Mutagenetix > Incidental Mutation

Incidental Mutation 'R6993:Pdcd2'

543997

Institutional Source

Beutler Lab

Gene Symbol

Pdcd2

Ensembl Gene

ENSMUSG00000014771

Gene Name

programmed cell death 2

Synonyms

RP-8

MMRRC Submission

045099-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6993 (G1)

Quality Score

219.009

Status

Not validated

Chromosome

Chromosomal Location

15739472-15747560 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 15747343 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 65 (Y65H)

Ref Sequence

ENSEMBL: ENSMUSP00000052523 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000054450
AA Change: Y65H

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000052523
Gene: ENSMUSG00000014771
AA Change: Y65H

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

probably damaging
Transcript: ENSMUST00000154293
AA Change: Y65H

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000118625
Gene: ENSMUSG00000014771
AA Change: Y65H

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

99% (66/67)

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700011L22Rik	T	C	8: 79,975,053 (GRCm39)	E10G	possibly damaging	Het
Akap9	A	G	5: 4,115,866 (GRCm39)	I3429V	possibly damaging	Het
Braf	T	A	6: 39,620,097 (GRCm39)	I441F	probably damaging	Het
C5ar1	A	T	7: 15,982,837 (GRCm39)	V61E	probably damaging	Het
Camk2a	C	A	18: 61,076,247 (GRCm39)		probably benign	Het
Cd163	A	G	6: 124,294,673 (GRCm39)	Y579C	probably damaging	Het
Celf1	T	C	2: 90,840,821 (GRCm39)	Y363H	probably damaging	Het
Cntn3	T	C	6: 102,255,365 (GRCm39)	T178A	probably damaging	Het
Cryab	C	T	9: 50,664,748 (GRCm39)	P58S	probably benign	Het
Ctsf	G	T	19: 4,908,511 (GRCm39)	R290L	probably benign	Het
Ctsw	T	A	19: 5,515,865 (GRCm39)	I258F	probably damaging	Het
Dnah7b	T	C	1: 46,234,299 (GRCm39)		probably null	Het
Drg1	TCATCTTCCA	TCA	11: 3,200,294 (GRCm39)		probably null	Het
Etfb	A	G	7: 43,105,978 (GRCm39)	T172A	possibly damaging	Het
Etfdh	A	G	3: 79,519,338 (GRCm39)	Y272H	probably benign	Het
Ewsr1	C	T	11: 5,021,573 (GRCm39)	R454Q	probably benign	Het
F2rl2	T	A	13: 95,837,642 (GRCm39)	I229N	probably damaging	Het
Fam162a	A	T	16: 35,870,215 (GRCm39)	I88N	probably damaging	Het
Fastkd5	A	G	2: 130,458,459 (GRCm39)	S44P	probably benign	Het
Fat3	T	G	9: 15,830,517 (GRCm39)	S4326R	probably damaging	Het
Fbf1	T	C	11: 116,043,610 (GRCm39)	K400E	probably benign	Het
Fndc7	A	G	3: 108,783,907 (GRCm39)	V234A	probably benign	Het
Gfi1	T	A	5: 107,865,634 (GRCm39)	H481L	probably damaging	Het
Gm5591	T	A	7: 38,218,647 (GRCm39)	H742L	probably benign	Het
Golm1	ACTTCTTCT	ACTTCT	13: 59,797,390 (GRCm39)		probably benign	Het
H2-DMb1	A	C	17: 34,376,324 (GRCm39)	T148P	possibly damaging	Het
H2-T3	A	G	17: 36,497,962 (GRCm39)	L317P	probably damaging	Het
Hes3	T	C	4: 152,371,380 (GRCm39)	T190A	probably benign	Het
Hivep1	C	T	13: 42,312,190 (GRCm39)	L1477F	possibly damaging	Het
Insr	C	T	8: 3,308,752 (GRCm39)	G95S	probably damaging	Het
Irf9	A	G	14: 55,846,414 (GRCm39)	I394V	probably benign	Het
Kat2b	T	C	17: 53,945,550 (GRCm39)	L323P	probably damaging	Het
Kdr	T	C	5: 76,133,071 (GRCm39)	D69G	probably benign	Het
Krt1c	C	T	15: 101,724,395 (GRCm39)	E290K	probably damaging	Het
Krtap4-6	G	T	11: 99,556,545 (GRCm39)	R61S	unknown	Het
Ldc1	A	G	4: 130,112,106 (GRCm39)	L192P	probably damaging	Het
Lrrc27	A	T	7: 138,822,540 (GRCm39)	K477M	probably damaging	Het
Lvrn	T	C	18: 47,015,365 (GRCm39)	V579A	probably benign	Het
Malrd1	A	T	2: 16,155,602 (GRCm39)	I2004L	unknown	Het
Mast4	A	T	13: 102,872,482 (GRCm39)	N2103K	probably benign	Het
Mast4	C	T	13: 102,941,155 (GRCm39)	V301I	probably damaging	Het
Myo18a	T	A	11: 77,749,900 (GRCm39)		probably benign	Het
Or10d5	T	A	9: 39,861,933 (GRCm39)	M45L	probably benign	Het
Or52ab2	G	T	7: 102,969,998 (GRCm39)		probably benign	Het
Pcdhga10	A	G	18: 37,882,309 (GRCm39)	Y690C	probably damaging	Het
Ppp1r12a	A	G	10: 108,076,698 (GRCm39)	E309G	probably benign	Het
Psmb8	A	G	17: 34,418,617 (GRCm39)	D123G	probably damaging	Het
Ptcd3	A	T	6: 71,862,299 (GRCm39)	W513R	probably damaging	Het
Ptx4	G	A	17: 25,343,898 (GRCm39)	V383I	possibly damaging	Het
Ric1	T	C	19: 29,564,013 (GRCm39)	L589S	probably damaging	Het
Rmnd5b	A	G	11: 51,515,427 (GRCm39)		probably benign	Het
Sec16a	A	T	2: 26,313,586 (GRCm39)	S1925T	probably damaging	Het
Slc16a11	T	A	11: 70,106,842 (GRCm39)	M360K	possibly damaging	Het
Slc19a2	T	A	1: 164,088,391 (GRCm39)	F79I	probably benign	Het
Slc2a6	G	T	2: 26,917,255 (GRCm39)	S45R	probably damaging	Het
Slco1a7	G	A	6: 141,711,468 (GRCm39)	T81I	possibly damaging	Het
Sppl3	T	A	5: 115,220,349 (GRCm39)	M87K	probably damaging	Het
Tbcel	A	T	9: 42,327,413 (GRCm39)	L330*	probably null	Het
Tbx5	A	T	5: 120,009,454 (GRCm39)	Y321F	possibly damaging	Het
Tenm3	C	T	8: 48,689,474 (GRCm39)	D2038N	probably damaging	Het
Tesk1	A	G	4: 43,447,006 (GRCm39)	T465A	probably benign	Het
Unc45a	A	T	7: 79,975,403 (GRCm39)	Y934N	probably damaging	Het
Unc80	A	T	1: 66,588,952 (GRCm39)	Q1039L	possibly damaging	Het
Vmn2r112	T	C	17: 22,822,195 (GRCm39)	L291P	probably benign	Het
Wwc2	A	T	8: 48,300,500 (GRCm39)	F988I	unknown	Het
Zfp947	G	A	17: 22,364,961 (GRCm39)	P238S	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
R5963:Pdcd2	UTSW	17	15,746,656 (GRCm39)	missense	possibly damaging	0.91
R6944:Pdcd2	UTSW	17	15,745,632 (GRCm39)	missense	possibly damaging	0.82
R9667:Pdcd2	UTSW	17	15,747,535 (GRCm39)	start codon destroyed	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- TTCCGGTACCTGAATACAACC -3'
(R):5'- ATAGGGTTACCTCCAGTCCG -3'

Sequencing Primer
(F):5'- GGTACCTGAATACAACCACTCG -3'
(R):5'- TTCCGGCCTAACACGTGAC -3'

Posted On

2019-05-13