Incidental Mutation 'R0931:Pdcd1'
ID 80851
Institutional Source Beutler Lab
Gene Symbol Pdcd1
Ensembl Gene ENSMUSG00000026285
Gene Name programmed cell death 1
Synonyms Pdc1, PD-1
MMRRC Submission 039075-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.339) question?
Stock # R0931 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 93966027-93980278 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 93967238 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 220 (V220A)
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: V220A

PolyPhen 2 Score 0.046 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000027507
Gene: ENSMUSG00000026285
AA Change: V220A

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
IG 39 145 3.33e-9 SMART
transmembrane domain 170 192 N/A INTRINSIC
Meta Mutation Damage Score 0.1065 question?
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.9%
  • 10x: 97.7%
  • 20x: 96.0%
Validation Efficiency 100% (42/42)
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: 40 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamtsl1 G A 4: 86,168,084 (GRCm39) A476T probably benign Het
Ajm1 T C 2: 25,468,501 (GRCm39) E470G possibly damaging Het
Aknad1 T C 3: 108,659,339 (GRCm39) S118P probably damaging Het
Arhgap20 A G 9: 51,728,041 (GRCm39) T85A probably benign Het
Astn2 A G 4: 65,566,530 (GRCm39) L824P probably damaging Het
Ccr1 C A 9: 123,763,827 (GRCm39) K234N probably damaging Het
Cfap46 T C 7: 139,235,757 (GRCm39) R203G probably damaging Het
Col8a1 A G 16: 57,448,931 (GRCm39) I193T unknown Het
Cpa2 T C 6: 30,552,070 (GRCm39) probably benign Het
Crabp1 T C 9: 54,675,717 (GRCm39) L100P possibly damaging Het
Cspp1 A T 1: 10,174,511 (GRCm39) R655W probably damaging Het
Ddx1 A T 12: 13,287,818 (GRCm39) probably benign Het
Dnah7b T G 1: 46,138,772 (GRCm39) probably benign Het
Dzip3 A G 16: 48,771,921 (GRCm39) S583P probably damaging Het
Exosc1 A G 19: 41,921,676 (GRCm39) probably benign Het
Fhip1a A G 3: 85,580,550 (GRCm39) S552P probably benign Het
Gas7 A T 11: 67,543,751 (GRCm39) probably benign Het
Gss A T 2: 155,409,609 (GRCm39) probably benign Het
Hdhd3 G A 4: 62,417,757 (GRCm39) R140* probably null Het
Irx2 T A 13: 72,779,675 (GRCm39) S320T possibly damaging Het
Kcnf1 T C 12: 17,225,142 (GRCm39) S360G possibly damaging Het
Klk1b4 T C 7: 43,860,480 (GRCm39) L166P probably damaging Het
Klri1 A T 6: 129,674,381 (GRCm39) probably benign Het
Mettl27 T C 5: 134,963,285 (GRCm39) probably benign Het
Myrfl T A 10: 116,675,354 (GRCm39) H193L probably benign Het
Nbas C T 12: 13,381,115 (GRCm39) probably benign Het
Or10ac1 C A 6: 42,515,020 (GRCm39) R312L probably benign Het
Or52b2 A T 7: 104,986,736 (GRCm39) Y62* probably null Het
Papolg A G 11: 23,832,257 (GRCm39) I177T probably damaging Het
Psmc1 T C 12: 100,085,341 (GRCm39) L234P probably damaging Het
Rasa2 A T 9: 96,434,457 (GRCm39) M610K possibly damaging Het
Ryr3 A G 2: 112,484,047 (GRCm39) F3930S probably damaging Het
Sacs G A 14: 61,440,944 (GRCm39) V997I probably benign Het
Setdb2 A G 14: 59,660,945 (GRCm39) probably benign Het
Ssu2 C A 6: 112,361,359 (GRCm39) L32F probably damaging Het
Taar1 A T 10: 23,797,181 (GRCm39) N293I probably damaging Het
Ttn A G 2: 76,611,846 (GRCm39) probably benign Het
Vmn2r49 T C 7: 9,720,325 (GRCm39) M389V possibly damaging Het
Wdr7 T C 18: 63,998,371 (GRCm39) V1106A probably benign Het
Zfp324 A G 7: 12,700,185 (GRCm39) I15V 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
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
R8876:Pdcd1 UTSW 1 93,980,155 (GRCm39) missense probably benign
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'- CCCAGCTTGTGGTAAACCTGAAGTG -3'
(R):5'- GAACCCCAAATCCAGTGTCAGTCTG -3'

Sequencing Primer
(F):5'- CATGCTAATGGCTGAAGAATCTG -3'
(R):5'- TCCAGTGTCAGTCTGGAAAC -3'
Posted On 2013-11-07