Incidental Mutation 'R2173:Phgdh'
ID 237606
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 040175-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2173 (G1)
Quality Score 202
Status Validated
Chromosome 3
Chromosomal Location 98220487-98247285 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 98222427 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 388 (V388A)
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: V388A

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000064755
Gene: ENSMUSG00000053398
AA Change: V388A

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 probably benign
Transcript: ENSMUST00000090746
SMART Domains Protein: ENSMUSP00000088249
Gene: ENSMUSG00000027875

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
Pfam:HMG_CoA_synt_N 50 223 7.2e-108 PFAM
Pfam:HMG_CoA_synt_C 224 506 1.8e-131 PFAM
Meta Mutation Damage Score 0.0691 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.6%
Validation Efficiency 97% (66/68)
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: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Alpk1 T A 3: 127,477,239 (GRCm39) H273L probably damaging Het
Alpk3 A G 7: 80,726,648 (GRCm39) Y111C probably damaging Het
Anapc2 T G 2: 25,163,288 (GRCm39) V175G probably benign Het
Arhgap30 T C 1: 171,235,335 (GRCm39) S570P probably damaging Het
AU040320 T C 4: 126,686,069 (GRCm39) L215P probably benign Het
Ccdc59 A T 10: 105,677,388 (GRCm39) K9M possibly damaging Het
Ccdc65 A G 15: 98,618,914 (GRCm39) N298D probably benign Het
Cfap70 T A 14: 20,458,630 (GRCm39) N727Y probably benign Het
Clcn7 A G 17: 25,364,583 (GRCm39) H63R probably benign Het
Corin A T 5: 72,661,422 (GRCm39) C24S probably benign Het
Cyp1a2 A G 9: 57,584,798 (GRCm39) W419R probably damaging Het
Dlgap4 C A 2: 156,604,732 (GRCm39) A256D probably damaging Het
Eif4enif1 A G 11: 3,192,367 (GRCm39) probably null Het
Eri2 A G 7: 119,385,766 (GRCm39) V245A possibly damaging Het
Erich6b T C 14: 75,896,332 (GRCm39) F73L probably benign Het
Fam110a A G 2: 151,812,429 (GRCm39) C114R probably damaging Het
Fam149a T C 8: 45,806,991 (GRCm39) D288G probably damaging Het
Fam171a1 T A 2: 3,226,656 (GRCm39) Y596* probably null Het
Fsd1 A G 17: 56,298,223 (GRCm39) T183A possibly damaging Het
Fut10 T A 8: 31,726,159 (GRCm39) Y305N probably damaging Het
Ganab A T 19: 8,879,624 (GRCm39) probably benign Het
Gm9922 G T 14: 101,967,012 (GRCm39) probably benign Het
Gp9 A G 6: 87,756,035 (GRCm39) T17A probably benign Het
Gxylt2 T C 6: 100,775,115 (GRCm39) Y345H probably damaging Het
Herc2 A G 7: 55,835,699 (GRCm39) H3269R probably benign Het
Hpx A T 7: 105,241,290 (GRCm39) S374T probably benign Het
Hspa5 T C 2: 34,664,674 (GRCm39) V376A probably damaging Het
Hyi T C 4: 118,219,381 (GRCm39) probably benign Het
Impdh2 G A 9: 108,442,593 (GRCm39) probably null Het
Kremen2 A C 17: 23,961,770 (GRCm39) W246G probably damaging Het
Krt87 A G 15: 101,385,818 (GRCm39) V259A probably damaging Het
L3mbtl4 A T 17: 68,894,188 (GRCm39) H398L probably damaging Het
Lama5 C A 2: 179,838,035 (GRCm39) V894L probably benign Het
Maml2 A G 9: 13,532,912 (GRCm39) probably benign Het
Nup153 A T 13: 46,855,076 (GRCm39) probably benign Het
Or10g6 T G 9: 39,934,550 (GRCm39) I287S probably damaging Het
Or2y15 G T 11: 49,350,967 (GRCm39) V154L probably benign Het
Or5k14 A G 16: 58,692,982 (GRCm39) F177S probably damaging Het
Or8b3b T C 9: 38,584,240 (GRCm39) I180V probably benign Het
Or9r7 G A 10: 129,962,372 (GRCm39) P185S probably benign Het
Otof C T 5: 30,543,718 (GRCm39) R582H probably damaging Het
Otud4 T C 8: 80,395,093 (GRCm39) S543P probably damaging Het
Pde6a A G 18: 61,387,453 (GRCm39) D448G probably damaging Het
Plin3 G T 17: 56,586,891 (GRCm39) D385E possibly damaging Het
Polg G T 7: 79,105,341 (GRCm39) D734E probably damaging Het
Pomt1 T C 2: 32,140,912 (GRCm39) Y515H probably damaging Het
Prr35 A C 17: 26,167,461 (GRCm39) H25Q probably damaging Het
Pwwp2a G A 11: 43,573,313 (GRCm39) A132T probably benign Het
Rbm6 A T 9: 107,729,390 (GRCm39) F419L possibly damaging Het
Rfx5 A G 3: 94,864,027 (GRCm39) probably null Het
Rnf135 G A 11: 80,080,066 (GRCm39) S119N probably benign Het
Scfd1 T A 12: 51,433,862 (GRCm39) D51E probably benign Het
Smox A T 2: 131,353,944 (GRCm39) E5D possibly damaging Het
Srpk2 T C 5: 23,723,613 (GRCm39) probably null Het
Syne2 T A 12: 76,147,763 (GRCm39) probably benign Het
Tcf20 A G 15: 82,738,893 (GRCm39) S853P possibly damaging Het
Tmem131l A G 3: 83,833,452 (GRCm39) F804L probably damaging Het
Ttll8 A G 15: 88,798,800 (GRCm39) L645P probably damaging Het
Ubr3 T A 2: 69,727,743 (GRCm39) H35Q probably benign Het
Uck1 GCCAACACC GCC 2: 32,146,088 (GRCm39) probably benign Het
Vmn2r70 A T 7: 85,214,290 (GRCm39) H287Q probably benign Het
Vps26a A T 10: 62,304,171 (GRCm39) I150N probably damaging Het
Zfp605 G A 5: 110,275,323 (GRCm39) R147H probably benign Het
Zfyve16 A G 13: 92,631,596 (GRCm39) M1333T probably damaging 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
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
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'- CAGGCTTCTAAGATGAGGGGTG -3'
(R):5'- AGCTGAGGGTTAAGTGCCTG -3'

Sequencing Primer
(F):5'- CCTGGCACTGGGGAGTTAATAGC -3'
(R):5'- GCCTGTGGCTCCCTTCC -3'
Posted On 2014-10-02