Incidental Mutation 'R5261:Pdcd11'
| ID |
401473 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pdcd11
|
| Ensembl Gene |
ENSMUSG00000025047 |
| Gene Name |
programmed cell death 11 |
| Synonyms |
ALG-4, 1110021I22Rik |
| MMRRC Submission |
042830-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.967)
|
| Stock # |
R5261 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
47079183-47119585 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 47101976 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 1054
(I1054V)
|
| 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: I1054V
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000072008
Gene: ENSMUSG00000025047
AA Change: I1054V
| 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 |
0.0898 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.5%
- 20x: 93.1%
|
| Validation Efficiency |
96% (64/67) |
| 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: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 6820408C15Rik |
C |
G |
2: 152,282,777 (GRCm39) |
P211A |
probably damaging |
Het |
| Ambra1 |
G |
A |
2: 91,715,951 (GRCm39) |
V761M |
probably damaging |
Het |
| Amfr |
T |
A |
8: 94,702,798 (GRCm39) |
|
probably null |
Het |
| Asphd1 |
C |
A |
7: 126,545,287 (GRCm39) |
A357S |
probably benign |
Het |
| Brd3 |
C |
A |
2: 27,353,931 (GRCm39) |
Q60H |
probably damaging |
Het |
| Cd96 |
T |
A |
16: 45,890,016 (GRCm39) |
M336L |
probably benign |
Het |
| Cep152 |
T |
A |
2: 125,406,125 (GRCm39) |
H1469L |
probably benign |
Het |
| Coro1a |
G |
T |
7: 126,299,816 (GRCm39) |
|
probably null |
Het |
| D630045J12Rik |
A |
T |
6: 38,171,555 (GRCm39) |
L871Q |
probably benign |
Het |
| Depdc5 |
C |
T |
5: 33,095,635 (GRCm39) |
P824L |
probably damaging |
Het |
| Enpep |
T |
G |
3: 129,099,075 (GRCm39) |
D467A |
probably damaging |
Het |
| Extl2 |
G |
A |
3: 115,821,013 (GRCm39) |
A273T |
probably benign |
Het |
| Foxi3 |
T |
A |
6: 70,937,500 (GRCm39) |
F218Y |
probably damaging |
Het |
| Golga2 |
A |
G |
2: 32,194,166 (GRCm39) |
M521V |
probably benign |
Het |
| Gpr142 |
T |
A |
11: 114,695,168 (GRCm39) |
N44K |
probably damaging |
Het |
| Gtf2ird2 |
A |
G |
5: 134,245,061 (GRCm39) |
I440V |
probably benign |
Het |
| Gucy1b2 |
T |
A |
14: 62,642,028 (GRCm39) |
K698I |
probably damaging |
Het |
| Hspa1b |
T |
C |
17: 35,177,983 (GRCm39) |
M1V |
probably null |
Het |
| Ints9 |
T |
A |
14: 65,245,521 (GRCm39) |
Y260N |
probably benign |
Het |
| Khdc3 |
T |
G |
9: 73,010,768 (GRCm39) |
V182G |
possibly damaging |
Het |
| Ky |
A |
G |
9: 102,414,798 (GRCm39) |
|
probably null |
Het |
| Map2k1 |
T |
A |
9: 64,098,843 (GRCm39) |
I263F |
probably damaging |
Het |
| Or13a18 |
A |
C |
7: 140,190,576 (GRCm39) |
I166L |
probably benign |
Het |
| Or2t47 |
T |
C |
11: 58,442,877 (GRCm39) |
S63G |
probably benign |
Het |
| Or5ak25 |
A |
G |
2: 85,269,241 (GRCm39) |
V87A |
probably benign |
Het |
| Otogl |
T |
A |
10: 107,613,453 (GRCm39) |
H2004L |
probably benign |
Het |
| Palmd |
T |
C |
3: 116,717,009 (GRCm39) |
H496R |
probably benign |
Het |
| Papolb |
C |
G |
5: 142,515,409 (GRCm39) |
R78P |
possibly damaging |
Het |
| Pcdh10 |
G |
A |
3: 45,336,247 (GRCm39) |
G854R |
probably damaging |
Het |
| Pik3ap1 |
A |
T |
19: 41,364,545 (GRCm39) |
L58Q |
probably damaging |
Het |
| Ppp2ca |
A |
G |
11: 51,989,937 (GRCm39) |
K21R |
probably benign |
Het |
| Prmt5 |
A |
C |
14: 54,745,373 (GRCm39) |
I598S |
probably damaging |
Het |
| Pycr1 |
T |
A |
11: 120,532,050 (GRCm39) |
I239F |
probably damaging |
Het |
| R3hdm2 |
C |
T |
10: 127,334,285 (GRCm39) |
R896C |
probably damaging |
Het |
| Rev3l |
C |
T |
10: 39,722,725 (GRCm39) |
P699S |
probably damaging |
Het |
| Samd1 |
CGAGGAGGAGGAGGAGGAGGA |
CGAGGAGGAGGAGGAGGA |
8: 84,725,625 (GRCm39) |
|
probably benign |
Het |
| Sel1l |
A |
T |
12: 91,791,658 (GRCm39) |
M351K |
possibly damaging |
Het |
| Sesn2 |
A |
G |
4: 132,226,617 (GRCm39) |
L159P |
probably damaging |
Het |
| Slc35f4 |
T |
A |
14: 49,540,946 (GRCm39) |
|
probably benign |
Het |
| Slc3a1 |
C |
A |
17: 85,359,403 (GRCm39) |
N409K |
probably damaging |
Het |
| Slc45a2 |
C |
T |
15: 11,027,871 (GRCm39) |
T480I |
probably damaging |
Het |
| Slco1c1 |
T |
C |
6: 141,492,502 (GRCm39) |
F246S |
probably damaging |
Het |
| Socs2 |
T |
G |
10: 95,228,681 (GRCm39) |
I190L |
unknown |
Het |
| Srsf1 |
T |
A |
11: 87,938,684 (GRCm39) |
I7N |
possibly damaging |
Het |
| Stox1 |
T |
A |
10: 62,503,620 (GRCm39) |
H145L |
probably damaging |
Het |
| Trap1 |
A |
T |
16: 3,874,286 (GRCm39) |
I243N |
probably damaging |
Het |
| Trav7-3 |
T |
C |
14: 53,681,207 (GRCm39) |
I83T |
probably benign |
Het |
| Trmt9b |
T |
C |
8: 36,979,078 (GRCm39) |
I227T |
probably benign |
Het |
| Tuft1 |
A |
T |
3: 94,546,712 (GRCm39) |
I42K |
possibly damaging |
Het |
| Umps |
A |
G |
16: 33,787,344 (GRCm39) |
V3A |
probably benign |
Het |
| Vim |
A |
C |
2: 13,579,643 (GRCm39) |
E134A |
probably null |
Het |
| Vmn1r28 |
C |
A |
6: 58,242,524 (GRCm39) |
H122Q |
probably benign |
Het |
| Vps51 |
T |
G |
19: 6,121,063 (GRCm39) |
E283D |
probably benign |
Het |
| Vsig10l |
T |
A |
7: 43,120,274 (GRCm39) |
V760D |
probably damaging |
Het |
| Xrn1 |
A |
G |
9: 95,927,596 (GRCm39) |
D1460G |
probably benign |
Het |
| Zfp282 |
A |
G |
6: 47,874,824 (GRCm39) |
D343G |
probably damaging |
Het |
| Zfp35 |
A |
G |
18: 24,136,778 (GRCm39) |
H374R |
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 |
|
|
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 |
|
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'- CCAGCTTCTAAGAGGACCAG -3'
(R):5'- ATAATTGCCACAGTCCCCTC -3'
Sequencing Primer
(F):5'- CTTCTAAGAGGACCAGGATGCC -3'
(R):5'- CAAACCTCATACTTAGATGTCTTCAC -3'
|
| Posted On |
2016-07-06 |
Incidental Mutation