Incidental Mutation 'R8876:Pdcd1'
ID 676552
Institutional Source Beutler Lab
Gene Symbol Pdcd1
Ensembl Gene ENSMUSG00000026285
Gene Name programmed cell death 1
Synonyms Pdc1, PD-1
MMRRC Submission 068688-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.339) question?
Stock # R8876 (G1)
Quality Score 225.009
Status Validated
Chromosome 1
Chromosomal Location 93966027-93980278 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 93980155 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 21 (S21P)
Ref Sequence ENSEMBL: ENSMUSP00000027507 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000027507]
AlphaFold Q02242
PDB Structure CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF MURINE PD-1 [X-RAY DIFFRACTION]
Crystal Structure of the PD-1/PD-L1 Complex [X-RAY DIFFRACTION]
Crystal structure of the mouse PD-1 and PD-L2 complex [X-RAY DIFFRACTION]
Crystal structure of the mouse PD-1 Mutant and PD-L2 complex [X-RAY DIFFRACTION]
Crystal structure of the complex between mouse PD-1 mutant and PD-L2 IgV domain [X-RAY DIFFRACTION]
Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and PD-L2 [X-RAY DIFFRACTION]
Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and human PD-L1 [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000027507
AA Change: S21P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000027507
Gene: ENSMUSG00000026285
AA Change: S21P

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
IG 39 145 3.33e-9 SMART
transmembrane domain 170 192 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
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 cell surface membrane protein of the immunoglobulin superfamily. This protein is expressed in pro-B-cells and is thought to play a role in their differentiation. In mice, expression of this gene is induced in the thymus when anti-CD3 antibodies are injected and large numbers of thymocytes undergo apoptosis. Mice deficient for this gene bred on a BALB/c background developed dilated cardiomyopathy and died from congestive heart failure. These studies suggest that this gene product may also be important in T cell function and contribute to the prevention of autoimmune diseases. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for disruptions in this gene display abnormalities in leukopoiesis and the immune system which vary considerably depending on the genetic background. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Accs A C 2: 93,668,403 (GRCm39) L356R probably damaging Het
Acvr1 A T 2: 58,338,422 (GRCm39) D433E possibly damaging Het
Aldh3b1 A G 19: 3,971,502 (GRCm39) L122P probably damaging Het
Ap3b1 T G 13: 94,540,586 (GRCm39) N169K possibly damaging Het
Apbb2 A G 5: 66,609,000 (GRCm39) S216P probably benign Het
Arap3 T A 18: 38,130,077 (GRCm39) H28L possibly damaging Het
Arhgap44 C T 11: 64,898,896 (GRCm39) M760I possibly damaging Het
Arhgef19 G T 4: 140,975,193 (GRCm39) A304S probably benign Het
Atpaf1 T C 4: 115,645,548 (GRCm39) I139T possibly damaging Het
BC024139 G T 15: 76,010,320 (GRCm39) T62K possibly damaging Het
Bmal2 G A 6: 146,723,492 (GRCm39) G274D probably benign Het
Capn5 T C 7: 97,780,902 (GRCm39) T292A probably benign Het
Card19 T C 13: 49,358,814 (GRCm39) N53S possibly damaging Het
Cep97 A G 16: 55,742,467 (GRCm39) V232A possibly damaging Het
Cfap298 A G 16: 90,724,281 (GRCm39) I164T possibly damaging Het
Clca3a2 G T 3: 144,777,360 (GRCm39) T837K probably benign Het
Col8a2 G C 4: 126,204,647 (GRCm39) G219A probably damaging Het
Ctu2 T C 8: 123,206,951 (GRCm39) S365P Het
Dnah2 T C 11: 69,382,348 (GRCm39) D1254G probably damaging Het
Dscam A G 16: 96,420,828 (GRCm39) L1686S probably damaging Het
Fgr A G 4: 132,726,071 (GRCm39) probably benign Het
Frmd4a T A 2: 4,606,111 (GRCm39) S612T probably damaging Het
Gadd45gip1 T C 8: 85,560,748 (GRCm39) I121T probably damaging Het
Gapvd1 A G 2: 34,568,560 (GRCm39) V1353A possibly damaging Het
Gdf3 G A 6: 122,583,942 (GRCm39) P142S probably damaging Het
Gm19965 G A 1: 116,749,776 (GRCm39) G486R unknown Het
Gpatch2l T C 12: 86,308,405 (GRCm39) L307P probably damaging Het
Grm3 T C 5: 9,561,580 (GRCm39) K757E probably damaging Het
Inppl1 T A 7: 101,472,750 (GRCm39) H1218L possibly damaging Het
Jag2 T C 12: 112,873,257 (GRCm39) I1055V probably benign Het
Krtap9-5 G T 11: 99,840,340 (GRCm39) C347F unknown Het
Magi2 T A 5: 20,856,190 (GRCm39) Y1050* probably null Het
Myrf A G 19: 10,206,378 (GRCm39) probably benign Het
Ntpcr T G 8: 126,464,785 (GRCm39) probably benign Het
Or13a19 T C 7: 139,902,716 (GRCm39) Y35H probably damaging Het
Or1p1b C T 11: 74,130,846 (GRCm39) T152I probably damaging Het
Or2y1c T C 11: 49,361,386 (GRCm39) M136T probably damaging Het
Palmd T G 3: 116,720,899 (GRCm39) D145A probably damaging Het
Pkn1 T C 8: 84,398,879 (GRCm39) T696A possibly damaging Het
Pnpt1 T A 11: 29,096,769 (GRCm39) probably benign Het
Sbf2 T A 7: 110,049,146 (GRCm39) I273F probably damaging Het
Skic3 T G 13: 76,323,403 (GRCm39) D1382E probably benign Het
Slc16a4 A T 3: 107,208,101 (GRCm39) N204Y probably benign Het
Slc38a1 T C 15: 96,514,091 (GRCm39) I44V possibly damaging Het
Smpdl3a T C 10: 57,685,166 (GRCm39) V312A probably damaging Het
Ston1 A G 17: 88,942,600 (GRCm39) Y2C probably benign Het
Syde1 A T 10: 78,425,325 (GRCm39) Y229N probably damaging Het
Ttc6 T A 12: 57,784,489 (GRCm39) C1853S possibly damaging Het
Ttn A G 2: 76,609,249 (GRCm39) I17650T possibly damaging Het
Upf1 T C 8: 70,796,918 (GRCm39) E105G possibly damaging Het
Wrn A G 8: 33,814,422 (GRCm39) W341R probably benign Het
Xndc1 C T 7: 101,729,754 (GRCm39) P267L probably benign Het
Zbtb26 T C 2: 37,326,896 (GRCm39) T47A probably benign Het
Zc3h10 A T 10: 128,380,163 (GRCm39) V398E probably damaging Het
Zfp652 G T 11: 95,639,921 (GRCm39) probably benign Het
Other mutations in Pdcd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00226:Pdcd1 APN 1 93,967,860 (GRCm39) splice site probably benign
IGL01522:Pdcd1 APN 1 93,968,571 (GRCm39) missense probably benign 0.00
IGL02337:Pdcd1 APN 1 93,968,582 (GRCm39) missense probably benign 0.08
IGL02750:Pdcd1 APN 1 93,967,269 (GRCm39) splice site probably benign
R6720_pdcd1_520 UTSW 1 93,969,114 (GRCm39) missense probably benign 0.00
R0092:Pdcd1 UTSW 1 93,980,149 (GRCm39) missense possibly damaging 0.49
R0554:Pdcd1 UTSW 1 93,967,107 (GRCm39) missense probably damaging 1.00
R0931:Pdcd1 UTSW 1 93,967,238 (GRCm39) missense probably benign 0.05
R3932:Pdcd1 UTSW 1 93,968,989 (GRCm39) missense probably benign 0.01
R5222:Pdcd1 UTSW 1 93,980,175 (GRCm39) missense probably damaging 0.99
R5914:Pdcd1 UTSW 1 93,968,550 (GRCm39) missense probably benign 0.15
R6186:Pdcd1 UTSW 1 93,967,846 (GRCm39) nonsense probably null
R6720:Pdcd1 UTSW 1 93,969,114 (GRCm39) missense probably benign 0.00
R6844:Pdcd1 UTSW 1 93,967,106 (GRCm39) missense probably benign 0.36
R7966:Pdcd1 UTSW 1 93,969,186 (GRCm39) missense probably damaging 1.00
R8233:Pdcd1 UTSW 1 93,967,142 (GRCm39) missense probably damaging 1.00
R8387:Pdcd1 UTSW 1 93,969,193 (GRCm39) missense probably damaging 1.00
R8677:Pdcd1 UTSW 1 93,968,952 (GRCm39) missense probably damaging 1.00
R8724:Pdcd1 UTSW 1 93,968,956 (GRCm39) missense probably damaging 1.00
R8823:Pdcd1 UTSW 1 93,969,220 (GRCm39) missense probably benign 0.00
R8875:Pdcd1 UTSW 1 93,967,092 (GRCm39) missense probably benign 0.06
R9041:Pdcd1 UTSW 1 93,969,091 (GRCm39) missense probably benign 0.33
R9081:Pdcd1 UTSW 1 93,968,880 (GRCm39) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- TGTCTGTCTAAAAGCAAGGAGG -3'
(R):5'- AAGAACAGGTCTCCTCCCTC -3'

Sequencing Primer
(F):5'- GGGGGCATTTCACCTGTAAAACC -3'
(R):5'- TCCCTCCAACATGACCTGGG -3'
Posted On 2021-07-15