Mutagenetix > Incidental Mutation

Incidental Mutation 'R5901:Pdcd11'

456350

Institutional Source

Beutler Lab

Gene Symbol

Pdcd11

Ensembl Gene

ENSMUSG00000025047

Gene Name

programmed cell death 11

Synonyms

ALG-4, 1110021I22Rik

MMRRC Submission

043239-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.968) question?

Stock #

R5901 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

47079183-47119585 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 47116771 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 1580 (S1580P)

Ref Sequence

ENSEMBL: ENSMUSP00000072008 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000035822] [ENSMUST00000072141] [ENSMUST00000140512]

AlphaFold

Q6NS46

Predicted Effect

probably benign
Transcript: ENSMUST00000035822

SMART Domains

Protein: ENSMUSP00000047278
Gene: ENSMUSG00000033033

Domain	Start	End	E-Value	Type
Pfam:Ca_hom_mod	6	256	2.3e-88	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000072141
AA Change: S1580P

PolyPhen 2 Score 0.761 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000072008
Gene: ENSMUSG00000025047
AA Change: S1580P

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

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.8%
20x: 93.5%

Validation Efficiency

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: 42 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2300003K06Rik	T	A	11: 99,728,163 (GRCm39)	S227C	unknown	Het
Acyp2	C	T	11: 30,456,354 (GRCm39)	E98K	possibly damaging	Het
Adamts15	C	T	9: 30,813,786 (GRCm39)	R793H	probably damaging	Het
Ankra2	A	G	13: 98,407,644 (GRCm39)	E38G	probably damaging	Het
Aqp8	G	A	7: 123,061,807 (GRCm39)	C8Y	probably damaging	Het
Atg9b	A	G	5: 24,597,017 (GRCm39)		probably benign	Het
Atp6v1b1	A	G	6: 83,735,339 (GRCm39)	E469G	possibly damaging	Het
B4gat1	T	A	19: 5,089,241 (GRCm39)	Y79*	probably null	Het
BB019430	T	A	10: 58,540,014 (GRCm39)		noncoding transcript	Het
Calhm3	T	C	19: 47,146,052 (GRCm39)	Y51C	probably damaging	Het
Ccr2	C	T	9: 123,906,239 (GRCm39)	T173I	possibly damaging	Het
Cfap43	T	C	19: 47,885,538 (GRCm39)	D359G	probably damaging	Het
Dop1b	A	G	16: 93,566,639 (GRCm39)	E1022G	possibly damaging	Het
Drd2	T	A	9: 49,318,259 (GRCm39)	C400*	probably null	Het
Efcab7	T	A	4: 99,766,941 (GRCm39)	H495Q	probably damaging	Het
Faim	T	C	9: 98,874,195 (GRCm39)	V29A	probably benign	Het
Fancd2	T	C	6: 113,526,326 (GRCm39)	S350P	probably damaging	Het
Fbxw16	T	C	9: 109,270,285 (GRCm39)	E152G	probably benign	Het
Kif17	T	C	4: 138,025,643 (GRCm39)		probably null	Het
Kif24	A	T	4: 41,428,604 (GRCm39)	S119T	probably damaging	Het
Ly6k	A	T	15: 74,670,429 (GRCm39)	S38T	probably benign	Het
Mapk10	A	G	5: 103,061,158 (GRCm39)	S430P	probably damaging	Het
Megf10	G	A	18: 57,410,180 (GRCm39)	A654T	probably benign	Het
Mlph	T	C	1: 90,867,536 (GRCm39)	L450P	probably damaging	Het
Otof	T	C	5: 30,532,323 (GRCm39)	D1603G	probably damaging	Het
Rad54b	G	A	4: 11,595,919 (GRCm39)	R232H	possibly damaging	Het
Sar1b	C	T	11: 51,670,576 (GRCm39)	T40I	possibly damaging	Het
Scyl2	C	T	10: 89,496,124 (GRCm39)	S242N	probably benign	Het
Sema4b	A	G	7: 79,874,715 (GRCm39)	N702D	possibly damaging	Het
Slc16a11	A	G	11: 70,107,172 (GRCm39)	I394V	probably benign	Het
Stard9	A	C	2: 120,531,851 (GRCm39)	T2703P	probably damaging	Het
Stat5b	A	T	11: 100,695,733 (GRCm39)	L83Q	possibly damaging	Het
Tas2r119	T	A	15: 32,177,932 (GRCm39)	V166D	possibly damaging	Het
Tmem117	T	A	15: 94,612,839 (GRCm39)	I125N	probably benign	Het
Tmem39a	T	C	16: 38,393,568 (GRCm39)	I89T	probably benign	Het
Ubr4	T	A	4: 139,178,565 (GRCm39)	H3272Q	probably damaging	Het
Vmn1r7	T	C	6: 57,001,591 (GRCm39)	E223G	probably damaging	Het
Vmn2r78	T	C	7: 86,603,796 (GRCm39)	V658A	probably damaging	Het
Xirp2	A	T	2: 67,343,410 (GRCm39)	T1884S	possibly damaging	Het
Xkr4	A	T	1: 3,286,901 (GRCm39)	F430I	probably damaging	Het
Yae1d1	A	G	13: 18,164,200 (GRCm39)	M1T	probably null	Het
Zfand4	T	C	6: 116,265,084 (GRCm39)	V183A	probably 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
R5592:Pdcd11	UTSW	19	47,091,164 (GRCm39)	missense	probably benign
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
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'- TCCAATTCCCAACTCTGACG -3'
(R):5'- AGCCCAGACCTGAATGAGATG -3'

Sequencing Primer
(F):5'- AACTCTGACGCCCTCTGTGG -3'
(R):5'- AATGAGATGGTCTTCAGGGCCC -3'

Posted On

2017-02-15