Incidental Mutation 'R4741:Ptcd3'
ID 358074
Institutional Source Beutler Lab
Gene Symbol Ptcd3
Ensembl Gene ENSMUSG00000063884
Gene Name pentatricopeptide repeat domain 3
Synonyms 2610034F17Rik, 2810422B04Rik
MMRRC Submission 042026-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4741 (G1)
Quality Score 225
Status Not validated
Chromosome 6
Chromosomal Location 71857622-71885734 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 71879933 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Phenylalanine at position 108 (L108F)
Ref Sequence ENSEMBL: ENSMUSP00000080743 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000082094] [ENSMUST00000206879]
AlphaFold Q14C51
Predicted Effect probably damaging
Transcript: ENSMUST00000082094
AA Change: L108F

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000080743
Gene: ENSMUSG00000063884
AA Change: L108F

DomainStartEndE-ValueType
low complexity region 2 8 N/A INTRINSIC
low complexity region 216 227 N/A INTRINSIC
Pfam:PPR_2 253 300 1.4e-10 PFAM
Pfam:PPR_3 331 366 2.1e-4 PFAM
low complexity region 671 684 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205293
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205420
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205761
Predicted Effect probably benign
Transcript: ENSMUST00000206284
Predicted Effect probably damaging
Transcript: ENSMUST00000206879
AA Change: L108F

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 94.1%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Angptl2 T C 2: 33,136,200 (GRCm39) Y462H probably benign Het
Arhgef12 A G 9: 42,883,449 (GRCm39) I1360T possibly damaging Het
Armc10 T G 5: 21,856,834 (GRCm39) L111R probably damaging Het
Atm T C 9: 53,364,907 (GRCm39) K2628E probably benign Het
Best3 A T 10: 116,859,901 (GRCm39) N387I probably benign Het
Bltp1 A G 3: 36,996,524 (GRCm39) T1079A probably damaging Het
Brpf3 T C 17: 29,036,758 (GRCm39) F721S possibly damaging Het
Cacna1c A G 6: 118,590,271 (GRCm39) S1411P probably damaging Het
Cldn8 G A 16: 88,359,296 (GRCm39) H210Y probably benign Het
Clip2 T A 5: 134,545,123 (GRCm39) T344S probably benign Het
Csmd1 A C 8: 15,960,447 (GRCm39) W3323G probably damaging Het
Doc2a A T 7: 126,450,617 (GRCm39) T298S possibly damaging Het
Dpp9 T C 17: 56,512,286 (GRCm39) N234S probably benign Het
Dtx2 C T 5: 136,055,371 (GRCm39) R353C probably benign Het
Epm2aip1 A G 9: 111,101,681 (GRCm39) H218R probably benign Het
F2rl1 G A 13: 95,650,651 (GRCm39) T77M probably damaging Het
Fsd2 A G 7: 81,201,643 (GRCm39) probably null Het
Grin2a T C 16: 9,481,376 (GRCm39) Y475C probably damaging Het
H2-Ob T A 17: 34,461,545 (GRCm39) S95T possibly damaging Het
Hddc3 A G 7: 79,995,464 (GRCm39) T160A probably benign Het
Hp A T 8: 110,302,104 (GRCm39) C281* probably null Het
Ighg1 T C 12: 113,290,178 (GRCm39) probably benign Het
Ints7 A G 1: 191,351,747 (GRCm39) I819V probably benign Het
Jam2 G A 16: 84,609,840 (GRCm39) V151M probably damaging Het
Jmjd1c A G 10: 67,060,718 (GRCm39) I737V possibly damaging Het
Krt74 C T 15: 101,669,876 (GRCm39) noncoding transcript Het
Lnpep T C 17: 17,791,920 (GRCm39) Y407C probably damaging Het
Lrp4 T G 2: 91,341,912 (GRCm39) C1842G probably damaging Het
Mug2 T A 6: 122,056,572 (GRCm39) N1172K probably benign Het
Npy6r A T 18: 44,408,791 (GRCm39) T71S probably damaging Het
Nsd3 A T 8: 26,163,382 (GRCm39) I591F probably damaging Het
Oog2 A C 4: 143,921,715 (GRCm39) E208D possibly damaging Het
Otogl A G 10: 107,615,121 (GRCm39) I1928T probably benign Het
Papss1 T C 3: 131,324,860 (GRCm39) L418P probably damaging Het
Pcdhb13 T A 18: 37,576,571 (GRCm39) D316E probably benign Het
Pcdhgb2 T A 18: 37,824,737 (GRCm39) probably null Het
Ralgps1 T C 2: 33,226,599 (GRCm39) S31G probably benign Het
Rnf225 A T 7: 12,661,857 (GRCm39) H12L probably benign Het
Ryr3 T A 2: 112,633,613 (GRCm39) M2047L probably damaging Het
Secisbp2l C T 2: 125,582,657 (GRCm39) G933D possibly damaging Het
Serpinb3b G T 1: 107,082,200 (GRCm39) Q355K probably benign Het
Slc8a2 T A 7: 15,868,233 (GRCm39) F155Y probably damaging Het
Taf1c A G 8: 120,330,134 (GRCm39) probably benign Het
Tln2 A G 9: 67,293,837 (GRCm39) probably null Het
Tmpo A G 10: 90,998,506 (GRCm39) V427A probably benign Het
Vmn1r17 A T 6: 57,338,337 (GRCm39) Y9* probably null Het
Vmn2r63 C T 7: 42,577,544 (GRCm39) M331I probably benign Het
Zdhhc1 CGGGGG CGGGGGG 8: 106,210,376 (GRCm39) probably null Het
Zfand5 C T 19: 21,253,845 (GRCm39) T16I probably damaging Het
Zfp352 A T 4: 90,113,177 (GRCm39) K439M possibly damaging Het
Zfp786 G A 6: 47,797,625 (GRCm39) H438Y probably damaging Het
Zfp808 T A 13: 62,319,763 (GRCm39) C331S probably damaging Het
Other mutations in Ptcd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00767:Ptcd3 APN 6 71,880,432 (GRCm39) missense probably damaging 0.96
IGL00903:Ptcd3 APN 6 71,884,828 (GRCm39) missense possibly damaging 0.93
IGL01545:Ptcd3 APN 6 71,865,561 (GRCm39) missense probably benign 0.01
IGL01924:Ptcd3 APN 6 71,875,411 (GRCm39) missense probably damaging 1.00
IGL02675:Ptcd3 APN 6 71,860,426 (GRCm39) critical splice donor site probably null
R0732:Ptcd3 UTSW 6 71,858,155 (GRCm39) unclassified probably benign
R1374:Ptcd3 UTSW 6 71,885,637 (GRCm39) nonsense probably null
R1393:Ptcd3 UTSW 6 71,866,605 (GRCm39) missense probably benign 0.00
R1498:Ptcd3 UTSW 6 71,870,479 (GRCm39) missense probably damaging 1.00
R1646:Ptcd3 UTSW 6 71,875,379 (GRCm39) missense probably benign 0.26
R1712:Ptcd3 UTSW 6 71,885,637 (GRCm39) nonsense probably null
R2022:Ptcd3 UTSW 6 71,862,537 (GRCm39) missense probably damaging 1.00
R2248:Ptcd3 UTSW 6 71,871,269 (GRCm39) critical splice donor site probably null
R2406:Ptcd3 UTSW 6 71,865,631 (GRCm39) missense probably damaging 1.00
R3418:Ptcd3 UTSW 6 71,860,470 (GRCm39) missense possibly damaging 0.93
R3419:Ptcd3 UTSW 6 71,860,470 (GRCm39) missense possibly damaging 0.93
R4677:Ptcd3 UTSW 6 71,870,498 (GRCm39) missense probably benign 0.17
R4752:Ptcd3 UTSW 6 71,878,296 (GRCm39) missense probably damaging 0.99
R5441:Ptcd3 UTSW 6 71,858,505 (GRCm39) missense possibly damaging 0.62
R5583:Ptcd3 UTSW 6 71,879,920 (GRCm39) missense probably damaging 1.00
R5681:Ptcd3 UTSW 6 71,884,643 (GRCm39) missense probably damaging 1.00
R6028:Ptcd3 UTSW 6 71,875,392 (GRCm39) missense probably damaging 1.00
R6324:Ptcd3 UTSW 6 71,862,311 (GRCm39) missense probably benign 0.00
R6537:Ptcd3 UTSW 6 71,874,094 (GRCm39) splice site probably null
R6600:Ptcd3 UTSW 6 71,860,530 (GRCm39) missense probably damaging 1.00
R6783:Ptcd3 UTSW 6 71,885,627 (GRCm39) missense probably benign 0.00
R6810:Ptcd3 UTSW 6 71,862,516 (GRCm39) missense probably damaging 0.99
R6860:Ptcd3 UTSW 6 71,874,094 (GRCm39) splice site probably null
R6993:Ptcd3 UTSW 6 71,862,299 (GRCm39) missense probably damaging 1.00
R7578:Ptcd3 UTSW 6 71,885,691 (GRCm39) missense probably benign
R7788:Ptcd3 UTSW 6 71,862,541 (GRCm39) missense probably benign 0.00
R7851:Ptcd3 UTSW 6 71,879,843 (GRCm39) missense probably damaging 1.00
R7888:Ptcd3 UTSW 6 71,860,431 (GRCm39) missense probably damaging 1.00
R7889:Ptcd3 UTSW 6 71,865,592 (GRCm39) missense probably damaging 1.00
R7919:Ptcd3 UTSW 6 71,880,438 (GRCm39) missense probably damaging 1.00
R8162:Ptcd3 UTSW 6 71,884,798 (GRCm39) missense probably benign 0.02
R8351:Ptcd3 UTSW 6 71,885,625 (GRCm39) missense probably benign 0.00
R8451:Ptcd3 UTSW 6 71,885,625 (GRCm39) missense probably benign 0.00
R8701:Ptcd3 UTSW 6 71,862,495 (GRCm39) missense possibly damaging 0.92
R8826:Ptcd3 UTSW 6 71,885,645 (GRCm39) missense probably benign 0.01
R8926:Ptcd3 UTSW 6 71,869,464 (GRCm39) missense probably damaging 1.00
R8969:Ptcd3 UTSW 6 71,880,431 (GRCm39) missense probably benign 0.44
R9031:Ptcd3 UTSW 6 71,880,458 (GRCm39) nonsense probably null
R9046:Ptcd3 UTSW 6 71,870,364 (GRCm39) critical splice donor site probably null
R9384:Ptcd3 UTSW 6 71,874,110 (GRCm39) missense possibly damaging 0.77
R9668:Ptcd3 UTSW 6 71,871,275 (GRCm39) missense possibly damaging 0.93
R9771:Ptcd3 UTSW 6 71,872,903 (GRCm39) nonsense probably null
X0024:Ptcd3 UTSW 6 71,878,258 (GRCm39) missense probably damaging 1.00
X0065:Ptcd3 UTSW 6 71,884,790 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- AAATGGCTAAATCTGCTGTGGAAG -3'
(R):5'- GCAAACCATGTGTGTCTGTGG -3'

Sequencing Primer
(F):5'- CTGCTGTGGAAGTATGATTTAATTTG -3'
(R):5'- GAAATCAGTACCATACTCAGAAGTG -3'
Posted On 2015-11-11