Mutagenetix > Incidental Mutation

Incidental Mutation 'R5592:Pdcd11'

437603

Institutional Source

Beutler Lab

Gene Symbol

Pdcd11

Ensembl Gene

ENSMUSG00000025047

Gene Name

programmed cell death 11

Synonyms

ALG-4, 1110021I22Rik

MMRRC Submission

043144-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.968) question?

Stock #

R5592 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

47079183-47119585 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 47091164 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 379 (N379K)

Ref Sequence

ENSEMBL: ENSMUSP00000072008 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000072141] [ENSMUST00000140512]

AlphaFold

Q6NS46

Predicted Effect

probably benign
Transcript: ENSMUST00000072141
AA Change: N379K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000072008
Gene: ENSMUSG00000025047
AA Change: N379K

Domain	Start	End	E-Value	Type
low complexity region	53	76	N/A	INTRINSIC
S1	81	171	1.05e-7	SMART
S1	185	258	2.32e-9	SMART
S1	279	346	1.44e-5	SMART
S1	363	436	8.55e-8	SMART
S1	451	522	3.89e-20	SMART
S1	540	611	1.14e-17	SMART
S1	634	707	2.76e-2	SMART
S1	727	798	2.02e-18	SMART
low complexity region	813	823	N/A	INTRINSIC
S1	844	911	6.13e0	SMART
Blast:S1	923	993	8e-39	BLAST
low complexity region	1018	1032	N/A	INTRINSIC
S1	1045	1120	1.3e-7	SMART
S1	1158	1233	6.09e-4	SMART
S1	1239	1309	4.14e-6	SMART
S1	1333	1407	1.57e-6	SMART
low complexity region	1433	1473	N/A	INTRINSIC
coiled coil region	1557	1588	N/A	INTRINSIC
HAT	1591	1622	6.53e2	SMART
HAT	1624	1661	4.12e1	SMART
HAT	1663	1694	3.49e2	SMART
HAT	1696	1728	3.18e-1	SMART
HAT	1730	1764	2.25e2	SMART
HAT	1766	1798	8.52e-2	SMART
HAT	1800	1835	1.33e1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000140512

SMART Domains

Protein: ENSMUSP00000121661
Gene: ENSMUSG00000033033

Domain	Start	End	E-Value	Type
Pfam:Ca_hom_mod	6	258	2.9e-93	PFAM

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.8%
20x: 96.7%

Validation Efficiency

100% (48/48)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] PDCD11 is a NF-kappa-B (NFKB1; 164011)-binding protein that colocalizes with U3 RNA (MIM 180710) in the nucleolus and is required for rRNA maturation and generation of 18S rRNA (Sweet et al., 2003 [PubMed 14624448]; Sweet et al., 2008 [PubMed 17654514]).[supplied by OMIM, Oct 2008]

Allele List at MGI

Other mutations in this stock

Total: 48 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A630001G21Rik	A	T	1: 85,654,332 (GRCm39)	F2I	probably damaging	Het
Adam17	C	T	12: 21,384,138 (GRCm39)	S454N	probably damaging	Het
Adcy1	A	T	11: 7,089,088 (GRCm39)	K501*	probably null	Het
Arhgap28	A	T	17: 68,165,267 (GRCm39)	M543K	probably damaging	Het
Art3	T	A	5: 92,540,679 (GRCm39)	Y141N	probably damaging	Het
Ccdc38	C	T	10: 93,386,064 (GRCm39)	T60I	possibly damaging	Het
Crmp1	A	C	5: 37,422,609 (GRCm39)	I139L	probably benign	Het
Cul9	G	A	17: 46,831,517 (GRCm39)	L1566F	probably benign	Het
Cysltr2	T	C	14: 73,266,931 (GRCm39)	K260E	probably benign	Het
Drd1	A	T	13: 54,208,190 (GRCm39)	M1K	probably null	Het
Flii	T	G	11: 60,611,225 (GRCm39)	M449L	probably benign	Het
Galnt16	T	C	12: 80,635,293 (GRCm39)	V343A	probably damaging	Het
Gimap4	A	T	6: 48,668,092 (GRCm39)	E154D	probably damaging	Het
Glmp	T	G	3: 88,233,333 (GRCm39)		probably benign	Het
Glt1d1	A	T	5: 127,734,183 (GRCm39)	D119V	probably benign	Het
Gm5930	C	T	14: 44,568,886 (GRCm39)	M245I	probably benign	Het
Golgb1	T	A	16: 36,746,125 (GRCm39)	H2901Q	probably benign	Het
Krt12	C	T	11: 99,311,650 (GRCm39)	V184I	probably benign	Het
Lyst	T	G	13: 13,917,918 (GRCm39)	I3326S	probably damaging	Het
Mier3	T	A	13: 111,843,195 (GRCm39)	Y182*	probably null	Het
Mlip	G	A	9: 77,137,764 (GRCm39)	S381L	probably damaging	Het
Mmp25	A	G	17: 23,859,176 (GRCm39)	V157A	possibly damaging	Het
Mplkipl1	C	T	19: 61,164,364 (GRCm39)	G24R	unknown	Het
Ms4a6c	A	G	19: 11,457,641 (GRCm39)		probably benign	Het
Ms4a6c	A	G	19: 11,458,496 (GRCm39)		probably benign	Het
Muc19	T	C	15: 91,828,199 (GRCm39)		noncoding transcript	Het
Mucl3	T	C	17: 35,954,535 (GRCm39)	Y9C	probably damaging	Het
Mycbp2	C	A	14: 103,432,113 (GRCm39)	M2308I	probably benign	Het
Myo1a	G	T	10: 127,549,908 (GRCm39)	V463F	probably damaging	Het
Ogdh	A	T	11: 6,266,763 (GRCm39)		probably null	Het
Or52h9	A	T	7: 104,202,938 (GRCm39)	N271Y	probably benign	Het
Or5l14	A	G	2: 87,792,684 (GRCm39)	L184P	probably damaging	Het
Otx1	C	A	11: 21,947,037 (GRCm39)	A91S	probably damaging	Het
Paip1	C	A	13: 119,587,334 (GRCm39)	D124E	probably damaging	Het
Pitpnm2	T	C	5: 124,280,212 (GRCm39)	E112G	probably damaging	Het
Prrg4	T	C	2: 104,663,123 (GRCm39)	Y161C	probably benign	Het
Rb1	A	G	14: 73,449,187 (GRCm39)	Y648H	probably damaging	Het
Rpa3	A	T	6: 8,257,694 (GRCm39)	M56K	probably benign	Het
Scarf1	A	T	11: 75,416,513 (GRCm39)	T652S	probably benign	Het
Slc16a5	A	G	11: 115,363,608 (GRCm39)	K423R	probably benign	Het
Sptan1	C	T	2: 29,876,731 (GRCm39)		probably benign	Het
Ssrp1	T	C	2: 84,875,863 (GRCm39)	I574T	probably benign	Het
Synm	A	G	7: 67,409,264 (GRCm39)	L38P	probably damaging	Het
Ubqln4	T	G	3: 88,464,171 (GRCm39)	M224R	probably damaging	Het
Uroc1	A	G	6: 90,332,326 (GRCm39)	N561S	probably damaging	Het
Vav1	A	G	17: 57,611,835 (GRCm39)	Y483C	probably benign	Het
Vps13a	G	A	19: 16,702,935 (GRCm39)	L673F	probably damaging	Het
Zfp418	G	T	7: 7,184,314 (GRCm39)	K92N	possibly damaging	Het

Other mutations in Pdcd11

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00646:Pdcd11	APN	19	47,105,767 (GRCm39)	missense	possibly damaging	0.83
IGL00656:Pdcd11	APN	19	47,086,609 (GRCm39)	missense	probably damaging	1.00
IGL00754:Pdcd11	APN	19	47,092,221 (GRCm39)	missense	possibly damaging	0.86
IGL00907:Pdcd11	APN	19	47,096,003 (GRCm39)	missense	probably benign	0.16
IGL00987:Pdcd11	APN	19	47,102,989 (GRCm39)	intron	probably benign
IGL01346:Pdcd11	APN	19	47,098,053 (GRCm39)	missense	probably benign	0.03
IGL01529:Pdcd11	APN	19	47,098,068 (GRCm39)	missense	probably benign	0.01
IGL01670:Pdcd11	APN	19	47,094,743 (GRCm39)	missense	probably damaging	0.98
IGL01917:Pdcd11	APN	19	47,089,604 (GRCm39)	missense	possibly damaging	0.92
IGL02096:Pdcd11	APN	19	47,094,860 (GRCm39)	missense	probably benign	0.10
IGL02300:Pdcd11	APN	19	47,115,381 (GRCm39)	missense	probably benign
IGL02515:Pdcd11	APN	19	47,113,516 (GRCm39)	missense	probably damaging	1.00
IGL02886:Pdcd11	APN	19	47,102,064 (GRCm39)	missense	possibly damaging	0.95
IGL03158:Pdcd11	APN	19	47,116,500 (GRCm39)	missense	possibly damaging	0.91
R0100:Pdcd11	UTSW	19	47,091,105 (GRCm39)	missense	probably benign	0.00
R0100:Pdcd11	UTSW	19	47,091,105 (GRCm39)	missense	probably benign	0.00
R0128:Pdcd11	UTSW	19	47,108,301 (GRCm39)	missense	probably benign	0.15
R0139:Pdcd11	UTSW	19	47,099,398 (GRCm39)	critical splice acceptor site	probably null
R0227:Pdcd11	UTSW	19	47,101,876 (GRCm39)	intron	probably benign
R0316:Pdcd11	UTSW	19	47,101,611 (GRCm39)	missense	probably damaging	0.97
R0480:Pdcd11	UTSW	19	47,113,476 (GRCm39)	intron	probably benign
R0577:Pdcd11	UTSW	19	47,087,271 (GRCm39)	missense	probably benign	0.01
R0725:Pdcd11	UTSW	19	47,115,730 (GRCm39)	missense	probably benign	0.17
R1344:Pdcd11	UTSW	19	47,118,516 (GRCm39)	missense	probably damaging	1.00
R1418:Pdcd11	UTSW	19	47,118,516 (GRCm39)	missense	probably damaging	1.00
R1856:Pdcd11	UTSW	19	47,086,626 (GRCm39)	missense	probably benign	0.00
R2146:Pdcd11	UTSW	19	47,093,191 (GRCm39)	missense	probably benign	0.00
R2147:Pdcd11	UTSW	19	47,093,191 (GRCm39)	missense	probably benign	0.00
R2447:Pdcd11	UTSW	19	47,102,995 (GRCm39)	missense	probably benign	0.01
R2916:Pdcd11	UTSW	19	47,101,876 (GRCm39)	intron	probably benign
R3177:Pdcd11	UTSW	19	47,101,703 (GRCm39)	missense	probably damaging	1.00
R3277:Pdcd11	UTSW	19	47,101,703 (GRCm39)	missense	probably damaging	1.00
R3712:Pdcd11	UTSW	19	47,115,684 (GRCm39)	intron	probably benign
R4495:Pdcd11	UTSW	19	47,099,445 (GRCm39)	missense	probably benign
R4697:Pdcd11	UTSW	19	47,114,786 (GRCm39)	missense	possibly damaging	0.83
R4941:Pdcd11	UTSW	19	47,108,325 (GRCm39)	missense	probably damaging	1.00
R4953:Pdcd11	UTSW	19	47,116,404 (GRCm39)	missense	probably benign	0.04
R5048:Pdcd11	UTSW	19	47,095,554 (GRCm39)	missense	probably benign
R5049:Pdcd11	UTSW	19	47,095,554 (GRCm39)	missense	probably benign
R5103:Pdcd11	UTSW	19	47,112,893 (GRCm39)	missense	probably benign	0.00
R5107:Pdcd11	UTSW	19	47,094,893 (GRCm39)	missense	probably damaging	1.00
R5139:Pdcd11	UTSW	19	47,095,554 (GRCm39)	missense	probably benign
R5261:Pdcd11	UTSW	19	47,101,976 (GRCm39)	missense	probably benign
R5302:Pdcd11	UTSW	19	47,096,083 (GRCm39)	missense	probably damaging	1.00
R5769:Pdcd11	UTSW	19	47,091,076 (GRCm39)	missense	possibly damaging	0.92
R5791:Pdcd11	UTSW	19	47,099,430 (GRCm39)	missense	possibly damaging	0.65
R5809:Pdcd11	UTSW	19	47,082,247 (GRCm39)	missense	probably benign	0.01
R5899:Pdcd11	UTSW	19	47,093,198 (GRCm39)	missense	possibly damaging	0.93
R5901:Pdcd11	UTSW	19	47,116,771 (GRCm39)	missense	possibly damaging	0.76
R5947:Pdcd11	UTSW	19	47,117,702 (GRCm39)	missense	probably benign	0.20
R6177:Pdcd11	UTSW	19	47,108,722 (GRCm39)	missense	probably damaging	1.00
R6489:Pdcd11	UTSW	19	47,098,191 (GRCm39)	missense	probably damaging	1.00
R6575:Pdcd11	UTSW	19	47,098,117 (GRCm39)	missense	probably damaging	0.98
R6578:Pdcd11	UTSW	19	47,099,520 (GRCm39)	missense	probably benign	0.11
R7009:Pdcd11	UTSW	19	47,101,581 (GRCm39)	missense	probably benign	0.17
R7015:Pdcd11	UTSW	19	47,086,665 (GRCm39)	missense	probably benign	0.00
R7060:Pdcd11	UTSW	19	47,099,418 (GRCm39)	missense	probably benign	0.30
R7260:Pdcd11	UTSW	19	47,117,673 (GRCm39)	missense	possibly damaging	0.62
R7392:Pdcd11	UTSW	19	47,116,436 (GRCm39)	missense	probably damaging	1.00
R7601:Pdcd11	UTSW	19	47,094,808 (GRCm39)	missense	not run
R7759:Pdcd11	UTSW	19	47,101,637 (GRCm39)	missense	possibly damaging	0.88
R7760:Pdcd11	UTSW	19	47,101,637 (GRCm39)	missense	possibly damaging	0.88
R7785:Pdcd11	UTSW	19	47,093,125 (GRCm39)	missense	probably benign	0.00
R7793:Pdcd11	UTSW	19	47,094,871 (GRCm39)	missense	probably benign	0.00
R7810:Pdcd11	UTSW	19	47,086,659 (GRCm39)	missense	possibly damaging	0.81
R7863:Pdcd11	UTSW	19	47,085,403 (GRCm39)	missense	probably damaging	1.00
R7950:Pdcd11	UTSW	19	47,101,876 (GRCm39)	intron	probably benign
R8062:Pdcd11	UTSW	19	47,119,152 (GRCm39)	missense	possibly damaging	0.50
R8184:Pdcd11	UTSW	19	47,101,791 (GRCm39)	nonsense	probably null
R8278:Pdcd11	UTSW	19	47,094,736 (GRCm39)	missense	probably damaging	1.00
R8404:Pdcd11	UTSW	19	47,093,231 (GRCm39)	missense	probably damaging	0.98
R8508:Pdcd11	UTSW	19	47,108,245 (GRCm39)	missense	probably damaging	1.00
R8525:Pdcd11	UTSW	19	47,081,337 (GRCm39)	missense	possibly damaging	0.52
R8787:Pdcd11	UTSW	19	47,097,019 (GRCm39)	missense	probably damaging	1.00
R9019:Pdcd11	UTSW	19	47,101,658 (GRCm39)	missense	probably damaging	1.00
R9534:Pdcd11	UTSW	19	47,108,718 (GRCm39)	missense	probably benign	0.01
R9660:Pdcd11	UTSW	19	47,082,191 (GRCm39)	missense	possibly damaging	0.67
R9712:Pdcd11	UTSW	19	47,117,741 (GRCm39)	missense	probably damaging	0.98
RF010:Pdcd11	UTSW	19	47,101,890 (GRCm39)	frame shift	probably null
RF027:Pdcd11	UTSW	19	47,101,888 (GRCm39)	frame shift	probably null
RF039:Pdcd11	UTSW	19	47,101,894 (GRCm39)	frame shift	probably null
RF061:Pdcd11	UTSW	19	47,101,884 (GRCm39)	frame shift	probably null
X0065:Pdcd11	UTSW	19	47,085,335 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGGGCGTTTGACCCTTAGAG -3'
(R):5'- ACAGCCTTTTACACTGGAGG -3'

Sequencing Primer
(F):5'- GTGGACGTCTCCTGCTCATCTG -3'
(R):5'- CAGCCTTTTACACTGGAGGCTAAG -3'

Posted On

2016-10-26