Mutagenetix > Incidental Mutation

Incidental Mutation 'R6944:Pdcd2'

540807

Institutional Source

Beutler Lab

Gene Symbol

Pdcd2

Ensembl Gene

ENSMUSG00000014771

Gene Name

programmed cell death 2

Synonyms

RP-8

MMRRC Submission

045058-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6944 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

15739472-15747560 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 15745632 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 185 (N185S)

Ref Sequence

ENSEMBL: ENSMUSP00000118625 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000054450
AA Change: N185S

PolyPhen 2 Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000052523
Gene: ENSMUSG00000014771
AA Change: N185S

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

possibly damaging
Transcript: ENSMUST00000154293
AA Change: N185S

PolyPhen 2 Score 0.819 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000118625
Gene: ENSMUSG00000014771
AA Change: N185S

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: 99.9%
10x: 99.5%
20x: 98.2%

Validation Efficiency

97% (75/77)

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb1b	T	G	5: 8,863,693 (GRCm39)	V216G	probably damaging	Het
Abcb5	T	C	12: 118,875,265 (GRCm39)	R636G	probably benign	Het
Ago1	G	T	4: 126,354,215 (GRCm39)	F198L	possibly damaging	Het
Ankrd42	C	T	7: 92,268,755 (GRCm39)		probably null	Het
Anxa11	T	A	14: 25,875,176 (GRCm39)	F274I	probably damaging	Het
Ascc1	T	C	10: 59,849,475 (GRCm39)	L122P	probably damaging	Het
Bptf	T	C	11: 106,971,649 (GRCm39)	S953G	probably damaging	Het
Chml	T	A	1: 175,515,727 (GRCm39)	N65Y	probably damaging	Het
Clcc1	A	G	3: 108,578,284 (GRCm39)	K262E	probably damaging	Het
Clhc1	T	G	11: 29,519,346 (GRCm39)	D384E	probably damaging	Het
Cnot2	G	A	10: 116,373,128 (GRCm39)		probably benign	Het
Cntnap1	T	C	11: 101,073,730 (GRCm39)	V627A	probably damaging	Het
Col6a4	A	G	9: 105,949,370 (GRCm39)	V755A	probably damaging	Het
Cyp4f18	T	A	8: 72,743,738 (GRCm39)	I406F	probably benign	Het
Dclre1a	T	C	19: 56,533,451 (GRCm39)	E381G	possibly damaging	Het
Dnah1	A	G	14: 30,990,861 (GRCm39)	Y3153H	probably damaging	Het
Dnah8	C	A	17: 31,013,633 (GRCm39)	D3791E	probably benign	Het
Dnah9	T	C	11: 65,975,975 (GRCm39)	E1358G	possibly damaging	Het
Eef1g	G	A	19: 8,945,656 (GRCm39)	R30H	probably benign	Het
Egln3	A	T	12: 54,230,738 (GRCm39)	I181N	probably benign	Het
Entpd6	A	G	2: 150,605,519 (GRCm39)	T250A	probably damaging	Het
Epb41l5	C	T	1: 119,536,859 (GRCm39)	R344Q	probably damaging	Het
Fam20b	T	C	1: 156,515,091 (GRCm39)	D258G	probably benign	Het
Fbxw18	A	T	9: 109,531,655 (GRCm39)	D21E	probably damaging	Het
Fbxw21	T	C	9: 108,986,603 (GRCm39)	E92G	probably damaging	Het
Fzd6	T	A	15: 38,889,212 (GRCm39)	M110K	possibly damaging	Het
Golgb1	C	T	16: 36,732,475 (GRCm39)	P574L	probably benign	Het
Gpr153	A	G	4: 152,363,820 (GRCm39)	E80G	probably damaging	Het
Gvin2	G	A	7: 105,551,187 (GRCm39)	Q622*	probably null	Het
Kcnt1	T	C	2: 25,767,840 (GRCm39)		probably benign	Het
Kcnt2	T	G	1: 140,511,803 (GRCm39)	V962G	probably benign	Het
Malt1	T	C	18: 65,570,991 (GRCm39)	V109A	probably benign	Het
Marchf7	A	G	2: 60,064,587 (GRCm39)	I288V	probably benign	Het
Mief1	C	T	15: 80,133,644 (GRCm39)	R234C	probably damaging	Het
Morc3	A	G	16: 93,667,460 (GRCm39)	S613G	probably benign	Het
Myt1	A	G	2: 181,439,387 (GRCm39)	E345G	possibly damaging	Het
Napb	T	C	2: 148,548,889 (GRCm39)	T133A	probably benign	Het
Nwd1	T	C	8: 73,380,162 (GRCm39)	V16A	possibly damaging	Het
Oas1f	G	A	5: 120,986,247 (GRCm39)	E67K	probably benign	Het
Obscn	T	C	11: 58,929,756 (GRCm39)	K5153R	probably damaging	Het
Or2w3b	T	A	11: 58,623,068 (GRCm39)	S308C	possibly damaging	Het
Or5a3	G	T	19: 12,400,628 (GRCm39)	M318I	probably benign	Het
Or5g26	C	T	2: 85,494,195 (GRCm39)	M194I	probably benign	Het
Or6d12	T	C	6: 116,492,791 (GRCm39)	F18L	possibly damaging	Het
Pgap1	A	T	1: 54,569,320 (GRCm39)	W349R	probably damaging	Het
Prpf39	T	A	12: 65,089,454 (GRCm39)	V64E	probably benign	Het
Ptpn13	T	A	5: 103,624,857 (GRCm39)	W54R	probably null	Het
Rbms3	G	T	9: 116,939,173 (GRCm39)	P29Q	probably damaging	Het
Rnf123	A	G	9: 107,940,822 (GRCm39)	L679P	probably benign	Het
Samd4	T	A	14: 47,254,092 (GRCm39)	D84E	possibly damaging	Het
Scarf1	T	C	11: 75,413,032 (GRCm39)	V426A	probably benign	Het
Slc12a1	A	G	2: 125,002,454 (GRCm39)	N145D	probably damaging	Het
Slc2a6	A	T	2: 26,916,076 (GRCm39)	M99K	probably damaging	Het
Slc34a2	A	T	5: 53,222,225 (GRCm39)	I306L	probably benign	Het
Slx4ip	A	G	2: 136,910,195 (GRCm39)	K397E	probably damaging	Het
Smr3a	C	T	5: 88,155,949 (GRCm39)		probably benign	Het
Spata31h1	A	C	10: 82,132,056 (GRCm39)	I318R	probably benign	Het
Spef2	T	C	15: 9,592,835 (GRCm39)	E1502G	probably damaging	Het
Sri	A	T	5: 8,113,365 (GRCm39)	T119S	probably benign	Het
Synrg	T	A	11: 83,915,912 (GRCm39)	L1085H	probably damaging	Het
Taf7	A	T	18: 37,775,910 (GRCm39)	L219H	probably damaging	Het
Tmco3	T	A	8: 13,353,729 (GRCm39)	V347E	probably damaging	Het
Tmem8b	A	T	4: 43,674,465 (GRCm39)	I250F	probably damaging	Het
Tom1l2	A	G	11: 60,139,817 (GRCm39)	V239A	probably damaging	Het
Trpm1	T	A	7: 63,893,181 (GRCm39)	M1011K	probably damaging	Het
Tspan9	A	T	6: 127,942,769 (GRCm39)	Y153N	probably benign	Het
Ttll11	T	C	2: 35,642,306 (GRCm39)	H675R	probably benign	Het
Unc50	C	T	1: 37,471,743 (GRCm39)	T131M	probably damaging	Het
Vgf	T	A	5: 137,061,206 (GRCm39)	I456N	probably damaging	Het
Vmn1r223	A	G	13: 23,433,483 (GRCm39)	I26V	unknown	Het
Vmn1r39	T	C	6: 66,782,205 (GRCm39)	M1V	probably null	Het
Vmn2r111	T	C	17: 22,778,032 (GRCm39)	N549S	possibly damaging	Het
Vmn2r14	T	C	5: 109,363,925 (GRCm39)	T664A	probably benign	Het
Vmn2r14	G	A	5: 109,364,140 (GRCm39)	T592I	probably benign	Het
Vmn2r96	T	A	17: 18,817,891 (GRCm39)	F489L	probably benign	Het
Vmn2r-ps158	T	C	7: 42,697,393 (GRCm39)	F817L	possibly damaging	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
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'- CTACCAAGACGTTCTCTGCC -3'
(R):5'- GATTGCCCTATTCCATAGCAGCTC -3'

Sequencing Primer
(F):5'- CACCACAGATACACACTGATGGTG -3'
(R):5'- AGCAGCTCTGATGTTCAACTG -3'

Posted On

2018-11-28