Mutagenetix > Incidental Mutation

Incidental Mutation 'R0893:Pdcd4'

83631

Institutional Source

Beutler Lab

Gene Symbol

Pdcd4

Ensembl Gene

ENSMUSG00000024975

Gene Name

programmed cell death 4

Synonyms

MA-3, TIS, D19Ucla1

MMRRC Submission

039056-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.252) question?

Stock #

R0893 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

53880662-53918291 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 53917525 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 454 (R454L)

Ref Sequence

ENSEMBL: ENSMUSP00000133135 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025931] [ENSMUST00000074371] [ENSMUST00000135402] [ENSMUST00000165617]

AlphaFold

Q61823

Predicted Effect

probably damaging
Transcript: ENSMUST00000025931
AA Change: R454L

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

SMART Domains

Protein: ENSMUSP00000025931
Gene: ENSMUSG00000024975
AA Change: R454L

Domain	Start	End	E-Value	Type
low complexity region	66	82	N/A	INTRINSIC
low complexity region	96	122	N/A	INTRINSIC
MA3	164	275	3.68e-41	SMART
MA3	327	440	5.01e-43	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000074371
AA Change: R454L

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

SMART Domains

Protein: ENSMUSP00000073975
Gene: ENSMUSG00000024975
AA Change: R454L

Domain	Start	End	E-Value	Type
low complexity region	66	82	N/A	INTRINSIC
low complexity region	96	122	N/A	INTRINSIC
MA3	164	275	3.68e-41	SMART
MA3	327	440	5.01e-43	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000135402

SMART Domains

Protein: ENSMUSP00000136324
Gene: ENSMUSG00000084957

Domain	Start	End	E-Value	Type
Pfam:BBIP10	1	64	2.7e-36	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000165617
AA Change: R454L

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

SMART Domains

Protein: ENSMUSP00000133135
Gene: ENSMUSG00000024975
AA Change: R454L

Domain	Start	End	E-Value	Type
low complexity region	66	82	N/A	INTRINSIC
low complexity region	96	122	N/A	INTRINSIC
MA3	164	275	3.68e-41	SMART
MA3	327	440	5.01e-43	SMART

Meta Mutation Damage Score

0.5848

Coding Region Coverage

1x: 99.4%
3x: 98.9%
10x: 97.4%
20x: 95.1%

Validation Efficiency

99% (77/78)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a tumor suppressor and encodes a protein that binds to the eukaryotic translation initiation factor 4A1 and inhibits its function by preventing RNA binding. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2010]
PHENOTYPE: Mice homozygous for a null allele have a higher prevalence of B cell derived lymphomas, multi-organ cysts and decreased susceptibility to experimentally induced autoimmune encephalomyelitis and type 1 diabetes. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700049A03Rik	T	A	12: 71,266,082 (GRCm39)		probably benign	Het
Adnp	A	T	2: 168,025,647 (GRCm39)	F549L	possibly damaging	Het
Agl	A	G	3: 116,546,935 (GRCm39)	I1305T	probably benign	Het
Aldh8a1	T	A	10: 21,267,593 (GRCm39)	M326K	probably benign	Het
Amdhd1	A	T	10: 93,363,513 (GRCm39)	M295K	probably damaging	Het
Arhgef4	T	A	1: 34,846,191 (GRCm39)	C324S	probably damaging	Het
Car8	A	T	4: 8,238,119 (GRCm39)		probably null	Het
Cc2d1a	T	C	8: 84,867,468 (GRCm39)		probably benign	Het
Cd81	G	A	7: 142,616,242 (GRCm39)	V27M	possibly damaging	Het
Ces1b	A	T	8: 93,806,056 (GRCm39)	S62T	probably benign	Het
Cfb	A	G	17: 35,077,031 (GRCm39)	S30P	probably damaging	Het
Cmtm3	A	G	8: 105,070,543 (GRCm39)	M101V	possibly damaging	Het
Cul7	T	A	17: 46,974,116 (GRCm39)	L1467H	probably damaging	Het
Ddb1	C	T	19: 10,590,280 (GRCm39)	S269L	probably benign	Het
Ddx25	G	A	9: 35,465,686 (GRCm39)	Q143*	probably null	Het
Dis3l2	T	A	1: 86,971,928 (GRCm39)		probably null	Het
Dlgap4	G	T	2: 156,587,898 (GRCm39)	E598*	probably null	Het
Dus1l	C	T	11: 120,680,262 (GRCm39)	G471D	possibly damaging	Het
Elp4	C	A	2: 105,727,290 (GRCm39)		probably benign	Het
Eya3	A	G	4: 132,417,097 (GRCm39)	N194S	probably benign	Het
Golgb1	G	T	16: 36,732,639 (GRCm39)	V629L	possibly damaging	Het
Hars2	G	A	18: 36,920,648 (GRCm39)	A164T	possibly damaging	Het
Hexb	T	A	13: 97,322,135 (GRCm39)	I217L	probably benign	Het
Hgh1	A	G	15: 76,253,848 (GRCm39)		probably null	Het
Hsd3b3	A	T	3: 98,649,757 (GRCm39)		probably null	Het
Ighg2c	T	A	12: 113,251,053 (GRCm39)	N321Y	unknown	Het
Il5	A	G	11: 53,611,763 (GRCm39)	T34A	probably benign	Het
Jph1	C	A	1: 17,074,507 (GRCm39)	E504*	probably null	Het
Kif2b	G	T	11: 91,466,420 (GRCm39)	T621K	probably benign	Het
Kmt2c	A	T	5: 25,556,268 (GRCm39)		probably benign	Het
Leprotl1	A	G	8: 34,606,006 (GRCm39)		probably null	Het
Lpar3	C	T	3: 145,946,348 (GRCm39)	R9C	possibly damaging	Het
Map1a	A	G	2: 121,131,014 (GRCm39)	E372G	probably damaging	Het
Map2	C	A	1: 66,419,927 (GRCm39)	T86K	probably damaging	Het
Map7	A	G	10: 20,149,629 (GRCm39)		probably null	Het
Mdn1	T	C	4: 32,701,713 (GRCm39)	V1482A	probably benign	Het
Mks1	G	A	11: 87,747,777 (GRCm39)		probably benign	Het
Morf4l1	T	G	9: 89,984,403 (GRCm39)	K102N	probably damaging	Het
Mroh1	T	A	15: 76,293,138 (GRCm39)	V304D	possibly damaging	Het
Mtg1	G	A	7: 139,729,665 (GRCm39)	V252M	probably damaging	Het
Myh13	A	T	11: 67,225,427 (GRCm39)	D264V	probably damaging	Het
Myh2	A	G	11: 67,077,334 (GRCm39)	Y823C	possibly damaging	Het
Myoz1	A	T	14: 20,701,252 (GRCm39)	S112R	probably benign	Het
Ncapd2	A	G	6: 125,150,445 (GRCm39)	V860A	probably benign	Het
Nfix	G	A	8: 85,453,155 (GRCm39)	R300C	probably damaging	Het
Npffr1	T	C	10: 61,450,010 (GRCm39)	F95L	possibly damaging	Het
Or51f1e	G	T	7: 102,747,641 (GRCm39)	R231L	probably benign	Het
Or8b9	T	C	9: 37,766,492 (GRCm39)	I126T	probably damaging	Het
Orc4	A	C	2: 48,822,622 (GRCm39)		probably benign	Het
P3h3	A	C	6: 124,822,476 (GRCm39)	I565R	probably damaging	Het
Pak4	T	C	7: 28,259,202 (GRCm39)	D552G	probably benign	Het
Pcdhb4	G	T	18: 37,442,423 (GRCm39)		probably null	Het
Phf8-ps	T	C	17: 33,284,263 (GRCm39)	I846M	probably benign	Het
Pkd1l2	A	G	8: 117,771,231 (GRCm39)	I1116T	probably damaging	Het
Plcb2	A	G	2: 118,555,586 (GRCm39)		probably benign	Het
Pmpca	T	C	2: 26,283,230 (GRCm39)		probably benign	Het
Pnpla7	T	A	2: 24,887,252 (GRCm39)	I32N	probably damaging	Het
Prpf8	A	G	11: 75,384,775 (GRCm39)	K718E	probably damaging	Het
Racgap1	C	T	15: 99,524,411 (GRCm39)	A359T	probably benign	Het
Rgs3	G	A	4: 62,523,798 (GRCm39)		probably null	Het
Rhpn1	A	G	15: 75,583,503 (GRCm39)	E356G	probably damaging	Het
Rps6ka5	T	C	12: 100,540,697 (GRCm39)	H488R	possibly damaging	Het
Scn11a	A	G	9: 119,632,396 (GRCm39)		probably null	Het
Sema4f	A	T	6: 82,912,948 (GRCm39)		probably benign	Het
Serpina1f	A	G	12: 103,660,094 (GRCm39)	S63P	probably damaging	Het
Slc9a3	T	C	13: 74,307,365 (GRCm39)	W386R	probably damaging	Het
Slc9b1	A	C	3: 135,100,651 (GRCm39)	L465F	probably benign	Het
Smc5	A	G	19: 23,241,017 (GRCm39)	V165A	possibly damaging	Het
Tex10	C	T	4: 48,456,800 (GRCm39)	R637Q	probably benign	Het
Tinagl1	G	T	4: 130,067,816 (GRCm39)	D59E	probably damaging	Het
Tns3	A	G	11: 8,443,302 (GRCm39)	Y354H	probably damaging	Het
Trappc9	C	T	15: 72,461,956 (GRCm39)	G1103D	probably damaging	Het
Unc79	A	T	12: 102,957,687 (GRCm39)	D34V	probably damaging	Het
Unc80	T	C	1: 66,560,645 (GRCm39)	L791P	probably damaging	Het
Unc93a2	A	G	17: 7,641,926 (GRCm39)	L174P	probably damaging	Het
Xpo7	G	T	14: 70,903,537 (GRCm39)		probably benign	Het
Zbtb1	T	A	12: 76,432,113 (GRCm39)	I33N	probably damaging	Het

Other mutations in Pdcd4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01563:Pdcd4	APN	19	53,917,552 (GRCm39)	missense	probably benign
IGL02608:Pdcd4	APN	19	53,915,638 (GRCm39)	splice site	probably null
seventh	UTSW	19	53,910,564 (GRCm39)	critical splice donor site	probably null
Uccidere	UTSW	19	53,899,379 (GRCm39)	missense	probably damaging	1.00
R1437:Pdcd4	UTSW	19	53,897,674 (GRCm39)	missense	probably damaging	0.99
R1836:Pdcd4	UTSW	19	53,914,650 (GRCm39)	missense	probably damaging	1.00
R4298:Pdcd4	UTSW	19	53,908,092 (GRCm39)	missense	probably damaging	1.00
R6365:Pdcd4	UTSW	19	53,910,564 (GRCm39)	critical splice donor site	probably null
R6436:Pdcd4	UTSW	19	53,915,362 (GRCm39)	splice site	probably null
R7523:Pdcd4	UTSW	19	53,899,379 (GRCm39)	missense	probably damaging	1.00
R8244:Pdcd4	UTSW	19	53,895,965 (GRCm39)	missense	probably benign
R8739:Pdcd4	UTSW	19	53,899,405 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- GGCTCACCTGCTTTCCAATAAGGTC -3'
(R):5'- AACACCCACACTTCGGTGGTTC -3'

Sequencing Primer
(F):5'- GGAAGAAAGTCCATTAGTAATCATGC -3'
(R):5'- agaaagaaaaTCCTTCAAAAAATCCC -3'

Posted On

2013-11-08