Incidental Mutation 'R4486:Nanog'
| ID |
331611 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nanog
|
| Ensembl Gene |
ENSMUSG00000012396 |
| Gene Name |
Nanog homeobox |
| Synonyms |
ENK, 2410002E02Rik, ecat4 |
| MMRRC Submission |
041742-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4486 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
6 |
| Chromosomal Location |
122684448-122691592 bp(+) (GRCm39) |
| Type of Mutation |
critical splice donor site (2 bp from exon) |
| DNA Base Change (assembly) |
T to C
at 122689676 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000108200
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000012540]
[ENSMUST00000112580]
[ENSMUST00000112581]
|
| AlphaFold |
Q80Z64 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000012540
|
| SMART Domains |
Protein: ENSMUSP00000012540
Gene: ENSMUSG00000012396
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
13 |
25 |
N/A |
INTRINSIC |
|
HOX
|
96 |
158 |
5.33e-22 |
SMART |
|
low complexity region
|
206 |
230 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000112580
|
| SMART Domains |
Protein: ENSMUSP00000108199
Gene: ENSMUSG00000012396
| Domain | Start | End | E-Value | Type |
|---|
|
HOX
|
71 |
133 |
5.33e-22 |
SMART |
|
low complexity region
|
181 |
205 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000112581
|
| SMART Domains |
Protein: ENSMUSP00000108200
Gene: ENSMUSG00000012396
| Domain | Start | End | E-Value | Type |
|---|
|
HOX
|
71 |
133 |
5.33e-22 |
SMART |
|
low complexity region
|
181 |
205 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.9478 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.7%
|
| Validation Efficiency |
94% (45/48) |
| MGI Phenotype |
FUNCTION: The protein encoded by this gene is a DNA binding homeobox transcription factor involved in embryonic stem (ES) cell proliferation, renewal, and pluripotency. The encoded protein can block ES cell differentiation and can also autorepress its own expression in differentiating cells. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mice homozygous for a disruption in this gene die between E3.5 and E5.5 with abnormal embryonic and extraembryonic tissue development. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcd2 |
A |
G |
15: 91,062,486 (GRCm39) |
V484A |
probably damaging |
Het |
| Adam22 |
A |
T |
5: 8,230,227 (GRCm39) |
|
probably benign |
Het |
| Adamts18 |
G |
T |
8: 114,439,825 (GRCm39) |
P923T |
probably benign |
Het |
| Ank3 |
C |
T |
10: 69,837,804 (GRCm39) |
T1604I |
possibly damaging |
Het |
| Armc10 |
A |
G |
5: 21,858,432 (GRCm39) |
Q159R |
probably damaging |
Het |
| Arnt2 |
T |
A |
7: 83,924,553 (GRCm39) |
T425S |
probably benign |
Het |
| B4galt3 |
A |
G |
1: 171,099,343 (GRCm39) |
T36A |
possibly damaging |
Het |
| Bbx |
A |
G |
16: 50,020,777 (GRCm39) |
V799A |
probably damaging |
Het |
| Bud23 |
T |
C |
5: 135,092,779 (GRCm39) |
|
probably null |
Het |
| Cnga2 |
T |
A |
X: 71,049,733 (GRCm39) |
F133I |
possibly damaging |
Het |
| Crispld1 |
A |
G |
1: 17,823,102 (GRCm39) |
T390A |
probably benign |
Het |
| Cyp4f39 |
T |
A |
17: 32,702,428 (GRCm39) |
D308E |
probably damaging |
Het |
| Dnah6 |
A |
G |
6: 73,015,729 (GRCm39) |
V3584A |
probably damaging |
Het |
| Ecpas |
A |
G |
4: 58,820,086 (GRCm39) |
|
probably benign |
Het |
| Frk |
T |
C |
10: 34,484,377 (GRCm39) |
I450T |
probably benign |
Het |
| Grm6 |
T |
C |
11: 50,750,816 (GRCm39) |
S660P |
probably damaging |
Het |
| Hao2 |
T |
A |
3: 98,789,341 (GRCm39) |
I116F |
probably damaging |
Het |
| Hyi |
G |
A |
4: 118,219,674 (GRCm39) |
G237D |
probably damaging |
Het |
| Jrkl |
T |
C |
9: 13,245,376 (GRCm39) |
N95S |
probably benign |
Het |
| Kifbp |
A |
G |
10: 62,398,806 (GRCm39) |
|
probably benign |
Het |
| Ngf |
G |
A |
3: 102,428,015 (GRCm39) |
D255N |
probably damaging |
Het |
| Nlrp4e |
A |
G |
7: 23,020,652 (GRCm39) |
I380V |
probably benign |
Het |
| Or52e7 |
T |
C |
7: 104,684,510 (GRCm39) |
F35S |
probably benign |
Het |
| Or6c76b |
T |
C |
10: 129,692,567 (GRCm39) |
F60S |
probably damaging |
Het |
| Pcdha3 |
T |
C |
18: 37,080,404 (GRCm39) |
V382A |
probably damaging |
Het |
| Pla2g4c |
T |
A |
7: 13,071,676 (GRCm39) |
N165K |
probably benign |
Het |
| Rexo5 |
T |
C |
7: 119,424,800 (GRCm39) |
I362T |
probably benign |
Het |
| Rpl7a-ps3 |
G |
A |
15: 36,308,429 (GRCm39) |
|
noncoding transcript |
Het |
| Rpusd2 |
T |
C |
2: 118,865,705 (GRCm39) |
V134A |
probably damaging |
Het |
| Serpina1c |
T |
A |
12: 103,863,259 (GRCm39) |
|
probably null |
Het |
| Slc6a19 |
A |
T |
13: 73,829,836 (GRCm39) |
I606N |
probably damaging |
Het |
| Smchd1 |
T |
C |
17: 71,714,230 (GRCm39) |
T878A |
probably benign |
Het |
| Tas2r143 |
A |
G |
6: 42,377,628 (GRCm39) |
M153V |
probably benign |
Het |
| Thrb |
G |
T |
14: 17,925,640 (GRCm38) |
M1I |
probably null |
Het |
| Trbc2 |
A |
G |
6: 41,523,814 (GRCm39) |
|
probably benign |
Het |
| Trim37 |
T |
A |
11: 87,087,651 (GRCm39) |
S587R |
probably benign |
Het |
| Ulbp1 |
T |
A |
10: 7,397,397 (GRCm39) |
H151L |
probably benign |
Het |
| Vmn2r54 |
A |
T |
7: 12,366,199 (GRCm39) |
L245* |
probably null |
Het |
| Vmn2r78 |
A |
C |
7: 86,569,959 (GRCm39) |
|
probably null |
Het |
| Xlr5b |
T |
C |
X: 72,201,504 (GRCm39) |
|
probably null |
Het |
| Xrcc4 |
A |
C |
13: 90,140,707 (GRCm39) |
S167R |
possibly damaging |
Het |
| Zfp994 |
C |
T |
17: 22,420,541 (GRCm39) |
C136Y |
probably damaging |
Het |
|
| Other mutations in Nanog |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00475:Nanog
|
APN |
6 |
122,688,495 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
IGL03278:Nanog
|
APN |
6 |
122,688,704 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03387:Nanog
|
APN |
6 |
122,688,731 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0280:Nanog
|
UTSW |
6 |
122,690,357 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R1443:Nanog
|
UTSW |
6 |
122,688,734 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2520:Nanog
|
UTSW |
6 |
122,690,418 (GRCm39) |
missense |
probably benign |
0.08 |
|
R3037:Nanog
|
UTSW |
6 |
122,690,227 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R4770:Nanog
|
UTSW |
6 |
122,688,550 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R4790:Nanog
|
UTSW |
6 |
122,684,874 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4825:Nanog
|
UTSW |
6 |
122,690,299 (GRCm39) |
missense |
probably benign |
0.09 |
|
R4931:Nanog
|
UTSW |
6 |
122,684,865 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R6010:Nanog
|
UTSW |
6 |
122,690,255 (GRCm39) |
missense |
probably benign |
0.16 |
|
R6025:Nanog
|
UTSW |
6 |
122,690,350 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R7661:Nanog
|
UTSW |
6 |
122,690,431 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R8236:Nanog
|
UTSW |
6 |
122,690,131 (GRCm39) |
missense |
probably benign |
|
|
R8272:Nanog
|
UTSW |
6 |
122,688,736 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8520:Nanog
|
UTSW |
6 |
122,690,475 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R9500:Nanog
|
UTSW |
6 |
122,690,219 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9632:Nanog
|
UTSW |
6 |
122,684,799 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9710:Nanog
|
UTSW |
6 |
122,684,799 (GRCm39) |
missense |
probably benign |
0.00 |
|
X0065:Nanog
|
UTSW |
6 |
122,684,752 (GRCm39) |
missense |
probably benign |
|
|
Z1176:Nanog
|
UTSW |
6 |
122,690,190 (GRCm39) |
nonsense |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- AAGAAAGAGTTTCACTTTACAGGCC -3'
(R):5'- CAGGACTAATGGACATAGATGGATC -3'
Sequencing Primer
(F):5'- TACAGGCCTGGCTGTCATG -3'
(R):5'- CATAGATGGATCAGGATGACACTG -3'
|
| Posted On |
2015-07-21 |
Incidental Mutation