Incidental Mutation 'R6494:Sox2'
| ID |
522926 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sox2
|
| Ensembl Gene |
ENSMUSG00000074637 |
| Gene Name |
SRY (sex determining region Y)-box 2 |
| Synonyms |
Sox-2, lcc, ysb |
| MMRRC Submission |
044626-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6494 (G1)
|
| Quality Score |
220.009 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
34704554-34706610 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 34705246 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Threonine
at position 228
(S228T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000096755
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000099151]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000099151
AA Change: S228T
PolyPhen 2
Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
|
| SMART Domains |
Protein: ENSMUSP00000096755
Gene: ENSMUSG00000074637
AA Change: S228T
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
19 |
35 |
N/A |
INTRINSIC |
|
HMG
|
42 |
112 |
1.8e-28 |
SMART |
|
low complexity region
|
137 |
156 |
N/A |
INTRINSIC |
|
low complexity region
|
248 |
263 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000184690
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000196243
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000196850
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000196987
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000197103
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000197258
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000200414
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000198758
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000200092
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000197977
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000199171
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 97.8%
- 20x: 92.4%
|
| Validation Efficiency |
98% (44/45) |
| MGI Phenotype |
FUNCTION: This intronless gene encodes a member of the SRY-related HMG-box (SOX) family of transcription factors involved in the regulation of embryonic development and in the determination of cell fate. The product of this gene is required for stem-cell maintenance in the central nervous system, and also regulates gene expression in the stomach. Mutations in a similar gene in human have been associated with optic nerve hypoplasia and with syndromic microphthalmia, a severe form of structural eye malformation. This gene lies within an intron of another gene called SOX2 overlapping transcript (Sox2ot). [provided by RefSeq, Sep 2015]
PHENOTYPE: Homozygotes for targeted null mutations implant but fail to develop an egg cylinder or epiblast, and die shortly thereafter. Other mutations that affect only regulatory elements show circling behavior and deafness, inner ear defects, and a yellow coat color. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Akt2 |
T |
C |
7: 27,315,774 (GRCm39) |
L52P |
possibly damaging |
Het |
| Chd1l |
G |
A |
3: 97,494,483 (GRCm39) |
A399V |
probably damaging |
Het |
| Chic2 |
T |
C |
5: 75,204,943 (GRCm39) |
E6G |
probably benign |
Het |
| Clca4a |
T |
A |
3: 144,663,059 (GRCm39) |
T597S |
probably benign |
Het |
| Col5a2 |
C |
A |
1: 45,417,487 (GRCm39) |
D1363Y |
probably damaging |
Het |
| Csmd1 |
C |
T |
8: 16,261,709 (GRCm39) |
|
probably null |
Het |
| Dnah7b |
A |
T |
1: 46,138,591 (GRCm39) |
Y211F |
probably damaging |
Het |
| Efcab3 |
A |
T |
11: 104,990,845 (GRCm39) |
Y5460F |
possibly damaging |
Het |
| Efcab6 |
T |
A |
15: 83,928,523 (GRCm39) |
|
probably null |
Het |
| Eno4 |
T |
A |
19: 58,951,226 (GRCm39) |
Y237N |
probably damaging |
Het |
| Fer1l4 |
T |
A |
2: 155,887,390 (GRCm39) |
D602V |
probably benign |
Het |
| Fgfr2 |
T |
C |
7: 129,800,280 (GRCm39) |
N337S |
probably damaging |
Het |
| Fras1 |
C |
T |
5: 96,907,423 (GRCm39) |
R3203C |
possibly damaging |
Het |
| Gbp2 |
T |
A |
3: 142,337,769 (GRCm39) |
V295E |
probably damaging |
Het |
| Gm10549 |
C |
A |
18: 33,597,358 (GRCm39) |
|
probably benign |
Het |
| Hyal4 |
A |
G |
6: 24,765,745 (GRCm39) |
I366M |
possibly damaging |
Het |
| Itsn2 |
C |
T |
12: 4,684,792 (GRCm39) |
R448* |
probably null |
Het |
| Klhl35 |
G |
T |
7: 99,122,106 (GRCm39) |
W69L |
probably damaging |
Het |
| Kpnb1 |
T |
C |
11: 97,072,474 (GRCm39) |
I154V |
probably benign |
Het |
| Lax1 |
T |
A |
1: 133,608,186 (GRCm39) |
Y185F |
probably damaging |
Het |
| Mmp12 |
C |
T |
9: 7,353,479 (GRCm39) |
P208L |
probably damaging |
Het |
| Ndufb8 |
C |
T |
19: 44,543,744 (GRCm39) |
V33M |
probably null |
Het |
| Nptn |
T |
G |
9: 58,531,035 (GRCm39) |
C169G |
probably damaging |
Het |
| Nuggc |
A |
T |
14: 65,885,671 (GRCm39) |
E766V |
probably damaging |
Het |
| Or10ag55-ps1 |
A |
T |
2: 87,139,520 (GRCm39) |
N149I |
possibly damaging |
Het |
| Or12e14 |
A |
T |
2: 87,187,976 (GRCm39) |
K63* |
probably null |
Het |
| Pcdhga6 |
T |
A |
18: 37,841,594 (GRCm39) |
I438N |
probably damaging |
Het |
| Pkn2 |
T |
C |
3: 142,509,429 (GRCm39) |
N721S |
possibly damaging |
Het |
| Pole |
T |
C |
5: 110,472,588 (GRCm39) |
W1590R |
possibly damaging |
Het |
| Prph2 |
A |
G |
17: 47,222,007 (GRCm39) |
T129A |
probably benign |
Het |
| Ptpro |
A |
T |
6: 137,359,640 (GRCm39) |
K403N |
probably benign |
Het |
| Rbck1 |
T |
C |
2: 152,172,886 (GRCm39) |
D54G |
possibly damaging |
Het |
| Serpinb7 |
T |
A |
1: 107,363,076 (GRCm39) |
L80* |
probably null |
Het |
| Setdb2 |
T |
A |
14: 59,639,863 (GRCm39) |
Y676F |
probably benign |
Het |
| Skint1 |
G |
T |
4: 111,867,909 (GRCm39) |
C12F |
probably benign |
Het |
| Slc22a26 |
T |
A |
19: 7,779,651 (GRCm39) |
D55V |
probably damaging |
Het |
| Slc9a8 |
G |
A |
2: 167,266,211 (GRCm39) |
V63I |
probably damaging |
Het |
| Spata31g1 |
A |
G |
4: 42,971,924 (GRCm39) |
N419S |
possibly damaging |
Het |
| Spg11 |
A |
G |
2: 121,943,706 (GRCm39) |
S149P |
probably damaging |
Het |
| Tbc1d19 |
T |
A |
5: 53,986,725 (GRCm39) |
S45T |
probably benign |
Het |
| Tsacc |
T |
C |
3: 88,202,703 (GRCm39) |
E11G |
probably benign |
Het |
| Ttc7b |
C |
T |
12: 100,461,666 (GRCm39) |
A104T |
possibly damaging |
Het |
| Uox |
C |
T |
3: 146,330,332 (GRCm39) |
R163* |
probably null |
Het |
| Zfp108 |
T |
A |
7: 23,960,782 (GRCm39) |
F458I |
probably damaging |
Het |
| Zfp616 |
A |
T |
11: 73,976,018 (GRCm39) |
K762N |
probably damaging |
Het |
|
| Other mutations in Sox2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02578:Sox2
|
APN |
3 |
34,704,745 (GRCm39) |
missense |
probably benign |
0.37 |
|
IGL03397:Sox2
|
APN |
3 |
34,704,686 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1164:Sox2
|
UTSW |
3 |
34,704,848 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1667:Sox2
|
UTSW |
3 |
34,704,568 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1829:Sox2
|
UTSW |
3 |
34,704,890 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1925:Sox2
|
UTSW |
3 |
34,704,820 (GRCm39) |
nonsense |
probably null |
|
|
R2066:Sox2
|
UTSW |
3 |
34,705,456 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R4170:Sox2
|
UTSW |
3 |
34,704,703 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4585:Sox2
|
UTSW |
3 |
34,705,193 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4586:Sox2
|
UTSW |
3 |
34,705,193 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4703:Sox2
|
UTSW |
3 |
34,704,862 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5509:Sox2
|
UTSW |
3 |
34,704,938 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5549:Sox2
|
UTSW |
3 |
34,705,142 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5637:Sox2
|
UTSW |
3 |
34,704,677 (GRCm39) |
missense |
probably benign |
0.03 |
|
R7117:Sox2
|
UTSW |
3 |
34,705,075 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R7210:Sox2
|
UTSW |
3 |
34,705,306 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7365:Sox2
|
UTSW |
3 |
34,705,121 (GRCm39) |
missense |
possibly damaging |
0.60 |
|
R7798:Sox2
|
UTSW |
3 |
34,704,791 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R7801:Sox2
|
UTSW |
3 |
34,704,791 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R8684:Sox2
|
UTSW |
3 |
34,705,016 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8889:Sox2
|
UTSW |
3 |
34,705,129 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
R9013:Sox2
|
UTSW |
3 |
34,704,746 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0024:Sox2
|
UTSW |
3 |
34,704,838 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- ATAAGTACACGCTTCCCGGAG -3'
(R):5'- TTCTCCAGTTCGCAGTCCAG -3'
Sequencing Primer
(F):5'- TACGCGCACATGAACGG -3'
(R):5'- TGGGCCATGTGCAGTCTAC -3'
|
| Posted On |
2018-06-06 |
Incidental Mutation