Incidental Mutation 'R1368:Pdcd2'
ID 155904
Institutional Source Beutler Lab
Gene Symbol Pdcd2
Ensembl Gene ENSMUSG00000014771
Gene Name programmed cell death 2
Synonyms RP-8
MMRRC Submission 039433-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1368 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 15739472-15747560 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 15746846 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 104 (N104K)
Ref Sequence ENSEMBL: ENSMUSP00000118625 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000054450] [ENSMUST00000154293] [ENSMUST00000162505]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000054450
AA Change: N104K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000052523
Gene: ENSMUSG00000014771
AA Change: N104K

DomainStartEndE-ValueType
low complexity region 35 50 N/A INTRINSIC
Pfam:zf-MYND 134 171 2.2e-10 PFAM
Pfam:PDCD2_C 188 338 6e-46 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125709
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137233
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139610
Predicted Effect probably damaging
Transcript: ENSMUST00000154293
AA Change: N104K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000118625
Gene: ENSMUSG00000014771
AA Change: N104K

DomainStartEndE-ValueType
low complexity region 35 50 N/A INTRINSIC
Pfam:zf-MYND 134 171 4.3e-11 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000162505
SMART Domains Protein: ENSMUSP00000124317
Gene: ENSMUSG00000014767

DomainStartEndE-ValueType
low complexity region 55 97 N/A INTRINSIC
low complexity region 103 115 N/A INTRINSIC
low complexity region 117 133 N/A INTRINSIC
Pfam:TBP 139 221 1.1e-34 PFAM
Pfam:TBP 229 312 8.5e-34 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232149
Meta Mutation Damage Score 0.4627 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 95.1%
Validation Efficiency 98% (55/56)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a nuclear protein expressed in a variety of tissues. Expression of this gene has been shown to be repressed by B-cell CLL/lymphoma 6 (BCL6), a transcriptional repressor required for lymph node germinal center development, suggesting that BCL6 regulates apoptosis by its effects on this protein. Alternative splicing results in multiple transcript variants and pseudogenes have been identified on chromosomes 9 and 12. [provided by RefSeq, Dec 2010]
PHENOTYPE: Mice homozygous for a null mutation display embryonic lethality before implantation with most arresting before the blastocyst satge. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 A G 11: 9,241,836 (GRCm39) D1233G probably benign Het
Abcc8 G A 7: 45,772,284 (GRCm39) R832W probably damaging Het
Atp10b A G 11: 43,092,981 (GRCm39) T439A probably damaging Het
Brd10 C A 19: 29,693,796 (GRCm39) S1966I probably damaging Het
C130073F10Rik T A 4: 101,747,953 (GRCm39) N74Y possibly damaging Het
Cct8 G A 16: 87,288,200 (GRCm39) S124L probably damaging Het
Cdh9 T A 15: 16,848,568 (GRCm39) probably benign Het
Cep290 C T 10: 100,330,828 (GRCm39) probably benign Het
Chrng T A 1: 87,133,575 (GRCm39) L10H probably damaging Het
Cnn3 T C 3: 121,250,786 (GRCm39) L189S probably benign Het
Cog4 A G 8: 111,585,157 (GRCm39) probably benign Het
Cxcl12 A G 6: 117,153,111 (GRCm39) probably benign Het
Eif2b2 G A 12: 85,270,230 (GRCm39) A257T probably damaging Het
Entrep2 A T 7: 64,469,625 (GRCm39) V41E probably damaging Het
Fanca G A 8: 124,031,020 (GRCm39) probably benign Het
Fcgbpl1 A G 7: 27,858,903 (GRCm39) Q2341R possibly damaging Het
Fktn G A 4: 53,734,880 (GRCm39) G173R probably damaging Het
Gabbr2 T C 4: 46,674,464 (GRCm39) N841S probably benign Het
Gm5622 T A 14: 51,899,647 (GRCm39) V167E possibly damaging Het
Gnaq T C 19: 16,355,651 (GRCm39) V289A probably benign Het
Gpatch2l T G 12: 86,307,439 (GRCm39) D272E possibly damaging Het
Gzmg G A 14: 56,395,263 (GRCm39) T74I probably benign Het
Ikzf2 G A 1: 69,578,474 (GRCm39) A271V possibly damaging Het
Lig4 T C 8: 10,021,176 (GRCm39) D868G possibly damaging Het
Mfsd6 T C 1: 52,747,764 (GRCm39) E367G possibly damaging Het
Mpz T C 1: 170,987,533 (GRCm39) L223P probably damaging Het
Muc17 T C 5: 137,175,674 (GRCm39) probably benign Het
Or2f1b C A 6: 42,739,613 (GRCm39) T209K possibly damaging Het
Pigg G T 5: 108,465,154 (GRCm39) G129V probably damaging Het
Ppp3cc T C 14: 70,483,311 (GRCm39) Y254C probably damaging Het
Prl3b1 G A 13: 27,427,848 (GRCm39) A53T probably benign Het
Psg23 A G 7: 18,348,645 (GRCm39) V54A probably benign Het
Psmd3 A G 11: 98,573,746 (GRCm39) D64G probably damaging Het
Psmg2 CTTCAGTT CTTCAGTTCAGTT 18: 67,779,095 (GRCm39) probably null Het
Ptgdr T A 14: 45,090,799 (GRCm39) I320F probably damaging Het
Rad50 T A 11: 53,574,072 (GRCm39) K722* probably null Het
Rasl10b G A 11: 83,308,665 (GRCm39) probably null Het
Rgs9 G A 11: 109,138,977 (GRCm39) S255L probably benign Het
Ror1 C T 4: 100,298,334 (GRCm39) P569L possibly damaging Het
Rsad2 T C 12: 26,497,147 (GRCm39) probably null Het
Scn8a A G 15: 100,933,422 (GRCm39) D1501G probably damaging Het
Sema3c A G 5: 17,883,330 (GRCm39) T313A possibly damaging Het
Serpinc1 T A 1: 160,821,094 (GRCm39) F59L probably damaging Het
Sike1 A G 3: 102,903,500 (GRCm39) D63G possibly damaging Het
Slc25a11 T A 11: 70,536,352 (GRCm39) probably null Het
Slc32a1 A G 2: 158,453,240 (GRCm39) M27V probably benign Het
Smc5 A G 19: 23,187,807 (GRCm39) V1003A probably damaging Het
Tll2 G A 19: 41,108,667 (GRCm39) R328C probably damaging Het
Topaz1 A G 9: 122,577,315 (GRCm39) E75G possibly damaging Het
Tspan3 A T 9: 56,054,783 (GRCm39) V48E probably benign Het
Ugt1a6b T C 1: 88,035,358 (GRCm39) I232T probably benign Het
Unc79 A G 12: 103,122,772 (GRCm39) K2290E probably damaging Het
Vmn1r19 T C 6: 57,381,656 (GRCm39) F70L probably benign Het
Other mutations in Pdcd2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02632:Pdcd2 APN 17 15,742,054 (GRCm39) missense probably damaging 0.99
R0433:Pdcd2 UTSW 17 15,746,646 (GRCm39) missense probably benign 0.37
R5083:Pdcd2 UTSW 17 15,743,084 (GRCm39) missense possibly damaging 0.50
R5508:Pdcd2 UTSW 17 15,742,001 (GRCm39) missense probably damaging 1.00
R5963:Pdcd2 UTSW 17 15,746,657 (GRCm39) missense probably damaging 1.00
R5963:Pdcd2 UTSW 17 15,746,656 (GRCm39) missense possibly damaging 0.91
R6944:Pdcd2 UTSW 17 15,745,632 (GRCm39) missense possibly damaging 0.82
R6993:Pdcd2 UTSW 17 15,747,343 (GRCm39) missense probably damaging 1.00
R9667:Pdcd2 UTSW 17 15,747,535 (GRCm39) start codon destroyed probably damaging 0.98
Predicted Primers PCR Primer
(F):5'- CGCCAGTCTAATGTCTGATGCTCC -3'
(R):5'- ATCCTGGGCACGGACTCCTTAAAG -3'

Sequencing Primer
(F):5'- AATGTCTGATGCTCCTTGCTG -3'
(R):5'- CCGGGTTTAAAAGCTCTTTAGC -3'
Posted On 2014-02-11