G probably damaging Het
Prex2 A G 1: 11,355,285 (GRCm39) T1529A probably damaging Het
Rcvrn A T 11: 67,586,514 (GRCm39) H91L possibly damaging Het
Rin2 C T 2: 145,702,366 (GRCm39) T354I probably benign Het
Tbx18 T C 9: 87,606,518 (GRCm39) Y209C probably damaging Het
Themis3 T C 17: 66,867,012 (GRCm39) N76S probably benign Het
Trhde A T 10: 114,623,975 (GRCm39) S310T possibly damaging Het
Vmn1r213 G A 13: 23,196,173 (GRCm39) C252Y possibly damaging Het
Zfp523 T C 17: 28,420,003 (GRCm39) V216A probably benign Het
Other mutations in Phgdh
AlleleSourceChrCoordTypePredicted EffectPPH 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
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'- TCCAATGTCCTGATAGGGAGATC -3'
(R):5'- ATTCCCCAGGCAACAGCTTC -3'

Sequencing Primer
(F):5'- TGTCCTGATAGGGAGATCAAAGTTCC -3'
(R):5'- AAGAAGGTGAGCTCTTGCC -3'
Posted On 2015-06-10