Incidental Mutation 'R5699:Pdp1'
ID 446554
Institutional Source Beutler Lab
Gene Symbol Pdp1
Ensembl Gene ENSMUSG00000049225
Gene Name pyruvate dehydrogenase phosphatase catalytic subunit 1
Synonyms LOC381511, Ppm2c
MMRRC Submission 043327-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5699 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 11958183-11966450 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 11960907 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 468 (D468G)
Ref Sequence ENSEMBL: ENSMUSP00000103937 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056050] [ENSMUST00000095144] [ENSMUST00000108297] [ENSMUST00000108299] [ENSMUST00000108301] [ENSMUST00000108302]
AlphaFold Q3UV70
Predicted Effect probably benign
Transcript: ENSMUST00000056050
AA Change: D428G

PolyPhen 2 Score 0.255 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000050521
Gene: ENSMUSG00000049225
AA Change: D428G

DomainStartEndE-ValueType
PP2Cc 99 523 3.36e-97 SMART
PP2C_SIG 177 525 2.77e0 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000095144
AA Change: D453G

PolyPhen 2 Score 0.792 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000092766
Gene: ENSMUSG00000049225
AA Change: D453G

DomainStartEndE-ValueType
PP2Cc 124 548 3.36e-97 SMART
PP2C_SIG 202 550 2.77e0 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000108297
AA Change: D428G

PolyPhen 2 Score 0.255 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000103932
Gene: ENSMUSG00000049225
AA Change: D428G

DomainStartEndE-ValueType
PP2Cc 99 523 3.36e-97 SMART
PP2C_SIG 177 525 2.77e0 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000108299
AA Change: D453G

PolyPhen 2 Score 0.792 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000103934
Gene: ENSMUSG00000049225
AA Change: D453G

DomainStartEndE-ValueType
PP2Cc 124 548 3.36e-97 SMART
PP2C_SIG 202 550 2.77e0 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000108301
AA Change: D487G

PolyPhen 2 Score 0.129 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000103936
Gene: ENSMUSG00000049225
AA Change: D487G

DomainStartEndE-ValueType
low complexity region 11 18 N/A INTRINSIC
PP2Cc 158 582 3.36e-97 SMART
PP2C_SIG 236 584 2.77e0 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000108302
AA Change: D468G

PolyPhen 2 Score 0.792 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000103937
Gene: ENSMUSG00000049225
AA Change: D468G

DomainStartEndE-ValueType
PP2Cc 139 563 3.36e-97 SMART
PP2C_SIG 217 565 2.77e0 SMART
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.6%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Pyruvate dehydrogenase (E1) is one of the three components (E1, E2, and E3) of the large pyruvate dehydrogenase complex. Pyruvate dehydrogenase kinases catalyze phosphorylation of serine residues of E1 to inactivate the E1 component and inhibit the complex. Pyruvate dehydrogenase phosphatases catalyze the dephosphorylation and activation of the E1 component to reverse the effects of pyruvate dehydrogenase kinases. Pyruvate dehydrogenase phosphatase is a heterodimer consisting of catalytic and regulatory subunits. Two catalytic subunits have been reported; one is predominantly expressed in skeletal muscle and another one is is much more abundant in the liver. The catalytic subunit, encoded by this gene, is the former, and belongs to the protein phosphatase 2C (PP2C) superfamily. Along with the pyruvate dehydrogenase complex and pyruvate dehydrogenase kinases, this enzyme is located in the mitochondrial matrix. Mutation in this gene causes pyruvate dehydrogenase phosphatase deficiency. Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Jun 2009]
Allele List at MGI
Other mutations in this stock
Total: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700128F08Rik A G 9: 8,225,320 (GRCm39) noncoding transcript Het
4930486L24Rik A G 13: 61,001,410 (GRCm39) F106L possibly damaging Het
Adam11 A T 11: 102,664,466 (GRCm39) M385L probably benign Het
Adgre1 C T 17: 57,788,007 (GRCm39) P925S probably benign Het
Adh7 G A 3: 137,932,087 (GRCm39) A234T probably benign Het
Ano2 A G 6: 125,849,703 (GRCm39) E475G probably damaging Het
C2cd4c A G 10: 79,448,385 (GRCm39) V254A probably benign Het
Car13 A G 3: 14,715,749 (GRCm39) Y89C probably damaging Het
Cd38 A G 5: 44,057,728 (GRCm39) K100R probably damaging Het
Cdh11 A G 8: 103,361,175 (GRCm39) I721T probably damaging Het
Cdh2 G A 18: 16,779,579 (GRCm39) Q161* probably null Het
Clk1 T C 1: 58,459,354 (GRCm39) K135R probably damaging Het
Col5a1 G A 2: 27,887,611 (GRCm39) G961R unknown Het
Cpt1b T A 15: 89,308,476 (GRCm39) I151F probably benign Het
Cyp51 A G 5: 4,151,213 (GRCm39) F139L probably damaging Het
Disp1 TTGA T 1: 182,870,119 (GRCm39) probably null Het
Dnah8 T C 17: 31,029,298 (GRCm39) I4089T probably benign Het
Dnali1 C T 4: 124,952,843 (GRCm39) V227M possibly damaging Het
Eml4 T G 17: 83,717,514 (GRCm39) S29A probably benign Het
Eps8l3 C A 3: 107,786,895 (GRCm39) P24T probably benign Het
Fancc A T 13: 63,478,446 (GRCm39) probably null Het
Firrm A T 1: 163,785,120 (GRCm39) V753D probably benign Het
Grid2 G A 6: 63,885,975 (GRCm39) A124T probably damaging Het
Ikbke C T 1: 131,204,204 (GRCm39) probably null Het
Kyat1 G A 2: 30,076,662 (GRCm39) A284V probably benign Het
Lgr6 C T 1: 134,921,748 (GRCm39) A199T probably damaging Het
Lmbrd2 G T 15: 9,175,269 (GRCm39) L393F probably benign Het
Lrrc26 T A 2: 25,180,536 (GRCm39) L179Q probably damaging Het
Mlx A G 11: 100,979,520 (GRCm39) D113G possibly damaging Het
Myod1 A G 7: 46,026,407 (GRCm39) K104R probably damaging Het
Nwd1 G A 8: 73,429,602 (GRCm39) probably null Het
Or56b2j T G 7: 104,353,200 (GRCm39) V142G probably damaging Het
Or5b118 A G 19: 13,448,336 (GRCm39) M1V probably null Het
Or6c3 A C 10: 129,308,746 (GRCm39) N62H probably damaging Het
Pacsin3 A T 2: 91,093,126 (GRCm39) Y206F probably damaging Het
Pcdhgb5 T A 18: 37,864,970 (GRCm39) V255E probably damaging Het
Pgr C T 9: 8,900,600 (GRCm39) probably benign Het
Prrt2 T A 7: 126,617,899 (GRCm39) Y345F probably benign Het
Rbbp8nl T C 2: 179,920,461 (GRCm39) T515A probably damaging Het
Rc3h1 G T 1: 160,757,823 (GRCm39) R47L probably damaging Het
Rfpl4b T A 10: 38,697,281 (GRCm39) I107F possibly damaging Het
Rsbn1 T C 3: 103,869,801 (GRCm39) F754S probably benign Het
Rufy4 T C 1: 74,186,822 (GRCm39) C537R probably damaging Het
Scn3a T C 2: 65,337,608 (GRCm39) T630A possibly damaging Het
Slc22a30 G A 19: 8,321,757 (GRCm39) Q436* probably null Het
Slco1a5 C A 6: 142,194,542 (GRCm39) C367F probably damaging Het
Slit1 A G 19: 41,613,959 (GRCm39) probably null Het
Slit2 G A 5: 48,378,333 (GRCm39) probably null Het
Snrnp40 G T 4: 130,258,958 (GRCm39) G122V possibly damaging Het
Stk16 T A 1: 75,190,248 (GRCm39) M111K probably damaging Het
Tbc1d2 T C 4: 46,616,298 (GRCm39) I477V probably benign Het
Tll1 T A 8: 64,570,974 (GRCm39) E199D probably damaging Het
Trhde A T 10: 114,424,407 (GRCm39) D459E probably benign Het
Ttn T C 2: 76,541,881 (GRCm39) R25375G possibly damaging Het
Tubgcp2 A T 7: 139,578,701 (GRCm39) M757K possibly damaging Het
Ubap1l T A 9: 65,279,337 (GRCm39) V212D possibly damaging Het
Ubqln5 A G 7: 103,778,632 (GRCm39) V64A possibly damaging Het
Usp47 A G 7: 111,709,204 (GRCm39) M1337V probably benign Het
Vmn1r201 T A 13: 22,659,409 (GRCm39) Y208N probably damaging Het
Xkr8 C T 4: 132,455,368 (GRCm39) R335H probably damaging Het
Zbtb49 A T 5: 38,373,870 (GRCm39) C25S probably damaging Het
Zeb2 T A 2: 44,887,800 (GRCm39) N404I probably damaging Het
Other mutations in Pdp1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02243:Pdp1 APN 4 11,961,873 (GRCm39) missense probably benign 0.20
IGL02643:Pdp1 APN 4 11,962,062 (GRCm39) missense probably benign
R1931:Pdp1 UTSW 4 11,962,074 (GRCm39) missense probably benign 0.01
R2162:Pdp1 UTSW 4 11,961,123 (GRCm39) missense probably damaging 0.98
R2418:Pdp1 UTSW 4 11,961,838 (GRCm39) missense probably damaging 0.98
R3843:Pdp1 UTSW 4 11,961,961 (GRCm39) missense probably benign 0.00
R6479:Pdp1 UTSW 4 11,961,327 (GRCm39) missense probably damaging 1.00
R7221:Pdp1 UTSW 4 11,961,004 (GRCm39) missense probably damaging 0.99
R7263:Pdp1 UTSW 4 11,960,821 (GRCm39) missense possibly damaging 0.82
R8483:Pdp1 UTSW 4 11,961,982 (GRCm39) missense probably benign
R9184:Pdp1 UTSW 4 11,962,143 (GRCm39) missense possibly damaging 0.80
R9712:Pdp1 UTSW 4 11,961,607 (GRCm39) missense probably benign 0.41
Z1177:Pdp1 UTSW 4 11,961,639 (GRCm39) missense possibly damaging 0.67
Predicted Primers PCR Primer
(F):5'- GTCGTTCATGATCAACAGCCCC -3'
(R):5'- AGAGTGATAGAGTCTGGCCCAG -3'

Sequencing Primer
(F):5'- GCCTACAGCATGGCGAATG -3'
(R):5'- TCTGGCCCAGACCAGTTGAATG -3'
Posted On 2016-11-21