Mutagenetix > Incidental Mutations

Incidental Mutation 'R3277:Pdcd11'

258293

Institutional Source

Beutler Lab

Gene Symbol

Pdcd11

Ensembl Gene

ENSMUSG00000025047

Gene Name

programmed cell death 11

Synonyms

ALG-4, 1110021I22Rik

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.969) question?

Stock #

R3277 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

47090766-47131143 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 47113264 bp

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 963 (F963L)

Ref Sequence

ENSEMBL: ENSMUSP00000072008 (fasta)

Gene Model

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

AlphaFold

Q6NS46

Predicted Effect

probably damaging
Transcript: ENSMUST00000072141
AA Change: F963L

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000072008
Gene: ENSMUSG00000025047
AA Change: F963L

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: 99.2%
3x: 98.5%
10x: 97.1%
20x: 94.6%

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: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921509C19Rik	T	C	2: 151,472,100	R553G	possibly damaging	Het
Adarb2	A	G	13: 8,752,627	N646S	probably damaging	Het
Adcy8	C	T	15: 64,699,159	G1242S	probably benign	Het
Ano9	T	A	7: 141,104,124	T543S	probably damaging	Het
Btnl10	A	G	11: 58,922,390	K282E	probably benign	Het
Btnl9	T	C	11: 49,169,676	D330G	probably damaging	Het
Ccdc178	G	T	18: 22,067,652	A416E	possibly damaging	Het
Cdx2	A	T	5: 147,303,192	S225T	probably benign	Het
Clca4b	T	C	3: 144,911,359	I843M	probably benign	Het
Cntn4	G	A	6: 106,437,964		probably null	Het
Cyp4f18	T	C	8: 71,993,200	D317G	possibly damaging	Het
Dennd4a	G	T	9: 64,888,993	R767L	probably damaging	Het
Dgkb	G	A	12: 38,084,217	V41M	probably damaging	Het
Duox1	T	C	2: 122,340,116	Y1206H	probably damaging	Het
Dync1i1	T	C	6: 5,972,211		probably null	Het
Fbxw2	T	C	2: 34,822,750	T100A	probably benign	Het
Fcgbp	C	A	7: 28,091,661	H782Q	probably damaging	Het
Flg2	A	T	3: 93,214,888	Q1455L	unknown	Het
Frrs1	T	C	3: 116,899,224	F49S	probably damaging	Het
Gli3	A	T	13: 15,725,982	Q1318L	probably benign	Het
Gm5592	A	G	7: 41,288,380	E362G	probably benign	Het
Gm7104	A	T	12: 88,285,728		noncoding transcript	Het
Gpatch2l	A	G	12: 86,244,315	T91A	possibly damaging	Het
Hacd4	T	C	4: 88,437,510	H46R	probably damaging	Het
Herc2	T	C	7: 56,153,428	V2175A	probably benign	Het
Hey1	T	C	3: 8,664,891	S169G	probably benign	Het
Hivep2	C	A	10: 14,128,969	T437K	probably benign	Het
Hlf	T	C	11: 90,345,835	K199E	probably damaging	Het
Hpgd	C	A	8: 56,298,413	A92E	probably damaging	Het
Hsp90aa1	T	A	12: 110,695,680	M1L	possibly damaging	Het
Hsp90aa1	C	A	12: 110,695,681		probably null	Het
Itgad	C	A	7: 128,190,981	H651N	possibly damaging	Het
Itgav	A	G	2: 83,776,542	D409G	probably damaging	Het
Kif2a	A	G	13: 106,976,756	I455T	probably damaging	Het
Klk14	G	A	7: 43,692,077	C51Y	probably damaging	Het
Lamc3	G	T	2: 31,908,625	G448C	probably damaging	Het
Ltbp1	G	A	17: 75,276,480	G425D	possibly damaging	Het
Ltbp1	T	A	17: 75,359,278		probably null	Het
Mag	C	T	7: 30,901,648		probably null	Het
Mdh1b	G	A	1: 63,711,531	T426M	possibly damaging	Het
Nr1h4	G	A	10: 89,478,788	T282I	possibly damaging	Het
Nsf	C	T	11: 103,930,752	E26K	possibly damaging	Het
Olfr1231	C	T	2: 89,303,218	V125M	possibly damaging	Het
Olfr1412	A	G	1: 92,588,813	N161S	probably benign	Het
Olfr552	T	C	7: 102,604,576	V74A	possibly damaging	Het
Padi6	A	G	4: 140,735,389	L307P	probably damaging	Het
Parp9	T	C	16: 35,948,208	S20P	probably damaging	Het
Pwp1	C	T	10: 85,882,079	L294F	probably benign	Het
Radil	A	G	5: 142,506,856	L339P	probably damaging	Het
Raver1	G	A	9: 21,079,277	P316S	possibly damaging	Het
Rell1	A	G	5: 63,926,987		probably null	Het
Rxrg	A	G	1: 167,635,700	D257G	possibly damaging	Het
Sema4c	C	T	1: 36,549,879	R722H	possibly damaging	Het
Sgk1	C	T	10: 21,996,601	R171W	probably damaging	Het
Spata7	A	G	12: 98,637,598	N75D	possibly damaging	Het
Ttc23l	A	G	15: 10,547,232	F99L	possibly damaging	Het
Unc13a	A	C	8: 71,629,695	C1642G	probably benign	Het
Usp36	C	T	11: 118,276,759		probably null	Het
Wrn	A	G	8: 33,317,554	M292T	probably damaging	Het
Zfp423	A	G	8: 87,782,331	Y462H	probably damaging	Het
Zscan5b	T	A	7: 6,231,346	Y124N	possibly damaging	Het
Zswim9	T	C	7: 13,277,270	T51A	possibly 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
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
R7009:Pdcd11	UTSW	19	47113142	missense	probably benign	0.17
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
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'- TTCAAATGAAACGCATGGGATG -3'
(R):5'- TTTGTCCCCAATAGCCAGGC -3'

Sequencing Primer
(F):5'- GAGAAGTGTTGCAAATTTTTCAGG -3'
(R):5'- GCTATGCCTTTTCTTAGACTTCACAG -3'

Posted On

2015-01-23