Incidental Mutation 'R0787:Phgdh'
ID 76893
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 038967-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0787 (G1)
Quality Score 174
Status Validated
Chromosome 3
Chromosomal Location 98313170-98339990 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to G at 98334549 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 83 (V83A)
Ref Sequence ENSEMBL: ENSMUSP00000064755 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000065793]
AlphaFold Q61753
Predicted Effect probably damaging
Transcript: ENSMUST00000065793
AA Change: V83A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000064755
Gene: ENSMUSG00000053398
AA Change: V83A

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: V54A
SMART Domains Protein: ENSMUSP00000117525
Gene: ENSMUSG00000053398
AA Change: V54A

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: ENSMUST00000153694
Meta Mutation Damage Score 0.8151 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 96.9%
  • 20x: 93.4%
Validation Efficiency 100% (56/56)
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: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700001F09Rik A T 14: 43,345,493 (GRCm38) probably null Het
Abca8a T A 11: 110,042,988 (GRCm38) Y1197F possibly damaging Het
Abcc2 T C 19: 43,798,516 (GRCm38) probably null Het
Adamts16 A T 13: 70,738,829 (GRCm38) C979S probably damaging Het
Agap2 T A 10: 127,085,150 (GRCm38) D523E unknown Het
Ankfy1 T A 11: 72,760,296 (GRCm38) I1024N probably damaging Het
Ankrd13c A G 3: 157,994,678 (GRCm38) S379G probably null Het
Arhgap40 T C 2: 158,547,790 (GRCm38) S625P probably benign Het
Armc12 G C 17: 28,538,766 (GRCm38) A291P probably damaging Het
Armc9 A G 1: 86,202,505 (GRCm38) N524D probably damaging Het
Col12a1 G T 9: 79,638,485 (GRCm38) T2305K probably damaging Het
Cyp2c54 T C 19: 40,047,635 (GRCm38) N277S probably benign Het
Czib T A 4: 107,890,129 (GRCm38) L6Q probably damaging Het
E130311K13Rik A T 3: 63,920,298 (GRCm38) V129E probably benign Het
Ehbp1l1 T C 19: 5,722,668 (GRCm38) D79G possibly damaging Het
Epb41l1 A G 2: 156,494,090 (GRCm38) E58G probably damaging Het
Fam217b T A 2: 178,420,909 (GRCm38) V222E probably benign Het
Fat1 T A 8: 45,040,555 (GRCm38) Y3913N probably damaging Het
Fgd4 A G 16: 16,423,901 (GRCm38) probably benign Het
Hltf A T 3: 20,106,446 (GRCm38) D759V probably damaging Het
Hsp90ab1 ACTTCTT ACTT 17: 45,569,499 (GRCm38) probably benign Het
Isg15 C T 4: 156,199,939 (GRCm38) R44H probably benign Het
Itga4 C T 2: 79,279,153 (GRCm38) T232I probably benign Het
Kntc1 C A 5: 123,796,104 (GRCm38) H1399Q probably benign Het
Lig1 A C 7: 13,299,069 (GRCm38) K499Q probably benign Het
Lrrn3 C A 12: 41,454,231 (GRCm38) C29F probably damaging Het
Mtmr10 T C 7: 64,300,615 (GRCm38) I136T possibly damaging Het
Naip1 A G 13: 100,426,096 (GRCm38) Y854H probably benign Het
Or6c201 T C 10: 129,133,526 (GRCm38) N81D possibly damaging Het
Pcdh9 G A 14: 93,886,757 (GRCm38) A659V possibly damaging Het
Phf20l1 T A 15: 66,615,630 (GRCm38) probably benign Het
Pik3r1 A T 13: 101,690,523 (GRCm38) M326K probably benign Het
Pirb A T 7: 3,717,638 (GRCm38) L287Q probably benign Het
Pkd1l2 T C 8: 117,076,177 (GRCm38) D235G possibly damaging Het
Pkhd1l1 C A 15: 44,529,264 (GRCm38) P1665Q probably damaging Het
Ppp1r7 A G 1: 93,364,956 (GRCm38) T326A probably damaging Het
Prr22 A T 17: 56,771,072 (GRCm38) Y75F possibly damaging Het
Ptov1 A C 7: 44,865,470 (GRCm38) probably null Het
Rasal2 A G 1: 157,158,696 (GRCm38) S766P probably damaging Het
Shmt1 T C 11: 60,792,976 (GRCm38) T337A probably benign Het
St5 G T 7: 109,525,620 (GRCm38) R1068S possibly damaging Het
Tbc1d4 A T 14: 101,449,209 (GRCm38) I1168N probably damaging Het
Tecpr2 T C 12: 110,946,343 (GRCm38) V1126A probably benign Het
Tep1 A T 14: 50,829,230 (GRCm38) S2304T possibly damaging Het
Tiam1 C A 16: 89,789,561 (GRCm38) R1446M probably damaging Het
Tmem87a T C 2: 120,370,484 (GRCm38) I425V probably benign Het
Ubr3 T C 2: 69,951,421 (GRCm38) probably benign Het
Ubxn7 T A 16: 32,381,763 (GRCm38) probably benign Het
Vmn2r13 A G 5: 109,156,847 (GRCm38) S573P probably damaging Het
Wdfy3 A T 5: 101,957,388 (GRCm38) V191E probably damaging Het
Zdhhc3 A T 9: 123,083,623 (GRCm38) C153* probably null Het
Zfp407 A T 18: 84,209,022 (GRCm38) V2154D probably damaging Het
Zfp407 A G 18: 84,209,346 (GRCm38) V2046A probably benign Het
Zfr T A 15: 12,140,548 (GRCm38) I227N unknown Het
Other mutations in Phgdh
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
R8373:Phgdh UTSW 3 98,321,245 (GRCm38) missense probably damaging 1.00
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

Sequencing Primer
Posted On 2013-10-16