Incidental Mutation 'R5865:Nfkb1'
| ID |
454115 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nfkb1
|
| Ensembl Gene |
ENSMUSG00000028163 |
| Gene Name |
nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105 |
| Synonyms |
p50, p50/p105, NF-kappaB, nuclear factor kappaB p50, NF kappaB1, p50 subunit of NF kappaB, NF-kappaB p50 |
| MMRRC Submission |
044074-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5865 (G1)
|
| Quality Score |
135 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
135290416-135397308 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 135309541 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Serine
at position 518
(T518S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000128345
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029812]
[ENSMUST00000164430]
[ENSMUST00000196469]
|
| AlphaFold |
P25799 |
| PDB Structure |
STRUCTURE OF NF-KB P50 HOMODIMER BOUND TO A KB SITE [X-RAY DIFFRACTION]
IKAPPABALPHA/NF-KAPPAB COMPLEX [X-RAY DIFFRACTION]
Crystal structure of a NF-kB heterodimer bound to an IFNb-kB [X-RAY DIFFRACTION]
Crystal structure of a NF-kB heterodimer bound to the Ig/HIV-kB siti [X-RAY DIFFRACTION]
The kB DNA sequence from the HLV-LTR functions as an allosteric regulator of HIV transcription [X-RAY DIFFRACTION]
STRUCTURE OF THE NUCLEAR FACTOR KAPPA-B (NF-KB) P50 HOMODIMER [X-RAY DIFFRACTION]
CRYSTAL STRUCTURE OF NF-kB(p50)2 COMPLEXED TO A HIGH-AFFINITY RNA APTAMER [X-RAY DIFFRACTION]
Crystal stucture of WLAC mutant of dimerisation domain of NF-kB p50 transcription factor [X-RAY DIFFRACTION]
Crystal stucture of MLAV mutant of dimerisation domain of NF-kB p50 transcription factor [X-RAY DIFFRACTION]
Crystal stucture of ILAC mutant of dimerisation domain of NF-kB p50 transcription factor [X-RAY DIFFRACTION]
>> 7 additional structures at PDB <<
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000029812
AA Change: T518S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000029812
Gene: ENSMUSG00000028163
AA Change: T518S
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RHD
|
42 |
240 |
2.9e-75 |
PFAM |
|
IPT
|
247 |
348 |
1.14e-22 |
SMART |
|
low complexity region
|
368 |
414 |
N/A |
INTRINSIC |
|
ANK
|
538 |
568 |
2.27e1 |
SMART |
|
ANK
|
577 |
606 |
1.11e-2 |
SMART |
|
ANK
|
610 |
640 |
2.47e0 |
SMART |
|
ANK
|
646 |
675 |
5.53e-3 |
SMART |
|
ANK
|
680 |
710 |
1.9e-1 |
SMART |
|
ANK
|
714 |
743 |
2.18e-1 |
SMART |
|
DEATH
|
801 |
888 |
1.9e-19 |
SMART |
|
low complexity region
|
890 |
902 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129428
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000132668
AA Change: T157S
|
| SMART Domains |
Protein: ENSMUSP00000114798
Gene: ENSMUSG00000028163
AA Change: T157S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
8 |
54 |
N/A |
INTRINSIC |
|
Blast:IPT
|
55 |
156 |
4e-22 |
BLAST |
|
ANK
|
178 |
208 |
2.27e1 |
SMART |
|
ANK
|
217 |
246 |
1.11e-2 |
SMART |
|
ANK
|
250 |
280 |
2.47e0 |
SMART |
|
ANK
|
286 |
315 |
5.53e-3 |
SMART |
|
ANK
|
320 |
350 |
1.9e-1 |
SMART |
|
ANK
|
354 |
383 |
2.18e-1 |
SMART |
|
Blast:DEATH
|
441 |
505 |
1e-34 |
BLAST |
|
PDB:2DBF|A
|
442 |
505 |
5e-32 |
PDB |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000164430
AA Change: T518S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000128345
Gene: ENSMUSG00000028163
AA Change: T518S
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RHD_DNA_bind
|
42 |
240 |
2.9e-75 |
PFAM |
|
IPT
|
247 |
348 |
1.14e-22 |
SMART |
|
low complexity region
|
368 |
414 |
N/A |
INTRINSIC |
|
ANK
|
538 |
568 |
2.27e1 |
SMART |
|
ANK
|
577 |
606 |
1.11e-2 |
SMART |
|
ANK
|
610 |
640 |
2.47e0 |
SMART |
|
ANK
|
646 |
675 |
5.53e-3 |
SMART |
|
ANK
|
680 |
710 |
1.9e-1 |
SMART |
|
ANK
|
714 |
743 |
2.18e-1 |
SMART |
|
DEATH
|
801 |
888 |
1.9e-19 |
SMART |
|
low complexity region
|
890 |
902 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000184550
AA Change: T6S
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000196469
|
| SMART Domains |
Protein: ENSMUSP00000143601
Gene: ENSMUSG00000028163
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RHD_DNA_bind
|
42 |
90 |
2.5e-19 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000199588
|
| Meta Mutation Damage Score |
0.4132 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.4%
- 10x: 96.7%
- 20x: 88.7%
|
| Validation Efficiency |
91% (59/65) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a 105 kD protein which can undergo cotranslational processing by the 26S proteasome to produce a 50 kD protein. The 105 kD protein is a Rel protein-specific transcription inhibitor and the 50 kD protein is a DNA binding subunit of the NF-kappa-B (NFKB) protein complex. NFKB is a transcription regulator that is activated by various intra- and extra-cellular stimuli such as cytokines, oxidant-free radicals, ultraviolet irradiation, and bacterial or viral products. Activated NFKB translocates into the nucleus and stimulates the expression of genes involved in a wide variety of biological functions. Inappropriate activation of NFKB has been associated with a number of inflammatory diseases while persistent inhibition of NFKB leads to inappropriate immune cell development or delayed cell growth. Alternative splicing results in multiple transcript variants encoding different isoforms, at least one of which is proteolytically processed. [provided by RefSeq, Feb 2016]
PHENOTYPE: Homozygous null mice have a decreased survivor rate, abnormal T cell development and decreased number of peripheral T cells, abnormal humoral responses with decreased immunoglobulin class switching, exhibit mild organ inflammation, and are susceptible toboth bacterial infections and hearing loss. [provided by MGI curators]
|
| Allele List at MGI |
All alleles(79) : Targeted(5) Gene trapped(74)
|
| Other mutations in this stock |
Total: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Actl6a |
G |
A |
3: 32,766,277 (GRCm39) |
V48M |
possibly damaging |
Het |
| Adamts2 |
T |
G |
11: 50,694,781 (GRCm39) |
Y1189* |
probably null |
Het |
| Bpifb9a |
T |
C |
2: 154,108,756 (GRCm39) |
I419T |
probably benign |
Het |
| Ccbe1 |
A |
T |
18: 66,216,222 (GRCm39) |
I167N |
possibly damaging |
Het |
| Ccdc187 |
T |
C |
2: 26,183,380 (GRCm39) |
T207A |
probably benign |
Het |
| Cd300lf |
G |
A |
11: 115,017,126 (GRCm39) |
L66F |
probably damaging |
Het |
| Cenpk |
A |
G |
13: 104,372,702 (GRCm39) |
*92W |
probably null |
Het |
| Col12a1 |
A |
T |
9: 79,511,760 (GRCm39) |
S2950R |
probably benign |
Het |
| Dnah3 |
T |
C |
7: 119,574,331 (GRCm39) |
T2154A |
probably benign |
Het |
| Ebna1bp2 |
A |
T |
4: 118,478,332 (GRCm39) |
|
probably benign |
Het |
| Elac2 |
G |
T |
11: 64,888,783 (GRCm39) |
C532F |
probably benign |
Het |
| Fam171a1 |
T |
A |
2: 3,226,374 (GRCm39) |
D377E |
probably benign |
Het |
| Haus6 |
A |
G |
4: 86,504,594 (GRCm39) |
C466R |
possibly damaging |
Het |
| Il4ra |
T |
C |
7: 125,174,348 (GRCm39) |
S297P |
probably benign |
Het |
| Itgb4 |
C |
T |
11: 115,881,748 (GRCm39) |
R766W |
probably damaging |
Het |
| Kank4 |
T |
C |
4: 98,659,630 (GRCm39) |
Y816C |
possibly damaging |
Het |
| Kcnc4 |
A |
T |
3: 107,365,515 (GRCm39) |
|
probably null |
Het |
| Kif21b |
C |
T |
1: 136,078,875 (GRCm39) |
R408* |
probably null |
Het |
| Lrrc31 |
A |
G |
3: 30,733,289 (GRCm39) |
V475A |
probably benign |
Het |
| Map2k1 |
C |
T |
9: 64,098,548 (GRCm39) |
|
probably null |
Het |
| Mc3r |
T |
A |
2: 172,091,592 (GRCm39) |
N271K |
possibly damaging |
Het |
| Ms4a14 |
A |
G |
19: 11,281,581 (GRCm39) |
S326P |
possibly damaging |
Het |
| Muc6 |
T |
A |
7: 141,236,769 (GRCm39) |
I358F |
probably damaging |
Het |
| Myo5c |
A |
G |
9: 75,204,770 (GRCm39) |
D1541G |
probably damaging |
Het |
| Myof |
T |
C |
19: 37,899,382 (GRCm39) |
S1793G |
probably damaging |
Het |
| Nphs1 |
T |
A |
7: 30,173,810 (GRCm39) |
I989N |
probably damaging |
Het |
| Or5m12 |
T |
C |
2: 85,734,865 (GRCm39) |
T178A |
probably benign |
Het |
| Pcdha5 |
T |
C |
18: 37,094,474 (GRCm39) |
F328L |
probably benign |
Het |
| Pclo |
T |
A |
5: 14,764,492 (GRCm39) |
S4322T |
probably benign |
Het |
| Peg10 |
A |
G |
6: 4,754,375 (GRCm39) |
N52S |
probably damaging |
Het |
| Phf10 |
A |
C |
17: 15,175,272 (GRCm39) |
|
probably benign |
Het |
| Pip4p1 |
A |
G |
14: 51,166,332 (GRCm39) |
|
probably benign |
Het |
| Psme4 |
T |
C |
11: 30,741,993 (GRCm39) |
I152T |
possibly damaging |
Het |
| Ptpn18 |
T |
A |
1: 34,510,644 (GRCm39) |
|
probably benign |
Het |
| Rufy4 |
A |
T |
1: 74,185,914 (GRCm39) |
Y527F |
probably damaging |
Het |
| Snx32 |
T |
C |
19: 5,546,382 (GRCm39) |
M293V |
probably benign |
Het |
| Sorl1 |
A |
T |
9: 41,894,330 (GRCm39) |
L1827M |
possibly damaging |
Het |
| Sstr5 |
T |
A |
17: 25,710,218 (GRCm39) |
D337V |
probably benign |
Het |
| Tcaf3 |
A |
G |
6: 42,573,631 (GRCm39) |
F194L |
probably benign |
Het |
| Tcerg1 |
T |
A |
18: 42,669,413 (GRCm39) |
W459R |
probably damaging |
Het |
| Tet2 |
T |
A |
3: 133,192,860 (GRCm39) |
I525L |
probably benign |
Het |
| Trim43b |
C |
T |
9: 88,967,659 (GRCm39) |
V325I |
probably benign |
Het |
| Txndc11 |
A |
T |
16: 10,940,552 (GRCm39) |
I180K |
probably damaging |
Het |
| Vmn1r193 |
A |
G |
13: 22,403,395 (GRCm39) |
L199P |
probably damaging |
Het |
| Vmn2r110 |
A |
G |
17: 20,804,557 (GRCm39) |
M121T |
probably benign |
Het |
| Zfhx4 |
G |
C |
3: 5,467,719 (GRCm39) |
A2626P |
probably damaging |
Het |
| Zfp445 |
C |
T |
9: 122,682,552 (GRCm39) |
S463N |
probably benign |
Het |
| Zwilch |
T |
A |
9: 64,080,190 (GRCm39) |
|
probably null |
Het |
|
| Other mutations in Nfkb1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01293:Nfkb1
|
APN |
3 |
135,296,600 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01345:Nfkb1
|
APN |
3 |
135,300,742 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01629:Nfkb1
|
APN |
3 |
135,307,228 (GRCm39) |
missense |
probably benign |
|
|
IGL02216:Nfkb1
|
APN |
3 |
135,300,724 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL02273:Nfkb1
|
APN |
3 |
135,310,968 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL02508:Nfkb1
|
APN |
3 |
135,296,579 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL03095:Nfkb1
|
APN |
3 |
135,324,591 (GRCm39) |
missense |
possibly damaging |
0.48 |
|
Conversely
|
UTSW |
3 |
135,332,420 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Finlay
|
UTSW |
3 |
135,300,814 (GRCm39) |
nonsense |
probably null |
|
|
Frisbee
|
UTSW |
3 |
135,319,704 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
Honeyeater
|
UTSW |
3 |
135,297,312 (GRCm39) |
splice site |
probably benign |
|
|
kookaburra
|
UTSW |
3 |
135,332,372 (GRCm39) |
nonsense |
probably null |
|
|
Murgatroyd
|
UTSW |
3 |
135,332,471 (GRCm39) |
missense |
possibly damaging |
0.72 |
|
Poderoso
|
UTSW |
3 |
135,319,751 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Puff
|
UTSW |
3 |
135,300,814 (GRCm39) |
nonsense |
probably null |
|
|
Roomba
|
UTSW |
3 |
135,318,173 (GRCm39) |
critical splice donor site |
probably null |
|
|
Wheelo
|
UTSW |
3 |
135,321,110 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R0026:Nfkb1
|
UTSW |
3 |
135,297,334 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0047:Nfkb1
|
UTSW |
3 |
135,300,814 (GRCm39) |
nonsense |
probably null |
|
|
R0989:Nfkb1
|
UTSW |
3 |
135,295,157 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1210:Nfkb1
|
UTSW |
3 |
135,300,688 (GRCm39) |
missense |
probably benign |
0.03 |
|
R1661:Nfkb1
|
UTSW |
3 |
135,300,718 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1665:Nfkb1
|
UTSW |
3 |
135,300,718 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1725:Nfkb1
|
UTSW |
3 |
135,373,519 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1984:Nfkb1
|
UTSW |
3 |
135,321,110 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R1985:Nfkb1
|
UTSW |
3 |
135,321,110 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R2154:Nfkb1
|
UTSW |
3 |
135,307,240 (GRCm39) |
missense |
probably benign |
0.44 |
|
R2281:Nfkb1
|
UTSW |
3 |
135,307,282 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2409:Nfkb1
|
UTSW |
3 |
135,319,704 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R2504:Nfkb1
|
UTSW |
3 |
135,295,090 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
R4032:Nfkb1
|
UTSW |
3 |
135,300,110 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R4232:Nfkb1
|
UTSW |
3 |
135,309,531 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4936:Nfkb1
|
UTSW |
3 |
135,319,743 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5085:Nfkb1
|
UTSW |
3 |
135,309,568 (GRCm39) |
missense |
probably benign |
0.36 |
|
R5262:Nfkb1
|
UTSW |
3 |
135,318,173 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5384:Nfkb1
|
UTSW |
3 |
135,318,303 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R5385:Nfkb1
|
UTSW |
3 |
135,318,303 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R5434:Nfkb1
|
UTSW |
3 |
135,332,372 (GRCm39) |
nonsense |
probably null |
|
|
R5663:Nfkb1
|
UTSW |
3 |
135,309,612 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R6006:Nfkb1
|
UTSW |
3 |
135,309,522 (GRCm39) |
nonsense |
probably null |
|
|
R6013:Nfkb1
|
UTSW |
3 |
135,332,445 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R6234:Nfkb1
|
UTSW |
3 |
135,332,471 (GRCm39) |
missense |
possibly damaging |
0.72 |
|
R6785:Nfkb1
|
UTSW |
3 |
135,321,064 (GRCm39) |
missense |
probably benign |
|
|
R7175:Nfkb1
|
UTSW |
3 |
135,319,751 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7227:Nfkb1
|
UTSW |
3 |
135,332,420 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7394:Nfkb1
|
UTSW |
3 |
135,319,458 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R7727:Nfkb1
|
UTSW |
3 |
135,291,162 (GRCm39) |
missense |
possibly damaging |
0.48 |
|
R7815:Nfkb1
|
UTSW |
3 |
135,309,552 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7849:Nfkb1
|
UTSW |
3 |
135,291,173 (GRCm39) |
missense |
|
|
|
R8004:Nfkb1
|
UTSW |
3 |
135,297,312 (GRCm39) |
splice site |
probably benign |
|
|
R8059:Nfkb1
|
UTSW |
3 |
135,299,613 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R8806:Nfkb1
|
UTSW |
3 |
135,295,213 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9169:Nfkb1
|
UTSW |
3 |
135,310,874 (GRCm39) |
missense |
probably benign |
0.00 |
|
X0050:Nfkb1
|
UTSW |
3 |
135,312,384 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GCATACTCGAGGTCTTGTCAG -3'
(R):5'- ATGCCCGATTGTGCTTGTTC -3'
Sequencing Primer
(F):5'- CATACTCGAGGTCTTGTCAGATGAG -3'
(R):5'- GCTTGTTCTAGTCAACACAATCCAG -3'
|
| Posted On |
2017-02-10 |
Incidental Mutation