Mutagenetix > Incidental Mutation

Incidental Mutation 'R3932:Pdcd1'

308486

Institutional Source

Beutler Lab

Gene Symbol

Pdcd1

Ensembl Gene

ENSMUSG00000026285

Gene Name

programmed cell death 1

Synonyms

Pdc1, PD-1

MMRRC Submission

040919-MU

Accession Numbers

Essential gene?

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

Stock #

R3932 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

93966027-93980278 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 93968989 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 110 (I110V)

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: I110V

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000027507
Gene: ENSMUSG00000026285
AA Change: I110V

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

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.4%
3x: 98.7%
10x: 97.1%
20x: 94.1%

Validation Efficiency

100% (52/52)

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: 48 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ap3b2	C	T	7: 81,123,598 (GRCm39)		probably benign	Het
Arl1	C	T	10: 88,569,398 (GRCm39)		probably benign	Het
Arsi	G	A	18: 61,049,723 (GRCm39)	G202E	probably benign	Het
Atp10a	T	C	7: 58,476,852 (GRCm39)	M1189T	possibly damaging	Het
Bcl2l14	A	G	6: 134,400,771 (GRCm39)	D64G	probably damaging	Het
Cdc34b	G	A	11: 94,633,441 (GRCm39)	V214M	probably benign	Het
Cfap54	T	C	10: 92,665,619 (GRCm39)	T2985A	probably benign	Het
Clcc1	T	C	3: 108,580,682 (GRCm39)	M332T	probably damaging	Het
Coch	T	C	12: 51,650,121 (GRCm39)	I370T	probably damaging	Het
Ctdnep1	A	G	11: 69,880,400 (GRCm39)		probably benign	Het
Edar	C	T	10: 58,446,164 (GRCm39)	C221Y	probably damaging	Het
Fam135b	T	A	15: 71,322,280 (GRCm39)	Q1295L	probably benign	Het
Fam184a	C	T	10: 53,575,397 (GRCm39)	A71T	probably damaging	Het
Fbxw10	A	G	11: 62,759,983 (GRCm39)		probably benign	Het
Frmd4a	T	C	2: 4,542,071 (GRCm39)	W247R	probably damaging	Het
Gcn1	A	G	5: 115,725,893 (GRCm39)	H553R	probably benign	Het
Grin3a	C	T	4: 49,672,472 (GRCm39)		probably null	Het
H2-Q6	C	T	17: 35,644,542 (GRCm39)		probably benign	Het
Hivep2	C	A	10: 14,004,713 (GRCm39)	T437K	probably benign	Het
Hspg2	T	C	4: 137,242,879 (GRCm39)	V670A	probably damaging	Het
Med10	A	G	13: 69,958,101 (GRCm39)	N18D	probably damaging	Het
Mgat4b	T	A	11: 50,124,165 (GRCm39)	H368Q	possibly damaging	Het
Morn5	C	A	2: 35,943,035 (GRCm39)	T45N	probably damaging	Het
Mrc2	G	A	11: 105,239,257 (GRCm39)		probably null	Het
Msl3	C	T	X: 167,454,813 (GRCm39)	A87T	probably damaging	Het
Myrf	T	C	19: 10,195,515 (GRCm39)	T432A	probably damaging	Het
Nalf2	G	A	X: 98,865,470 (GRCm39)	V266M	possibly damaging	Het
Nav3	T	A	10: 109,529,896 (GRCm39)	E2148D	probably damaging	Het
Nfe2l3	A	G	6: 51,433,595 (GRCm39)	T236A	possibly damaging	Het
Odc1	T	A	12: 17,598,801 (GRCm39)	F227Y	probably benign	Het
Opa1	A	T	16: 29,429,698 (GRCm39)	E401D	probably damaging	Het
Or5b21	T	C	19: 12,839,994 (GRCm39)	M285T	possibly damaging	Het
Pde5a	G	A	3: 122,554,545 (GRCm39)	E212K	probably damaging	Het
Plin4	A	G	17: 56,413,704 (GRCm39)	I307T	probably benign	Het
Rag1	T	C	2: 101,473,384 (GRCm39)	Y586C	probably damaging	Het
Rgs7bp	T	C	13: 105,189,506 (GRCm39)	M98V	probably benign	Het
Rgs9	A	G	11: 109,166,639 (GRCm39)		probably benign	Het
Rin3	A	G	12: 102,356,342 (GRCm39)	D961G	probably damaging	Het
Rubcn	A	G	16: 32,649,629 (GRCm39)		probably null	Het
Slc13a2	T	A	11: 78,289,226 (GRCm39)	Y495F	probably damaging	Het
Tfec	T	A	6: 16,845,458 (GRCm39)	D67V	probably damaging	Het
Tmem94	T	C	11: 115,680,080 (GRCm39)	M30T	probably benign	Het
Tsbp1	A	G	17: 34,662,417 (GRCm39)	T86A	possibly damaging	Het
Tubgcp6	A	G	15: 88,988,617 (GRCm39)		probably benign	Het
Vmn2r10	C	A	5: 109,150,088 (GRCm39)	A319S	possibly damaging	Het
Vmn2r85	T	C	10: 130,254,336 (GRCm39)	M783V	probably damaging	Het
Zfp422	T	C	6: 116,603,420 (GRCm39)	K193R	probably benign	Het
Zfp94	T	G	7: 24,003,112 (GRCm39)	D110A	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
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'- CAGTGTCGTCAAGGCTCTAG -3'
(R):5'- TGTCAGAGGGAGCAAATGCC -3'

Sequencing Primer
(F):5'- CAGAGCCATGGCAGAGAGC -3'
(R):5'- GAGGGAGCAAATGCCACCTTC -3'

Posted On

2015-04-17