Mutagenetix > Incidental Mutation

Incidental Mutation 'R8724:Pdcd1'

662257

Institutional Source

Beutler Lab

Gene Symbol

Pdcd1

Ensembl Gene

ENSMUSG00000026285

Gene Name

programmed cell death 1

Synonyms

Pdc1, PD-1

MMRRC Submission

068573-MU

Accession Numbers

Essential gene?

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

Stock #

R8724 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

93966027-93980278 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 93968956 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 121 (Y121H)

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: Y121H

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

SMART Domains

Protein: ENSMUSP00000027507
Gene: ENSMUSG00000026285
AA Change: Y121H

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: 100.0%
10x: 99.8%
20x: 99.5%

Validation Efficiency

99% (69/70)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamtsl4	C	T	3: 95,584,426 (GRCm39)	R990Q	possibly damaging	Het
Ampd2	C	A	3: 107,987,432 (GRCm39)	V134L	probably benign	Het
Ank2	A	T	3: 126,737,405 (GRCm39)	D2826E	unknown	Het
Asb3	A	T	11: 31,051,120 (GRCm39)	I486F	probably damaging	Het
Atg4b	A	T	1: 93,696,023 (GRCm39)	Y54F	probably damaging	Het
Atp1a2	T	A	1: 172,106,945 (GRCm39)	I792F	probably benign	Het
Bltp1	G	A	3: 36,945,042 (GRCm39)	V334I	probably damaging	Het
Ccser1	A	C	6: 61,288,199 (GRCm39)	S121R	probably damaging	Het
Cdc40	C	T	10: 40,717,480 (GRCm39)	D404N	probably damaging	Het
Cep120	A	T	18: 53,856,199 (GRCm39)	V406E	possibly damaging	Het
Ces2g	C	A	8: 105,692,955 (GRCm39)	A331D	probably benign	Het
Csnk1g2	G	A	10: 80,474,760 (GRCm39)	R299H	probably damaging	Het
Dlat	G	T	9: 50,560,967 (GRCm39)	A360E	probably damaging	Het
Dock10	T	G	1: 80,570,344 (GRCm39)	I371L	probably benign	Het
Dpp9	T	A	17: 56,512,867 (GRCm39)	T114S	probably benign	Het
Dusp13b	T	C	14: 21,796,475 (GRCm39)	R160G	probably benign	Het
Dync2i2	T	C	2: 29,923,961 (GRCm39)	D188G	probably benign	Het
Edem3	A	G	1: 151,651,624 (GRCm39)	K122R	possibly damaging	Het
Ehbp1l1	A	G	19: 5,765,886 (GRCm39)	S1486P	possibly damaging	Het
Elf3	A	G	1: 135,182,098 (GRCm39)	I361T	probably damaging	Het
Epha3	C	T	16: 63,403,818 (GRCm39)	C761Y	probably damaging	Het
Ephb2	A	G	4: 136,498,368 (GRCm39)	I237T	probably damaging	Het
Eya1	A	T	1: 14,279,206 (GRCm39)	D346E	probably benign	Het
Fat2	T	C	11: 55,173,786 (GRCm39)	Y2309C	probably damaging	Het
Fbn1	T	C	2: 125,202,066 (GRCm39)	D1269G	probably damaging	Het
Fmn2	CCCTCCTCTCCCTGGAATGGGAATACCTCCCCCACCTCCTCTCCCTGGAATGGGAATACCTCCCCCACCTCCTCTCCCTGGAATGGGAATATCTCCCCTACCTCCTCTCCCTGGAATGGGAATACCTCC	CCCTCCTCTCCCTGGAATGGGAATACCTCCCCCACCTCCTCTCCCTGGAATGGGAATATCTCCCCTACCTCCTCTCCCTGGAATGGGAATACCTCC	1: 174,436,769 (GRCm39)		probably benign	Het
Fnbp4	T	C	2: 90,577,097 (GRCm39)	V143A	probably damaging	Het
Foxo6	A	G	4: 120,144,109 (GRCm39)	I114T	probably damaging	Het
Gm6741	T	C	17: 91,544,564 (GRCm39)	I109T	probably benign	Het
Gtf2h5	C	CA	17: 6,134,833 (GRCm39)		probably null	Het
Hsf1	C	T	15: 76,381,999 (GRCm39)	S199L	probably damaging	Het
Htr3a	T	C	9: 48,815,981 (GRCm39)	N152S	probably damaging	Het
Ikzf2	T	A	1: 69,617,100 (GRCm39)	E82D	probably benign	Het
Kank2	T	G	9: 21,705,917 (GRCm39)	K367T	possibly damaging	Het
Kif20b	T	A	19: 34,916,146 (GRCm39)		probably benign	Het
Ktn1	G	A	14: 47,931,335 (GRCm39)	V643I	probably benign	Het
Lipk	G	A	19: 33,996,120 (GRCm39)	V11M	probably benign	Het
Med4	T	A	14: 73,751,249 (GRCm39)	L66*	probably null	Het
Mtus1	T	C	8: 41,451,500 (GRCm39)	K379E	probably damaging	Het
Nat1	T	A	8: 67,944,443 (GRCm39)	I276N	probably damaging	Het
Nav2	G	A	7: 49,141,184 (GRCm39)	V910M	possibly damaging	Het
Or10ag53	T	A	2: 87,082,704 (GRCm39)	I141N	probably damaging	Het
Or4a80	A	T	2: 89,582,373 (GRCm39)	D266E	probably damaging	Het
Pcdh9	A	G	14: 94,124,583 (GRCm39)	V529A	probably benign	Het
Pcdhga7	C	T	18: 37,848,146 (GRCm39)	T51I	probably benign	Het
Pdia6	A	G	12: 17,333,982 (GRCm39)	D438G	unknown	Het
Pgm1	A	G	4: 99,786,964 (GRCm39)	T68A	probably benign	Het
Pik3c2g	G	A	6: 139,913,619 (GRCm39)	V1006I	unknown	Het
Plk4	C	T	3: 40,768,022 (GRCm39)	T855I	probably damaging	Het
Pnldc1	T	A	17: 13,111,703 (GRCm39)	N335Y	probably damaging	Het
Prkcq	C	T	2: 11,304,784 (GRCm39)	P658S	probably benign	Het
Rbl2	T	C	8: 91,841,837 (GRCm39)	I1011T	possibly damaging	Het
Rev1	A	C	1: 38,127,150 (GRCm39)	V370G	probably damaging	Het
Rtn4	A	G	11: 29,643,316 (GRCm39)	E43G	unknown	Het
Rtp2	C	T	16: 23,746,064 (GRCm39)	G189D	possibly damaging	Het
Ryr1	G	A	7: 28,816,802 (GRCm39)	A78V	probably benign	Het
Sel1l3	A	C	5: 53,293,165 (GRCm39)	Y850*	probably null	Het
Senp3	T	C	11: 69,564,419 (GRCm39)	Q547R	probably damaging	Het
Siglecf	T	C	7: 43,004,976 (GRCm39)	L402P	probably damaging	Het
Slc24a1	T	C	9: 64,855,453 (GRCm39)	I485V	probably benign	Het
Slc45a2	T	A	15: 11,012,610 (GRCm39)	H204Q	probably benign	Het
Slc9a4	T	G	1: 40,623,301 (GRCm39)	I180S	probably damaging	Het
Smyd1	T	A	6: 71,193,767 (GRCm39)	Y420F	probably damaging	Het
Sorcs1	A	G	19: 50,139,658 (GRCm39)	I1168T	probably benign	Het
Syne1	T	C	10: 5,033,861 (GRCm39)	E7737G	possibly damaging	Het
Trappc4	T	A	9: 44,316,560 (GRCm39)	H145L	probably benign	Het
Wdr75	T	A	1: 45,856,560 (GRCm39)	W528R	probably damaging	Het
Zc3h13	T	C	14: 75,569,512 (GRCm39)	V1453A	probably benign	Het
Zfp143	T	C	7: 109,681,110 (GRCm39)	I318T	probably benign	Het
Zfp846	G	A	9: 20,505,352 (GRCm39)	R404H	possibly 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
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
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'- AGCCCTTCCATCCCTTAAAGG -3'
(R):5'- TTATGCTGAACTGGAACCGC -3'

Sequencing Primer
(F):5'- AATGGGCATCTGAGGATTTCCAC -3'
(R):5'- TGAACTGGAACCGCCTGAGTC -3'

Posted On

2021-03-08