Mutagenetix > Incidental Mutation

Incidental Mutation 'R7759:Pdcd11'

597772

Institutional Source

Beutler Lab

Gene Symbol

Pdcd11

Ensembl Gene

ENSMUSG00000025047

Gene Name

programmed cell death 11

Synonyms

ALG-4, 1110021I22Rik

MMRRC Submission

Accession Numbers

Essential gene?

Probably essential (E-score: 0.970) question?

Stock #

R7759 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

47090766-47131143 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 47113198 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Methionine at position 941 (V941M)

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: V941M

PolyPhen 2 Score 0.878 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000072008
Gene: ENSMUSG00000025047
AA Change: V941M

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

0.1712

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930562C15Rik	G	T	16: 4,864,650	G215V	probably benign	Het
Adamts1	C	A	16: 85,797,795	G652C	probably damaging	Het
Adck1	G	A	12: 88,402,117	A122T	possibly damaging	Het
Akap1	A	C	11: 88,845,833	M34R	probably damaging	Het
Apc2	C	T	10: 80,311,196	R695C	probably damaging	Het
Apon	T	A	10: 128,254,515	W21R	probably benign	Het
Arhgef16	T	C	4: 154,286,975	T254A	probably benign	Het
Arid5b	T	A	10: 68,097,802	S757C	probably damaging	Het
B020004C17Rik	A	C	14: 57,016,785	I122L	possibly damaging	Het
Bckdhb	T	G	9: 84,010,326	V270G	probably damaging	Het
Cacna1d	A	G	14: 30,099,188	Y1146H	probably benign	Het
Carmil2	A	G	8: 105,697,036	D1214G	possibly damaging	Het
Ccdc142	T	C	6: 83,107,931	V636A	probably benign	Het
Chd9	T	C	8: 90,977,550		probably null	Het
Csmd3	A	G	15: 47,698,173	S1336P		Het
Cubn	A	G	2: 13,348,150	Y1926H	probably damaging	Het
Ddx58	C	A	4: 40,225,104	A298S	probably damaging	Het
Dock4	A	T	12: 40,817,736	D1437V	probably damaging	Het
Eme1	A	T	11: 94,645,840	Y504*	probably null	Het
Enah	G	A	1: 181,918,444	A687V	unknown	Het
Endou	A	C	15: 97,713,866	V339G	probably damaging	Het
Ephb6	G	A	6: 41,614,605	R232H	probably benign	Het
Ephx2	G	A	14: 66,089,519	A409V	possibly damaging	Het
Esd	T	A	14: 74,745,567	C219*	probably null	Het
Fscb	A	T	12: 64,474,092	M200K	probably benign	Het
Gabra6	A	T	11: 42,317,681	V108D	probably damaging	Het
Gm11555	A	G	11: 99,649,742	V137A	unknown	Het
Gpld1	A	G	13: 24,962,400	D209G	probably damaging	Het
Ikzf1	T	A	11: 11,769,256	I408N	probably damaging	Het
Itgb4	A	G	11: 116,003,710	R1364G	possibly damaging	Het
Kif26b	A	C	1: 178,678,944	K195T	probably damaging	Het
Mfsd12	T	C	10: 81,363,593	W440R	probably benign	Het
Mtrr	C	T	13: 68,570,027	E373K	probably damaging	Het
Mug2	T	A	6: 122,081,358	V1293E	probably damaging	Het
Myof	C	A	19: 37,939,898	A1068S	probably benign	Het
Ncam2	A	G	16: 81,615,784	D720G	probably damaging	Het
Nova2	G	T	7: 18,958,251	G435V		Het
Oacyl	T	A	18: 65,710,560	D109E	probably damaging	Het
Olfr1393	A	T	11: 49,280,636	M163L	probably benign	Het
Olfr684	G	A	7: 105,157,025	S219F	probably damaging	Het
Pdzd8	C	A	19: 59,299,926	R1014L	probably damaging	Het
Ppm1h	T	G	10: 122,904,113	D364E	probably benign	Het
Rp1	T	C	1: 4,344,884	N2002D	probably benign	Het
Sall1	C	T	8: 89,042,351		probably null	Het
Scn10a	C	T	9: 119,648,132	W728*	probably null	Het
Setdb2	G	T	14: 59,419,364	T168K	probably damaging	Het
Sgms1	T	C	19: 32,159,876	I97V	probably benign	Het
Slc8a3	A	T	12: 81,314,551	M498K	probably benign	Het
Smpd4	A	T	16: 17,638,633	E362D	probably damaging	Het
Ssc5d	A	T	7: 4,937,530	K881*	probably null	Het
Strn4	A	G	7: 16,830,384	E313G	probably damaging	Het
Tas2r113	A	T	6: 132,893,927	N306I	possibly damaging	Het
Tdrd6	G	T	17: 43,624,839	R1773S	probably benign	Het
Thbs2	T	C	17: 14,677,059	E729G	probably damaging	Het
Tnfrsf23	G	A	7: 143,670,835	T135I	probably damaging	Het
Tollip	A	G	7: 141,884,539	M218T	probably benign	Het
Tyk2	A	T	9: 21,120,258		probably null	Het
Ubr2	G	A	17: 46,986,048	R269C	probably damaging	Het
Uggt1	A	T	1: 36,146,725	M1459K	possibly damaging	Het
Upf1	A	G	8: 70,334,080	V929A	probably benign	Het
Usp48	T	C	4: 137,594,452	S24P	probably benign	Het
Vmn1r214	G	A	13: 23,034,461	E42K	not run	Het
Vmn1r83	G	T	7: 12,321,433	D232E	probably benign	Het
Vmn2r25	C	T	6: 123,823,380	V668I	probably damaging	Het
Vmn2r6	A	G	3: 64,556,570	I281T	probably damaging	Het
Ywhag	A	T	5: 135,911,189	Y184N	probably damaging	Het
Zdbf2	A	C	1: 63,308,376	E1971D	possibly damaging	Het
Zfp568	G	A	7: 30,023,414	A595T	possibly damaging	Het
Zfy2	T	C	Y: 2,117,083	D248G	probably benign	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
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
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'- CGAAATCTGTAGAAGTATTCTTTGGG -3'
(R):5'- GAACTGGCATCCTGGTCCTC -3'

Sequencing Primer
(F):5'- AAGTATTCTTTGGGTAAGGTGTACAG -3'
(R):5'- GGCATCCTGGTCCTCTTAGAAG -3'

Posted On

2019-11-26