Mutagenetix > Incidental Mutation

Incidental Mutation 'R8387:Pdcd1'

647183

Institutional Source

Beutler Lab

Gene Symbol

Pdcd1

Ensembl Gene

ENSMUSG00000026285

Gene Name

programmed cell death 1

Synonyms

Pdc1, PD-1

MMRRC Submission

067876-MU

Accession Numbers

Essential gene?

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

Stock #

R8387 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

93966027-93980278 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 93969193 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Phenylalanine at position 42 (L42F)

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 damaging
Transcript: ENSMUST00000027507
AA Change: L42F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000027507
Gene: ENSMUSG00000026285
AA Change: L42F

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: 99.7%
20x: 99.0%

Validation Efficiency

98% (46/47)

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: 46 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb1b	G	A	5: 8,874,698 (GRCm39)	D453N	probably damaging	Het
Arl14ep	T	C	2: 106,799,562 (GRCm39)	D93G	probably damaging	Het
Bcl7b	T	C	5: 135,197,413 (GRCm39)	I18T	probably damaging	Het
Cdh1	A	G	8: 107,390,501 (GRCm39)	I614V	probably benign	Het
Cpa3	T	C	3: 20,281,400 (GRCm39)	I169V	probably benign	Het
Cpeb4	T	C	11: 31,858,877 (GRCm39)		probably null	Het
Csmd1	G	A	8: 16,050,484 (GRCm39)	H2251Y	possibly damaging	Het
Dab2ip	T	A	2: 35,609,870 (GRCm39)	I695K	probably damaging	Het
Dhtkd1	C	A	2: 5,934,479 (GRCm39)	L230F	possibly damaging	Het
Emc1	T	C	4: 139,088,600 (GRCm39)	S353P	probably benign	Het
Erc2	T	A	14: 27,375,253 (GRCm39)	L157Q	possibly damaging	Het
Flvcr1	A	G	1: 190,743,731 (GRCm39)		probably null	Het
Fryl	A	C	5: 73,293,663 (GRCm39)		probably null	Het
Gnl2	T	C	4: 124,949,127 (GRCm39)	*729Q	probably null	Het
Gpr63	G	A	4: 25,008,301 (GRCm39)	V342M	possibly damaging	Het
Guf1	C	T	5: 69,723,810 (GRCm39)	P463L	probably damaging	Het
Hmmr	G	A	11: 40,612,499 (GRCm39)	S206F	probably damaging	Het
Ifngr2	T	C	16: 91,358,535 (GRCm39)	L245P	probably damaging	Het
Igsf10	A	G	3: 59,236,564 (GRCm39)	F1206L	probably damaging	Het
Ktn1	T	A	14: 47,944,744 (GRCm39)		probably null	Het
Lekr1	A	G	3: 65,591,520 (GRCm39)	K86E	possibly damaging	Het
Lrrc3	C	T	10: 77,737,346 (GRCm39)	G30D	possibly damaging	Het
Mapk8ip2	T	C	15: 89,344,897 (GRCm39)	F765L	probably damaging	Het
Myo6	A	G	9: 80,183,632 (GRCm39)	T676A	unknown	Het
Nr4a1	T	C	15: 101,171,053 (GRCm39)	S510P	probably damaging	Het
Or2o1	T	C	11: 49,051,497 (GRCm39)	S219P	probably damaging	Het
Or4c113	T	C	2: 88,885,646 (GRCm39)	I41M	probably benign	Het
Or4c11c	G	A	2: 88,661,633 (GRCm39)	M57I	possibly damaging	Het
Or51e1	C	T	7: 102,359,402 (GRCm39)	T312I	probably benign	Het
Or5a1	A	G	19: 12,097,785 (GRCm39)	L97P	probably damaging	Het
Pdzd7	T	C	19: 45,018,490 (GRCm39)	D621G	probably damaging	Het
Peg10	GC	GCTCC	6: 4,756,452 (GRCm39)		probably benign	Het
Pias4	G	A	10: 80,990,342 (GRCm39)	R398C	probably benign	Het
Plekha6	A	T	1: 133,219,893 (GRCm39)		probably null	Het
Prkag3	A	G	1: 74,784,854 (GRCm39)		probably null	Het
Ptpn7	A	G	1: 135,061,606 (GRCm39)	T23A	probably benign	Het
Ptprd	T	C	4: 75,873,526 (GRCm39)	D1069G	probably damaging	Het
Ptprr	A	G	10: 116,087,030 (GRCm39)	Y503C	probably damaging	Het
Slc26a8	T	C	17: 28,866,899 (GRCm39)	D610G	probably benign	Het
Smyd4	A	G	11: 75,292,984 (GRCm39)	N638S	probably benign	Het
Tenm3	A	G	8: 48,740,883 (GRCm39)	F1200S	probably damaging	Het
Tox3	A	G	8: 90,984,595 (GRCm39)	S195P	probably benign	Het
Trim44	T	C	2: 102,230,518 (GRCm39)	E171G	probably damaging	Het
Vars1	T	A	17: 35,229,490 (GRCm39)	M369K	probably damaging	Het
Vmn2r77	C	A	7: 86,450,947 (GRCm39)	Q278K	probably benign	Het
Zfp345	T	C	2: 150,314,740 (GRCm39)	T266A	probably damaging	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
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'- TAGATGCCACTGTCATTGCG -3'
(R):5'- GCTTACGATATTCTGCCCTGG -3'

Sequencing Primer
(F):5'- CAAGGATGTTCATGTGGAAGTCATGC -3'
(R):5'- ACGATATTCTGCCCTGGAATGG -3'

Posted On

2020-09-02