Mutagenetix > Incidental Mutation

Incidental Mutation 'R8875:Pdcd1'

676503

Institutional Source

Beutler Lab

Gene Symbol

Pdcd1

Ensembl Gene

ENSMUSG00000026285

Gene Name

programmed cell death 1

Synonyms

Pdc1, PD-1

MMRRC Submission

068687-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.339) question?

Stock #

R8875 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

93966027-93980278 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 93967092 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Asparagine at position 269 (D269N)

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: D269N

PolyPhen 2 Score 0.057 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000027507
Gene: ENSMUSG00000026285
AA Change: D269N

Domain	Start	End	E-Value	Type
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: 98.8%

Validation Efficiency

100% (49/49)

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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610010K14Rik	A	G	11: 70,126,380 (GRCm39)	V140A		Het
Ablim1	G	T	19: 57,119,386 (GRCm39)	H233N	probably benign	Het
Adra1a	A	T	14: 66,875,214 (GRCm39)	Y63F	possibly damaging	Het
Ank3	A	G	10: 69,660,233 (GRCm39)	D245G	unknown	Het
Ap4e1	T	C	2: 126,877,100 (GRCm39)	I279T	probably damaging	Het
Bap1	T	G	14: 30,975,522 (GRCm39)	F122C	probably damaging	Het
Cdc5l	T	C	17: 45,703,915 (GRCm39)		probably benign	Het
Chd2	A	T	7: 73,151,783 (GRCm39)	I309N	probably damaging	Het
Cnpy3	T	C	17: 47,048,185 (GRCm39)	I177V	probably damaging	Het
Cp	A	G	3: 20,027,994 (GRCm39)	K467E	possibly damaging	Het
D630039A03Rik	T	G	4: 57,910,320 (GRCm39)	N164T	probably benign	Het
Dnah7a	C	A	1: 53,682,682 (GRCm39)	A263S	probably benign	Het
Eif2s1	G	A	12: 78,913,461 (GRCm39)	R54Q	probably damaging	Het
Fasn	A	T	11: 120,703,224 (GRCm39)	D1600E	possibly damaging	Het
Fat1	T	A	8: 45,493,600 (GRCm39)	F3915L	probably damaging	Het
Fiz1	A	T	7: 5,012,093 (GRCm39)	S142T	probably benign	Het
Fnip1	A	G	11: 54,406,380 (GRCm39)	Y1159C	probably damaging	Het
Fsip2	T	A	2: 82,820,782 (GRCm39)	V5505D	possibly damaging	Het
Gabrg3	A	G	7: 56,379,514 (GRCm39)	M296T	probably damaging	Het
Gm11562	A	T	11: 99,511,177 (GRCm39)	S8T	unknown	Het
Hoxd11	A	G	2: 74,513,365 (GRCm39)	D210G	probably benign	Het
Hsd17b2	T	C	8: 118,469,101 (GRCm39)	V171A	possibly damaging	Het
Ifi206	T	C	1: 173,301,353 (GRCm39)	Y775C	unknown	Het
Nherf2	T	A	17: 24,866,703 (GRCm39)		probably null	Het
Nr2f1	A	C	13: 78,337,970 (GRCm39)	I382S	probably damaging	Het
Nrp1	T	A	8: 129,207,472 (GRCm39)		probably null	Het
Or51l4	G	A	7: 103,404,462 (GRCm39)	S110F	probably damaging	Het
Or52h7	A	G	7: 104,213,670 (GRCm39)	T81A	probably benign	Het
Pira12	A	G	7: 3,897,256 (GRCm39)	S527P	probably damaging	Het
Plbd2	A	G	5: 120,637,121 (GRCm39)	Y114H	probably damaging	Het
Plch1	A	G	3: 63,618,391 (GRCm39)	C715R	probably damaging	Het
Plin4	G	A	17: 56,411,010 (GRCm39)	A1007V	probably benign	Het
Ptprs	G	T	17: 56,742,946 (GRCm39)	P399T	probably damaging	Het
Pum1	T	A	4: 130,507,186 (GRCm39)	I1181N	possibly damaging	Het
Qrich1	A	G	9: 108,436,502 (GRCm39)		probably benign	Het
Rbm12	T	C	2: 155,938,841 (GRCm39)	E477G	probably damaging	Het
Rpl7	T	C	1: 16,173,753 (GRCm39)	K57R	probably benign	Het
Spata31h1	G	A	10: 82,123,476 (GRCm39)	A3178V	probably benign	Het
Stab2	C	T	10: 86,832,728 (GRCm39)	C99Y	probably damaging	Het
Tas1r1	T	A	4: 152,113,047 (GRCm39)	T669S	probably benign	Het
Tle5	A	T	10: 81,400,534 (GRCm39)	I73F	probably benign	Het
Tm2d2	T	C	8: 25,507,443 (GRCm39)	L20P	possibly damaging	Het
Tmem158	G	T	9: 123,089,132 (GRCm39)	A160E	possibly damaging	Het
Tpst2	T	A	5: 112,457,714 (GRCm39)	Y347*	probably null	Het
Trpm3	T	C	19: 22,887,493 (GRCm39)	I876T	probably damaging	Het
Ttc6	T	C	12: 57,751,199 (GRCm39)	F1364L	probably damaging	Het
Ttc6	T	A	12: 57,776,194 (GRCm39)	S1713T	possibly damaging	Het
Vmn2r85	A	G	10: 130,254,171 (GRCm39)	S838P	probably damaging	Het
Zc2hc1c	T	C	12: 85,336,549 (GRCm39)	S69P	possibly damaging	Het
Zfp982	C	A	4: 147,595,320 (GRCm39)	N47K	probably benign	Het

Other mutations in Pdcd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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'- TGTCACTCCAGCTAGCTCAGAC -3'
(R):5'- TATGGGATGCACACACCACC -3'

Sequencing Primer
(F):5'- AGCTAGCTCAGACCCTGG -3'
(R):5'- TCCCCTGCCCCTTGAAGAAG -3'

Posted On

2021-07-15