Mutagenetix > Incidental Mutation

Incidental Mutation 'R9534:Pdcd11'

719632

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: 0.967) question?

Stock #

R9534 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

47079183-47119585 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 47108718 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Valine at position 1245 (M1245V)

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: M1245V

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000072008
Gene: ENSMUSG00000025047
AA Change: M1245V

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: 99.9%
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: 41 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actn3	C	A	19: 4,913,477 (GRCm39)	Q651H	probably benign	Het
Ahnak	G	T	19: 8,980,976 (GRCm39)	M753I	probably benign	Het
Ap1ar	T	C	3: 127,602,364 (GRCm39)	T225A	probably damaging	Het
Asic1	T	G	15: 99,594,397 (GRCm39)	I281S	probably benign	Het
Bard1	C	T	1: 71,114,189 (GRCm39)	C264Y	probably benign	Het
Bltp1	A	G	3: 37,052,419 (GRCm39)	T3040A	probably benign	Het
Bnip3l	G	A	14: 67,246,214 (GRCm39)	P7L	possibly damaging	Het
Cacna1e	T	C	1: 154,320,693 (GRCm39)	H1354R	possibly damaging	Het
Cc2d2b	G	T	19: 40,799,068 (GRCm39)	E860*	probably null	Het
Cenpn	T	A	8: 117,661,474 (GRCm39)	L191*	probably null	Het
Cep68	T	C	11: 20,190,686 (GRCm39)	R109G	probably benign	Het
Col9a1	T	A	1: 24,224,250 (GRCm39)	V144E	unknown	Het
Coro2a	T	C	4: 46,548,884 (GRCm39)	T137A	probably benign	Het
Ecpas	A	G	4: 58,807,867 (GRCm39)	V1667A	probably benign	Het
Eml6	T	C	11: 29,734,155 (GRCm39)	D1195G	possibly damaging	Het
Hspg2	G	A	4: 137,268,072 (GRCm39)	V2130I	probably benign	Het
Ifi214	A	T	1: 173,354,092 (GRCm39)	S193T	probably benign	Het
Iqsec3	C	A	6: 121,367,077 (GRCm39)	V724L	possibly damaging	Het
Lamb2	G	T	9: 108,365,830 (GRCm39)	G1445W	probably damaging	Het
Mis18bp1	A	T	12: 65,205,234 (GRCm39)	S313T	possibly damaging	Het
Or1f19	A	T	16: 3,410,937 (GRCm39)	I226F	probably benign	Het
Or4a68	A	C	2: 89,269,999 (GRCm39)	V208G	probably benign	Het
Or5b104	T	C	19: 13,072,121 (GRCm39)	E124G	probably damaging	Het
Pcdh9	C	T	14: 94,123,656 (GRCm39)	C838Y	probably damaging	Het
Ppp3r1	A	G	11: 17,132,123 (GRCm39)	Y7C	probably benign	Het
Rdx	C	T	9: 51,984,482 (GRCm39)	R330*	probably null	Het
Scaf11	T	G	15: 96,318,209 (GRCm39)	N452H	possibly damaging	Het
Scube1	A	G	15: 83,606,102 (GRCm39)	Y57H	probably damaging	Het
Slc35d3	T	C	10: 19,725,116 (GRCm39)	T247A	probably damaging	Het
Slfn5	A	T	11: 82,849,523 (GRCm39)	M341L	probably benign	Het
Smc2	T	A	4: 52,462,870 (GRCm39)	M620K	probably damaging	Het
Smg5	T	A	3: 88,252,759 (GRCm39)	S182T	probably benign	Het
Tdrd6	G	T	17: 43,936,510 (GRCm39)	L1513I	probably benign	Het
Tet2	A	T	3: 133,173,689 (GRCm39)	Y1524*	probably null	Het
Tex15	A	G	8: 34,060,999 (GRCm39)	N143S	probably benign	Het
Urb1	A	G	16: 90,583,096 (GRCm39)	I591T	possibly damaging	Het
Usp21	A	G	1: 171,110,942 (GRCm39)	S435P	probably benign	Het
Usp24	T	C	4: 106,264,312 (GRCm39)	Y1748H	probably damaging	Het
Vmn2r54	C	A	7: 12,366,093 (GRCm39)	K280N	probably benign	Het
Zan	G	T	5: 137,407,945 (GRCm39)	C3616*	probably null	Het
Zfp804b	T	C	5: 6,819,115 (GRCm39)	D1316G	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
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
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'- GGCTTGTGTGACTCTATCGCTC -3'
(R):5'- TTAGGCAAAGAAGAACTCTCTGGC -3'

Sequencing Primer
(F):5'- GTGTGACTCTATCGCTCTCTTAGG -3'
(R):5'- GAAGAACTCTCTGGCTCACCTG -3'

Posted On

2022-07-18