Mutagenetix > Incidental Mutation

Incidental Mutation 'R5963:Pdcd2'

471904

Institutional Source

Beutler Lab

Gene Symbol

Pdcd2

Ensembl Gene

ENSMUSG00000014771

Gene Name

programmed cell death 2

Synonyms

RP-8

MMRRC Submission

044148-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5963 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

15739472-15747560 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 15746656 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Glutamic Acid at position 168 (K168E)

Ref Sequence

ENSEMBL: ENSMUSP00000118625 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000054450] [ENSMUST00000154293] [ENSMUST00000162505]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000054450
AA Change: K168E

PolyPhen 2 Score 0.908 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000052523
Gene: ENSMUSG00000014771
AA Change: K168E

Domain	Start	End	E-Value	Type
low complexity region	35	50	N/A	INTRINSIC
Pfam:zf-MYND	134	171	2.2e-10	PFAM
Pfam:PDCD2_C	188	338	6e-46	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125709

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137233

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139610

Predicted Effect

possibly damaging
Transcript: ENSMUST00000154293
AA Change: K168E

PolyPhen 2 Score 0.908 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000118625
Gene: ENSMUSG00000014771
AA Change: K168E

Domain	Start	End	E-Value	Type
low complexity region	35	50	N/A	INTRINSIC
Pfam:zf-MYND	134	171	4.3e-11	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162505

SMART Domains

Protein: ENSMUSP00000124317
Gene: ENSMUSG00000014767

Domain	Start	End	E-Value	Type
low complexity region	55	97	N/A	INTRINSIC
low complexity region	103	115	N/A	INTRINSIC
low complexity region	117	133	N/A	INTRINSIC
Pfam:TBP	139	221	1.1e-34	PFAM
Pfam:TBP	229	312	8.5e-34	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232149

Meta Mutation Damage Score

0.2507

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.7%
20x: 92.5%

Validation Efficiency

99% (68/69)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a nuclear protein expressed in a variety of tissues. Expression of this gene has been shown to be repressed by B-cell CLL/lymphoma 6 (BCL6), a transcriptional repressor required for lymph node germinal center development, suggesting that BCL6 regulates apoptosis by its effects on this protein. Alternative splicing results in multiple transcript variants and pseudogenes have been identified on chromosomes 9 and 12. [provided by RefSeq, Dec 2010]
PHENOTYPE: Mice homozygous for a null mutation display embryonic lethality before implantation with most arresting before the blastocyst satge. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Alg8	A	G	7: 97,029,037 (GRCm39)	K131E	probably benign	Het
Ank3	T	A	10: 69,823,056 (GRCm39)	L575*	probably null	Het
Aqr	T	C	2: 113,957,442 (GRCm39)	T819A	probably damaging	Het
Bbs2	A	T	8: 94,807,659 (GRCm39)	S407T	probably benign	Het
Bmper	T	A	9: 23,286,889 (GRCm39)	C272S	probably benign	Het
Btbd9	C	T	17: 30,553,192 (GRCm39)		probably null	Het
C5ar1	A	G	7: 15,982,747 (GRCm39)	V91A	possibly damaging	Het
Ccdc138	A	G	10: 58,411,579 (GRCm39)	H649R	possibly damaging	Het
Cfap43	A	T	19: 47,734,013 (GRCm39)	V1451E	probably benign	Het
Cfap46	T	A	7: 139,231,511 (GRCm39)	M901L	probably damaging	Het
Cherp	G	T	8: 73,215,379 (GRCm39)		probably benign	Het
D430041D05Rik	C	T	2: 104,078,630 (GRCm39)	V1229I	possibly damaging	Het
Fat4	A	C	3: 39,064,696 (GRCm39)	D4884A	probably damaging	Het
Fcrl5	T	C	3: 87,351,480 (GRCm39)	F243L	probably damaging	Het
Garem1	T	A	18: 21,262,487 (GRCm39)	I776F	probably benign	Het
Gpr87	T	A	3: 59,086,690 (GRCm39)	R272*	probably null	Het
Gsdmc	A	T	15: 63,651,965 (GRCm39)		probably null	Het
Hydin	T	A	8: 111,220,926 (GRCm39)	F1441I	possibly damaging	Het
Ints11	T	A	4: 155,957,369 (GRCm39)	C63*	probably null	Het
Kdm4b	A	T	17: 56,706,732 (GRCm39)	T908S	probably damaging	Het
Lipn	A	G	19: 34,058,700 (GRCm39)	D304G	probably damaging	Het
Man2a1	T	G	17: 64,982,117 (GRCm39)	N544K	probably benign	Het
Mapkapk5	G	T	5: 121,676,544 (GRCm39)	H66N	probably damaging	Het
Mog	G	A	17: 37,323,240 (GRCm39)	R233*	probably null	Het
Mrps24	A	T	11: 5,657,481 (GRCm39)		probably benign	Het
Nom1	T	C	5: 29,642,768 (GRCm39)	L423P	probably damaging	Het
Or51b6	T	A	7: 103,556,168 (GRCm39)	V174E	probably benign	Het
Pcdha1	T	A	18: 37,064,224 (GRCm39)	V296E	probably damaging	Het
Pla2g12b	T	A	10: 59,239,780 (GRCm39)	V63D	probably damaging	Het
Pnn	C	T	12: 59,114,617 (GRCm39)	R56*	probably null	Het
Primpol	T	A	8: 47,046,615 (GRCm39)	E227V	possibly damaging	Het
Rad54l	A	T	4: 115,967,584 (GRCm39)	W233R	probably damaging	Het
Rims2	A	T	15: 39,300,578 (GRCm39)	D103V	probably damaging	Het
Rttn	T	C	18: 89,091,819 (GRCm39)	S1511P	probably benign	Het
Septin5	T	C	16: 18,442,962 (GRCm39)		probably null	Het
Simc1	T	A	13: 54,673,632 (GRCm39)	I660K	possibly damaging	Het
Slc15a5	A	G	6: 138,056,691 (GRCm39)	L75P	probably damaging	Het
Slc9a2	A	G	1: 40,721,196 (GRCm39)	S55G	possibly damaging	Het
Slit3	C	T	11: 35,591,063 (GRCm39)	R1292C	probably damaging	Het
Slitrk3	A	G	3: 72,958,046 (GRCm39)	V242A	probably benign	Het
St14	A	T	9: 31,017,853 (GRCm39)		probably benign	Het
Tnnt2	T	C	1: 135,771,600 (GRCm39)		probably benign	Het
Traf5	G	A	1: 191,731,977 (GRCm39)	T288I	probably benign	Het
Trerf1	C	T	17: 47,625,263 (GRCm39)		noncoding transcript	Het
Vegfc	A	G	8: 54,634,319 (GRCm39)	N333D	probably benign	Het
Vmn1r65	T	A	7: 6,011,608 (GRCm39)	I209F	probably damaging	Het
Vps51	A	G	19: 6,118,320 (GRCm39)	L725P	probably damaging	Het
Vps8	T	C	16: 21,288,871 (GRCm39)	I408T	possibly damaging	Het
Wdr72	T	C	9: 74,052,310 (GRCm39)	Y114H	probably damaging	Het
Ybx2	A	G	11: 69,831,918 (GRCm39)	E164G	probably damaging	Het
Zcchc14	A	T	8: 122,355,362 (GRCm39)		probably benign	Het
Zfp383	A	G	7: 29,615,103 (GRCm39)	T453A	possibly damaging	Het
Zfp84	G	T	7: 29,476,378 (GRCm39)	G357C	probably damaging	Het
Zmynd11	G	T	13: 9,745,931 (GRCm39)		probably benign	Het

Other mutations in Pdcd2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02632:Pdcd2	APN	17	15,742,054 (GRCm39)	missense	probably damaging	0.99
R0433:Pdcd2	UTSW	17	15,746,646 (GRCm39)	missense	probably benign	0.37
R1368:Pdcd2	UTSW	17	15,746,846 (GRCm39)	missense	probably damaging	1.00
R5083:Pdcd2	UTSW	17	15,743,084 (GRCm39)	missense	possibly damaging	0.50
R5508:Pdcd2	UTSW	17	15,742,001 (GRCm39)	missense	probably damaging	1.00
R5963:Pdcd2	UTSW	17	15,746,657 (GRCm39)	missense	probably damaging	1.00
R6944:Pdcd2	UTSW	17	15,745,632 (GRCm39)	missense	possibly damaging	0.82
R6993:Pdcd2	UTSW	17	15,747,343 (GRCm39)	missense	probably damaging	1.00
R9667:Pdcd2	UTSW	17	15,747,535 (GRCm39)	start codon destroyed	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- TGCATGACCACGGTTAACTACTC -3'
(R):5'- ACGCATTCTACTCCTATGAGCC -3'

Sequencing Primer
(F):5'- CTAGTCGGCCATTACTGGGAAG -3'
(R):5'- TATGAGCCCCCTTCTGAAACAG -3'

Posted On

2017-03-31