Mutagenetix > Incidental Mutation

Incidental Mutation 'R5899:Pdcd11'

457754

Institutional Source

Beutler Lab

Gene Symbol

Pdcd11

Ensembl Gene

ENSMUSG00000025047

Gene Name

programmed cell death 11

Synonyms

ALG-4, 1110021I22Rik

MMRRC Submission

044098-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.968) question?

Stock #

R5899 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

47079183-47119585 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 47093198 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 492 (N492S)

Ref Sequence

ENSEMBL: ENSMUSP00000072008 (fasta)

Gene Model

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

AlphaFold

Q6NS46

Predicted Effect

possibly damaging
Transcript: ENSMUST00000072141
AA Change: N492S

PolyPhen 2 Score 0.927 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000072008
Gene: ENSMUSG00000025047
AA Change: N492S

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

0.1294

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.6%
20x: 92.5%

Validation Efficiency

93% (56/60)

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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ahi1	T	C	10: 20,876,465 (GRCm39)	I792T	probably benign	Het
Anks1b	T	A	10: 90,759,379 (GRCm39)		probably null	Het
Ano3	T	G	2: 110,693,232 (GRCm39)	D122A	probably benign	Het
Atp12a	T	C	14: 56,610,801 (GRCm39)	V315A	probably benign	Het
B230104I21Rik	G	T	4: 154,433,986 (GRCm39)	G57*	probably null	Het
Bpifb2	A	G	2: 153,733,050 (GRCm39)	K378E	probably damaging	Het
Cdk5rap2	T	C	4: 70,161,830 (GRCm39)		probably benign	Het
Ceacam23	A	G	7: 17,651,369 (GRCm39)	D840G	possibly damaging	Het
Cflar	A	G	1: 58,791,927 (GRCm39)	D410G	probably benign	Het
Clcn6	A	G	4: 148,102,049 (GRCm39)	V345A	probably benign	Het
Cnga1	C	T	5: 72,776,404 (GRCm39)	V20I	possibly damaging	Het
Ddx50	T	A	10: 62,476,596 (GRCm39)	K226*	probably null	Het
Dnah5	T	C	15: 28,448,513 (GRCm39)	V4192A	possibly damaging	Het
Dnah8	G	A	17: 30,875,659 (GRCm39)	D494N	probably benign	Het
Dock7	A	T	4: 98,879,660 (GRCm39)	C965S	probably benign	Het
Dst	C	T	1: 34,334,370 (GRCm39)	A5083V	probably damaging	Het
E130208F15Rik	T	C	7: 30,021,726 (GRCm39)	Q10R	probably damaging	Het
Fbxw15	T	C	9: 109,384,741 (GRCm39)		probably null	Het
Fxr2	A	G	11: 69,543,511 (GRCm39)	N671D	probably damaging	Het
Gbp7	A	G	3: 142,252,303 (GRCm39)	T629A	probably benign	Het
Grm1	T	C	10: 10,565,092 (GRCm39)	Y1072C	probably benign	Het
Hmcn2	A	T	2: 31,244,685 (GRCm39)	E714V	possibly damaging	Het
Hsd17b13	T	A	5: 104,113,730 (GRCm39)	E205D	probably benign	Het
Igf2bp3	A	G	6: 49,094,084 (GRCm39)		probably benign	Het
Il2ra	A	G	2: 11,689,248 (GRCm39)	H259R	probably benign	Het
Klk15	G	T	7: 43,588,247 (GRCm39)	R185L	probably benign	Het
Map3k11	T	G	19: 5,745,937 (GRCm39)		probably null	Het
Morn3	A	G	5: 123,179,166 (GRCm39)	W95R	probably damaging	Het
Nipbl	A	G	15: 8,364,328 (GRCm39)		probably null	Het
Nrap	A	T	19: 56,329,006 (GRCm39)	V1145D	possibly damaging	Het
Or1e35	A	G	11: 73,797,755 (GRCm39)	S188P	probably damaging	Het
Or2l13b	C	T	16: 19,349,551 (GRCm39)	G40R	probably damaging	Het
Or9k2	T	A	10: 129,998,542 (GRCm39)	I218F	probably benign	Het
Ptgfr	C	T	3: 151,540,738 (GRCm39)	V257I	probably damaging	Het
Racgap1	T	C	15: 99,521,509 (GRCm39)	E549G	possibly damaging	Het
Rfx3	T	C	19: 27,808,165 (GRCm39)	T193A	probably damaging	Het
Rplp0	T	A	5: 115,699,489 (GRCm39)	I149N	probably benign	Het
Samd7	T	G	3: 30,810,883 (GRCm39)	I300S	probably benign	Het
Scpep1	A	G	11: 88,825,402 (GRCm39)		probably null	Het
Senp6	T	C	9: 80,049,352 (GRCm39)		probably benign	Het
Serpinb2	G	T	1: 107,447,446 (GRCm39)	G78V	probably damaging	Het
Sesn1	T	C	10: 41,687,189 (GRCm39)	S58P	probably benign	Het
Skic3	A	G	13: 76,259,938 (GRCm39)		probably null	Het
Spg11	T	C	2: 121,928,680 (GRCm39)	D591G	possibly damaging	Het
Spire2	A	C	8: 124,080,833 (GRCm39)	S26R	probably damaging	Het
Strip2	T	A	6: 29,956,957 (GRCm39)		probably benign	Het
Ttn	G	A	2: 76,697,519 (GRCm39)		probably benign	Het
Vmn2r77	A	G	7: 86,460,924 (GRCm39)	Y750C	probably damaging	Het
Wnt11	T	A	7: 98,488,383 (GRCm39)	Y23*	probably null	Het
Zbp1	T	A	2: 173,052,340 (GRCm39)	D272V	probably benign	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
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'- ACACATAGCCAGGCTACGTC -3'
(R):5'- CCACTGCTAGGTGAAGTACTG -3'

Sequencing Primer
(F):5'- TGGCTTTCCCACATGAGATC -3'
(R):5'- CCACTGCTAGGTGAAGTACTGAATAC -3'

Posted On

2017-02-15