Mutagenetix > Incidental Mutation

Incidental Mutation 'R7009:Pdcd11'

544946

Institutional Source

Beutler Lab

Gene Symbol

Pdcd11

Ensembl Gene

ENSMUSG00000025047

Gene Name

programmed cell death 11

Synonyms

ALG-4, 1110021I22Rik

MMRRC Submission

045111-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.969) question?

Stock #

R7009 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

47090766-47131143 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 47113142 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 922 (L922P)

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: L922P

PolyPhen 2 Score 0.174 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000072008
Gene: ENSMUSG00000025047
AA Change: L922P

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: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

99% (82/83)

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700007G11Rik	A	T	5: 98,784,520	D193V	probably damaging	Het
4921517D22Rik	G	T	13: 59,690,810	D69E	possibly damaging	Het
Abat	A	C	16: 8,602,367	M177L	probably benign	Het
Acadvl	A	G	11: 70,014,791		probably null	Het
Adam5	T	C	8: 24,806,438	N331S	probably benign	Het
Ager	A	G	17: 34,600,736	E372G	probably damaging	Het
Angpt1	T	A	15: 42,523,595	Q121L	possibly damaging	Het
Apoa4	A	T	9: 46,242,880	I260F	possibly damaging	Het
Arhgap32	A	T	9: 32,245,976	I90F	probably damaging	Het
Arhgap5	A	T	12: 52,519,639	Q1131L	probably benign	Het
Bach1	G	A	16: 87,719,291	R240Q	probably benign	Het
Cacna2d3	A	T	14: 28,969,365	M1K	probably null	Het
Ccdc18	G	A	5: 108,173,862		probably null	Het
Ccdc42	T	C	11: 68,594,616	F267S	probably damaging	Het
Cdh23	T	A	10: 60,337,306	Y1700F	probably damaging	Het
Cenpe	G	A	3: 135,235,202	S704N	probably benign	Het
Cenpe	A	T	3: 135,235,201	S704C	probably damaging	Het
Cfap54	A	T	10: 92,875,019	S2727T	unknown	Het
Clu	T	A	14: 65,971,832	V113D	probably damaging	Het
Cnbd2	A	G	2: 156,320,034	I98V	probably benign	Het
Copa	G	T	1: 172,091,000	R97L	probably damaging	Het
Epb41l1	C	A	2: 156,534,683		probably null	Het
Etnk1	T	A	6: 143,203,154		probably null	Het
Fnip1	A	T	11: 54,502,935	K732N	probably damaging	Het
G6pd2	A	G	5: 61,808,891	E3G	probably benign	Het
Gal3st2	A	G	1: 93,873,759	T95A	probably benign	Het
Gapvd1	A	G	2: 34,700,817	S948P	probably damaging	Het
Ggps1	A	T	13: 14,054,165	Y8*	probably null	Het
Gria2	T	C	3: 80,706,972	E587G	probably damaging	Het
Hpse	T	C	5: 100,692,279	E324G	probably benign	Het
Il16	G	A	7: 83,646,388	T493I	probably benign	Het
Ints1	T	C	5: 139,768,462	T652A	possibly damaging	Het
Ism1	A	G	2: 139,757,279	I391V	probably damaging	Het
Katnb1	A	G	8: 95,098,384	D598G	probably damaging	Het
Kif5c	A	G	2: 49,757,429	S880G	probably benign	Het
Klra8	T	C	6: 130,125,184	N96S	probably benign	Het
Krt79	T	A	15: 101,931,441	D373V	probably damaging	Het
Lamtor4	G	A	5: 138,259,112	R92Q	probably benign	Het
Lce1d	C	A	3: 92,686,046	C20F	unknown	Het
Limk1	T	C	5: 134,672,699	T117A	probably benign	Het
Medag	A	T	5: 149,427,243	K61M	probably benign	Het
Mkrn3	T	C	7: 62,419,618	M142V	probably benign	Het
Mob3c	G	A	4: 115,831,582	R104H	probably benign	Het
Morc1	G	T	16: 48,627,070	R903L	possibly damaging	Het
Myh6	T	C	14: 54,952,292	E1099G	probably damaging	Het
Nphp3	T	G	9: 104,016,116	C434G	probably null	Het
Npr3	C	T	15: 11,905,248	C131Y	probably damaging	Het
Oacyl	C	A	18: 65,722,538	Y112*	probably null	Het
Oprl1	A	G	2: 181,718,381	T77A	probably damaging	Het
Osgep	A	G	14: 50,924,708	V24A	probably damaging	Het
Otx2	T	A	14: 48,658,797	K260M	probably damaging	Het
Phldb1	A	G	9: 44,694,408	V375A	probably damaging	Het
Pip5k1b	C	T	19: 24,359,935		probably null	Het
Psmd3	G	A	11: 98,682,766	D13N	probably benign	Het
Ptprc	G	A	1: 138,064,553	H1140Y	probably damaging	Het
Ranbp3l	A	T	15: 9,062,984	H291L	probably damaging	Het
Rasa4	T	A	5: 136,101,363	D324E	probably damaging	Het
Rilpl1	T	A	5: 124,503,692		silent	Het
Rin2	A	C	2: 145,883,475	D794A	probably damaging	Het
Ripk1	A	G	13: 34,030,062	I522M	probably damaging	Het
Rnf31	T	C	14: 55,592,551	Y143H	probably benign	Het
Rp1	T	G	1: 4,042,068	I1187L	unknown	Het
Rps6ka5	G	A	12: 100,619,537	H166Y	probably damaging	Het
Rrm1	T	C	7: 102,460,334	V455A	probably damaging	Het
Runx2	G	A	17: 44,814,192	P80L	probably damaging	Het
Scn5a	T	G	9: 119,485,930	E1904A	probably damaging	Het
Sec16a	G	T	2: 26,436,002	S240*	probably null	Het
Slc22a8	C	T	19: 8,605,417	T154I	probably benign	Het
Slc25a16	T	A	10: 62,937,454	V156E	possibly damaging	Het
Slc28a3	A	T	13: 58,610,804	S2T	probably benign	Het
Srd5a3	G	A	5: 76,149,866	V48I	probably benign	Het
Srebf1	A	C	11: 60,200,526	H1025Q	probably damaging	Het
Stard9	A	G	2: 120,697,191	K1310E	probably benign	Het
Swt1	A	G	1: 151,370,630	V848A	possibly damaging	Het
Tanc2	A	T	11: 105,840,699	T434S	possibly damaging	Het
Tcf20	G	A	15: 82,854,682	T856I	probably benign	Het
Tcf7l2	T	C	19: 55,894,733		probably null	Het
Tmem246	A	T	4: 49,586,325	M281K	probably benign	Het
Trim45	A	G	3: 100,931,879		probably benign	Het
Tsen2	T	A	6: 115,547,972	M44K	possibly damaging	Het
Ttc21a	T	A	9: 119,958,073	C715*	probably null	Het
Vmn2r102	G	A	17: 19,694,194	V674I	probably damaging	Het
Zfp87	A	G	13: 67,517,054	S430P	probably damaging	Het

Other mutations in Pdcd11

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00646:Pdcd11	APN	19	47117328	missense	possibly damaging	0.83
IGL00656:Pdcd11	APN	19	47098170	missense	probably damaging	1.00
IGL00754:Pdcd11	APN	19	47103782	missense	possibly damaging	0.86
IGL00907:Pdcd11	APN	19	47107564	missense	probably benign	0.16
IGL00987:Pdcd11	APN	19	47114550	intron	probably benign
IGL01346:Pdcd11	APN	19	47109614	missense	probably benign	0.03
IGL01529:Pdcd11	APN	19	47109629	missense	probably benign	0.01
IGL01670:Pdcd11	APN	19	47106304	missense	probably damaging	0.98
IGL01917:Pdcd11	APN	19	47101165	missense	possibly damaging	0.92
IGL02096:Pdcd11	APN	19	47106421	missense	probably benign	0.10
IGL02300:Pdcd11	APN	19	47126942	missense	probably benign
IGL02515:Pdcd11	APN	19	47125077	missense	probably damaging	1.00
IGL02886:Pdcd11	APN	19	47113625	missense	possibly damaging	0.95
IGL03158:Pdcd11	APN	19	47128061	missense	possibly damaging	0.91
R0100:Pdcd11	UTSW	19	47102666	missense	probably benign	0.00
R0100:Pdcd11	UTSW	19	47102666	missense	probably benign	0.00
R0128:Pdcd11	UTSW	19	47119862	missense	probably benign	0.15
R0139:Pdcd11	UTSW	19	47110959	critical splice acceptor site	probably null
R0227:Pdcd11	UTSW	19	47113437	intron	probably benign
R0316:Pdcd11	UTSW	19	47113172	missense	probably damaging	0.97
R0480:Pdcd11	UTSW	19	47125037	intron	probably benign
R0577:Pdcd11	UTSW	19	47098832	missense	probably benign	0.01
R0725:Pdcd11	UTSW	19	47127291	missense	probably benign	0.17
R1344:Pdcd11	UTSW	19	47130077	missense	probably damaging	1.00
R1418:Pdcd11	UTSW	19	47130077	missense	probably damaging	1.00
R1856:Pdcd11	UTSW	19	47098187	missense	probably benign	0.00
R2146:Pdcd11	UTSW	19	47104752	missense	probably benign	0.00
R2147:Pdcd11	UTSW	19	47104752	missense	probably benign	0.00
R2447:Pdcd11	UTSW	19	47114556	missense	probably benign	0.01
R2916:Pdcd11	UTSW	19	47113437	intron	probably benign
R3177:Pdcd11	UTSW	19	47113264	missense	probably damaging	1.00
R3277:Pdcd11	UTSW	19	47113264	missense	probably damaging	1.00
R3712:Pdcd11	UTSW	19	47127245	intron	probably benign
R4495:Pdcd11	UTSW	19	47111006	missense	probably benign
R4697:Pdcd11	UTSW	19	47126347	missense	possibly damaging	0.83
R4941:Pdcd11	UTSW	19	47119886	missense	probably damaging	1.00
R4953:Pdcd11	UTSW	19	47127965	missense	probably benign	0.04
R5048:Pdcd11	UTSW	19	47107115	missense	probably benign
R5049:Pdcd11	UTSW	19	47107115	missense	probably benign
R5103:Pdcd11	UTSW	19	47124454	missense	probably benign	0.00
R5107:Pdcd11	UTSW	19	47106454	missense	probably damaging	1.00
R5139:Pdcd11	UTSW	19	47107115	missense	probably benign
R5261:Pdcd11	UTSW	19	47113537	missense	probably benign
R5302:Pdcd11	UTSW	19	47107644	missense	probably damaging	1.00
R5592:Pdcd11	UTSW	19	47102725	missense	probably benign
R5769:Pdcd11	UTSW	19	47102637	missense	possibly damaging	0.92
R5791:Pdcd11	UTSW	19	47110991	missense	possibly damaging	0.65
R5809:Pdcd11	UTSW	19	47093808	missense	probably benign	0.01
R5899:Pdcd11	UTSW	19	47104759	missense	possibly damaging	0.93
R5901:Pdcd11	UTSW	19	47128332	missense	possibly damaging	0.76
R5947:Pdcd11	UTSW	19	47129263	missense	probably benign	0.20
R6177:Pdcd11	UTSW	19	47120283	missense	probably damaging	1.00
R6489:Pdcd11	UTSW	19	47109752	missense	probably damaging	1.00
R6575:Pdcd11	UTSW	19	47109678	missense	probably damaging	0.98
R6578:Pdcd11	UTSW	19	47111081	missense	probably benign	0.11
R7015:Pdcd11	UTSW	19	47098226	missense	probably benign	0.00
R7060:Pdcd11	UTSW	19	47110979	missense	probably benign	0.30
R7260:Pdcd11	UTSW	19	47129234	missense	possibly damaging	0.62
R7392:Pdcd11	UTSW	19	47127997	missense	probably damaging	1.00
R7601:Pdcd11	UTSW	19	47106369	missense	not run
R7759:Pdcd11	UTSW	19	47113198	missense	possibly damaging	0.88
R7760:Pdcd11	UTSW	19	47113198	missense	possibly damaging	0.88
R7785:Pdcd11	UTSW	19	47104686	missense	probably benign	0.00
R7793:Pdcd11	UTSW	19	47106432	missense	probably benign	0.00
R7810:Pdcd11	UTSW	19	47098220	missense	possibly damaging	0.81
R7863:Pdcd11	UTSW	19	47096964	missense	probably damaging	1.00
R7950:Pdcd11	UTSW	19	47113437	intron	probably benign
R8062:Pdcd11	UTSW	19	47130713	missense	possibly damaging	0.50
R8184:Pdcd11	UTSW	19	47113352	nonsense	probably null
R8278:Pdcd11	UTSW	19	47106297	missense	probably damaging	1.00
R8404:Pdcd11	UTSW	19	47104792	missense	probably damaging	0.98
R8508:Pdcd11	UTSW	19	47119806	missense	probably damaging	1.00
R8525:Pdcd11	UTSW	19	47092898	missense	possibly damaging	0.52
R8787:Pdcd11	UTSW	19	47108580	missense	probably damaging	1.00
R9019:Pdcd11	UTSW	19	47113219	missense	probably damaging	1.00
R9534:Pdcd11	UTSW	19	47120279	missense	probably benign	0.01
R9660:Pdcd11	UTSW	19	47093752	missense	possibly damaging	0.67
R9712:Pdcd11	UTSW	19	47129302	missense	probably damaging	0.98
RF010:Pdcd11	UTSW	19	47113451	frame shift	probably null
RF027:Pdcd11	UTSW	19	47113449	frame shift	probably null
RF039:Pdcd11	UTSW	19	47113455	frame shift	probably null
RF061:Pdcd11	UTSW	19	47113445	frame shift	probably null
X0065:Pdcd11	UTSW	19	47096896	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GTCTGTCCTGACACCTCTGTAAG -3'
(R):5'- TTGAGGGTAAGGCAGACACC -3'

Sequencing Primer
(F):5'- ATTTCTGAGTTCCAGGACAGCCAG -3'
(R):5'- GACACCCTGCCCCACAC -3'

Posted On

2019-05-13