Incidental Mutation 'R5947:Pdcd11'
| ID |
472264 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pdcd11
|
| Ensembl Gene |
ENSMUSG00000025047 |
| Gene Name |
programmed cell death 11 |
| Synonyms |
ALG-4, 1110021I22Rik |
| MMRRC Submission |
044138-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.967)
|
| Stock # |
R5947 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
47079183-47119585 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 47117702 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Isoleucine
at position 1684
(V1684I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000072008
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000035822]
[ENSMUST00000072141]
[ENSMUST00000140512]
|
| AlphaFold |
Q6NS46 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000035822
|
| SMART Domains |
Protein: ENSMUSP00000047278
Gene: ENSMUSG00000033033
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Ca_hom_mod
|
6 |
256 |
2.3e-88 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000072141
AA Change: V1684I
PolyPhen 2
Score 0.199 (Sensitivity: 0.92; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000072008
Gene: ENSMUSG00000025047
AA Change: V1684I
| 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 |
0.0975 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 97.8%
- 20x: 93.1%
|
| Validation Efficiency |
100% (70/70) |
| 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: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb10 |
T |
C |
8: 124,694,737 (GRCm39) |
|
probably null |
Het |
| Abt1 |
T |
C |
13: 23,606,225 (GRCm39) |
E243G |
possibly damaging |
Het |
| Afap1l1 |
A |
G |
18: 61,876,771 (GRCm39) |
S361P |
probably damaging |
Het |
| Alms1 |
T |
C |
6: 85,596,694 (GRCm39) |
S507P |
probably benign |
Het |
| Atp13a3 |
A |
G |
16: 30,181,518 (GRCm39) |
V34A |
probably benign |
Het |
| Atpaf2 |
A |
T |
11: 60,296,708 (GRCm39) |
|
probably benign |
Het |
| Bbs1 |
A |
C |
19: 4,943,022 (GRCm39) |
L456R |
probably benign |
Het |
| Bri3bp |
G |
T |
5: 125,529,217 (GRCm39) |
G84* |
probably null |
Het |
| Bri3bp |
G |
C |
5: 125,529,218 (GRCm39) |
|
probably benign |
Het |
| Car10 |
A |
C |
11: 93,381,439 (GRCm39) |
H134P |
probably damaging |
Het |
| Cntrl |
A |
G |
2: 35,006,691 (GRCm39) |
E119G |
probably damaging |
Het |
| Cxcl3 |
C |
T |
5: 90,934,175 (GRCm39) |
|
probably benign |
Het |
| Dppa4 |
T |
C |
16: 48,111,471 (GRCm39) |
V100A |
possibly damaging |
Het |
| Elmo1 |
G |
T |
13: 20,474,553 (GRCm39) |
E105* |
probably null |
Het |
| Esrp2 |
T |
G |
8: 106,859,565 (GRCm39) |
|
probably benign |
Het |
| Exoc3l4 |
A |
G |
12: 111,388,835 (GRCm39) |
K108R |
possibly damaging |
Het |
| Exph5 |
G |
A |
9: 53,286,522 (GRCm39) |
R1201H |
probably benign |
Het |
| Galnt3 |
A |
C |
2: 65,914,500 (GRCm39) |
|
probably benign |
Het |
| Gm14486 |
C |
T |
2: 30,548,813 (GRCm39) |
|
noncoding transcript |
Het |
| Gna12 |
T |
A |
5: 140,746,717 (GRCm39) |
I243F |
probably damaging |
Het |
| Itga5 |
A |
T |
15: 103,265,212 (GRCm39) |
W232R |
probably damaging |
Het |
| Lekr1 |
A |
T |
3: 65,680,498 (GRCm39) |
|
noncoding transcript |
Het |
| Lrp1 |
C |
T |
10: 127,425,423 (GRCm39) |
|
probably null |
Het |
| Mast4 |
T |
C |
13: 102,872,148 (GRCm39) |
M2215V |
probably benign |
Het |
| Mfap5 |
T |
C |
6: 122,502,945 (GRCm39) |
Y52H |
probably damaging |
Het |
| Mrps31 |
A |
G |
8: 22,904,991 (GRCm39) |
K127E |
possibly damaging |
Het |
| Mto1 |
C |
T |
9: 78,368,311 (GRCm39) |
T485M |
probably damaging |
Het |
| Mybbp1a |
G |
A |
11: 72,333,257 (GRCm39) |
C107Y |
probably damaging |
Het |
| Nedd4 |
G |
A |
9: 72,638,132 (GRCm39) |
|
probably benign |
Het |
| Nek2 |
A |
G |
1: 191,561,597 (GRCm39) |
E360G |
probably benign |
Het |
| Notch1 |
T |
A |
2: 26,352,540 (GRCm39) |
|
probably benign |
Het |
| Nubp1 |
T |
C |
16: 10,238,050 (GRCm39) |
|
probably benign |
Het |
| Pcdhb1 |
G |
A |
18: 37,399,726 (GRCm39) |
R559H |
possibly damaging |
Het |
| Pggt1b |
G |
T |
18: 46,382,007 (GRCm39) |
N258K |
probably benign |
Het |
| Pou6f1 |
C |
T |
15: 100,484,001 (GRCm39) |
V166M |
possibly damaging |
Het |
| Pprc1 |
A |
G |
19: 46,052,111 (GRCm39) |
D546G |
possibly damaging |
Het |
| Psapl1 |
T |
C |
5: 36,361,651 (GRCm39) |
V81A |
probably benign |
Het |
| Rin2 |
T |
A |
2: 145,686,863 (GRCm39) |
|
probably benign |
Het |
| Rpf1 |
A |
G |
3: 146,212,299 (GRCm39) |
F347S |
probably damaging |
Het |
| Rrp12 |
A |
T |
19: 41,859,247 (GRCm39) |
|
probably null |
Het |
| Ryr1 |
A |
T |
7: 28,771,349 (GRCm39) |
L2557Q |
probably null |
Het |
| Slc1a7 |
T |
C |
4: 107,867,497 (GRCm39) |
|
probably benign |
Het |
| Slc35e2 |
T |
A |
4: 155,696,171 (GRCm39) |
M186K |
possibly damaging |
Het |
| Slc49a4 |
T |
C |
16: 35,550,676 (GRCm39) |
T308A |
probably benign |
Het |
| Snx6 |
G |
T |
12: 54,817,549 (GRCm39) |
S116* |
probably null |
Het |
| Sptan1 |
T |
C |
2: 29,884,379 (GRCm39) |
|
probably null |
Het |
| Sucla2 |
T |
A |
14: 73,830,109 (GRCm39) |
M382K |
probably damaging |
Het |
| Susd5 |
T |
C |
9: 113,886,659 (GRCm39) |
L16P |
possibly damaging |
Het |
| Tmem260 |
G |
A |
14: 48,724,258 (GRCm39) |
A369T |
possibly damaging |
Het |
| Tmprss6 |
A |
G |
15: 78,336,722 (GRCm39) |
Y393H |
probably damaging |
Het |
| Tnrc6c |
A |
T |
11: 117,613,345 (GRCm39) |
Q501L |
probably damaging |
Het |
| Trim17 |
A |
G |
11: 58,856,369 (GRCm39) |
Y142C |
probably damaging |
Het |
| Trim65 |
T |
C |
11: 116,019,108 (GRCm39) |
R144G |
probably damaging |
Het |
| Trpm1 |
A |
G |
7: 63,873,547 (GRCm39) |
T601A |
probably benign |
Het |
| Ttn |
A |
T |
2: 76,564,688 (GRCm39) |
V28483E |
probably damaging |
Het |
| Ube2l3 |
T |
C |
16: 17,019,340 (GRCm39) |
|
probably null |
Het |
| Ube2l3 |
G |
T |
16: 17,019,336 (GRCm39) |
|
probably benign |
Het |
| Yme1l1 |
T |
C |
2: 23,085,318 (GRCm39) |
|
probably benign |
Het |
| Zfat |
A |
G |
15: 68,051,806 (GRCm39) |
S663P |
probably benign |
Het |
| Zfp647 |
G |
A |
15: 76,796,285 (GRCm39) |
P125L |
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 |
|
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'- TCTCTGTACTTACAAGTGGCCG -3'
(R):5'- CCTGAGGCTGAGATGTGATAG -3'
Sequencing Primer
(F):5'- GAAATAGTTCTCGGGCATCCAGC -3'
(R):5'- GGCTGAGATGTGATAGCATGG -3'
|
| Posted On |
2017-03-31 |
Incidental Mutation