Incidental Mutation 'R4471:Sox5'
| ID |
329427 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sox5
|
| Ensembl Gene |
ENSMUSG00000041540 |
| Gene Name |
SRY (sex determining region Y)-box 5 |
| Synonyms |
A730017D01Rik |
| MMRRC Submission |
041728-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4471 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
6 |
| Chromosomal Location |
143774151-144727703 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 143790491 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Threonine
at position 523
(M523T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000047567
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000038815]
[ENSMUST00000077160]
[ENSMUST00000111748]
[ENSMUST00000111749]
[ENSMUST00000144289]
[ENSMUST00000170367]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000038815
AA Change: M523T
PolyPhen 2
Score 0.540 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000047567
Gene: ENSMUSG00000041540
AA Change: M523T
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
167 |
178 |
N/A |
INTRINSIC |
|
coiled coil region
|
193 |
272 |
N/A |
INTRINSIC |
|
low complexity region
|
336 |
348 |
N/A |
INTRINSIC |
|
low complexity region
|
431 |
445 |
N/A |
INTRINSIC |
|
coiled coil region
|
449 |
483 |
N/A |
INTRINSIC |
|
low complexity region
|
494 |
505 |
N/A |
INTRINSIC |
|
HMG
|
555 |
625 |
2.84e-26 |
SMART |
|
low complexity region
|
686 |
708 |
N/A |
INTRINSIC |
|
low complexity region
|
729 |
750 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000077160
AA Change: M475T
PolyPhen 2
Score 0.479 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000076403
Gene: ENSMUSG00000041540
AA Change: M475T
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
167 |
178 |
N/A |
INTRINSIC |
|
coiled coil region
|
193 |
277 |
N/A |
INTRINSIC |
|
low complexity region
|
383 |
397 |
N/A |
INTRINSIC |
|
coiled coil region
|
401 |
435 |
N/A |
INTRINSIC |
|
low complexity region
|
446 |
457 |
N/A |
INTRINSIC |
|
HMG
|
507 |
577 |
2.84e-26 |
SMART |
|
low complexity region
|
638 |
660 |
N/A |
INTRINSIC |
|
low complexity region
|
681 |
702 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000111746
|
| SMART Domains |
Protein: ENSMUSP00000107375
Gene: ENSMUSG00000041540
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
60 |
74 |
N/A |
INTRINSIC |
|
coiled coil region
|
78 |
112 |
N/A |
INTRINSIC |
|
low complexity region
|
123 |
134 |
N/A |
INTRINSIC |
|
HMG
|
184 |
234 |
1.72e-2 |
SMART |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000111748
AA Change: M152T
PolyPhen 2
Score 0.479 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000107377
Gene: ENSMUSG00000041540
AA Change: M152T
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
60 |
74 |
N/A |
INTRINSIC |
|
coiled coil region
|
78 |
112 |
N/A |
INTRINSIC |
|
low complexity region
|
123 |
134 |
N/A |
INTRINSIC |
|
HMG
|
184 |
254 |
2.84e-26 |
SMART |
|
low complexity region
|
315 |
337 |
N/A |
INTRINSIC |
|
low complexity region
|
358 |
379 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111749
AA Change: M439T
PolyPhen 2
Score 0.024 (Sensitivity: 0.95; Specificity: 0.81)
|
| SMART Domains |
Protein: ENSMUSP00000107378
Gene: ENSMUSG00000041540
AA Change: M439T
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
132 |
143 |
N/A |
INTRINSIC |
|
coiled coil region
|
158 |
237 |
N/A |
INTRINSIC |
|
low complexity region
|
347 |
361 |
N/A |
INTRINSIC |
|
coiled coil region
|
365 |
399 |
N/A |
INTRINSIC |
|
low complexity region
|
410 |
421 |
N/A |
INTRINSIC |
|
HMG
|
471 |
541 |
2.84e-26 |
SMART |
|
low complexity region
|
602 |
624 |
N/A |
INTRINSIC |
|
low complexity region
|
645 |
666 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141102
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000144289
|
| SMART Domains |
Protein: ENSMUSP00000122786
Gene: ENSMUSG00000041540
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
14 |
26 |
N/A |
INTRINSIC |
|
low complexity region
|
109 |
123 |
N/A |
INTRINSIC |
|
coiled coil region
|
127 |
161 |
N/A |
INTRINSIC |
|
low complexity region
|
172 |
183 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000170367
AA Change: M474T
PolyPhen 2
Score 0.479 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000133041
Gene: ENSMUSG00000041540
AA Change: M474T
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
167 |
178 |
N/A |
INTRINSIC |
|
coiled coil region
|
193 |
272 |
N/A |
INTRINSIC |
|
low complexity region
|
382 |
396 |
N/A |
INTRINSIC |
|
coiled coil region
|
400 |
434 |
N/A |
INTRINSIC |
|
low complexity region
|
445 |
456 |
N/A |
INTRINSIC |
|
HMG
|
506 |
576 |
2.84e-26 |
SMART |
|
low complexity region
|
637 |
659 |
N/A |
INTRINSIC |
|
low complexity region
|
680 |
701 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.0719 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.4%
|
| Validation Efficiency |
99% (69/70) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. The encoded protein may play a role in chondrogenesis. A pseudogene of this gene is located on chromosome 8. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous null mice fail to breathe and die at birth exhibiting a narrow thoracic cage, irregularly mineralized sternum, cleft secondary palate, and delayed bone mineralization. Homozygotes for a transposon induced insertion die shortly after birth exhibiting cyanosis and respiratory distress. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 65 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Alpk1 |
A |
G |
3: 127,473,175 (GRCm39) |
S943P |
probably damaging |
Het |
| Ankdd1a |
T |
C |
9: 65,410,791 (GRCm39) |
D398G |
probably damaging |
Het |
| Ankrd13b |
T |
A |
11: 77,367,040 (GRCm39) |
K49M |
probably damaging |
Het |
| Asah1 |
A |
G |
8: 41,796,761 (GRCm39) |
|
probably null |
Het |
| Cdc34b |
A |
G |
11: 94,633,064 (GRCm39) |
E88G |
probably benign |
Het |
| Cdh2 |
T |
C |
18: 16,907,533 (GRCm39) |
|
probably null |
Het |
| Ceacam1 |
T |
A |
7: 25,174,025 (GRCm39) |
N210I |
possibly damaging |
Het |
| Celf3 |
A |
G |
3: 94,395,585 (GRCm39) |
|
probably null |
Het |
| Cfap20dc |
A |
G |
14: 8,536,571 (GRCm38) |
L212P |
probably damaging |
Het |
| Cmya5 |
A |
T |
13: 93,228,833 (GRCm39) |
M2085K |
probably benign |
Het |
| Cpne6 |
G |
A |
14: 55,754,089 (GRCm39) |
V469M |
probably damaging |
Het |
| Cyp2j12 |
A |
G |
4: 96,021,306 (GRCm39) |
V100A |
probably benign |
Het |
| Dnajb4 |
A |
T |
3: 151,890,799 (GRCm39) |
H333Q |
probably benign |
Het |
| Eif3f |
T |
C |
7: 108,540,153 (GRCm39) |
V316A |
possibly damaging |
Het |
| Eml1 |
T |
C |
12: 108,472,894 (GRCm39) |
|
probably benign |
Het |
| Ern1 |
C |
A |
11: 106,310,868 (GRCm39) |
V302L |
possibly damaging |
Het |
| Fam110b |
A |
T |
4: 5,799,092 (GRCm39) |
H170L |
probably benign |
Het |
| Fn3krp |
T |
G |
11: 121,317,499 (GRCm39) |
D146E |
probably benign |
Het |
| Git1 |
A |
G |
11: 77,390,650 (GRCm39) |
T129A |
probably benign |
Het |
| Glrp1 |
T |
A |
1: 88,431,196 (GRCm39) |
Q58L |
unknown |
Het |
| Gpatch2 |
A |
G |
1: 186,965,337 (GRCm39) |
E281G |
probably damaging |
Het |
| Hipk2 |
T |
A |
6: 38,713,857 (GRCm39) |
|
probably benign |
Het |
| Hydin |
A |
G |
8: 111,313,764 (GRCm39) |
N4214S |
probably damaging |
Het |
| Icam5 |
T |
A |
9: 20,946,802 (GRCm39) |
C443* |
probably null |
Het |
| Impdh1 |
G |
A |
6: 29,204,631 (GRCm39) |
Q307* |
probably null |
Het |
| Ivns1abp |
C |
T |
1: 151,236,990 (GRCm39) |
T447M |
probably benign |
Het |
| Lman1 |
A |
T |
18: 66,124,797 (GRCm39) |
|
probably benign |
Het |
| Mdn1 |
A |
G |
4: 32,668,860 (GRCm39) |
E306G |
probably benign |
Het |
| Msc |
G |
C |
1: 14,825,902 (GRCm39) |
P24R |
probably damaging |
Het |
| Mtif2 |
T |
C |
11: 29,490,053 (GRCm39) |
|
probably benign |
Het |
| Mvp |
C |
T |
7: 126,601,130 (GRCm39) |
M1I |
probably null |
Het |
| Myh7 |
A |
T |
14: 55,229,311 (GRCm39) |
Y162* |
probably null |
Het |
| Nemf |
G |
A |
12: 69,361,216 (GRCm39) |
H956Y |
probably benign |
Het |
| Nktr |
T |
C |
9: 121,577,962 (GRCm39) |
|
probably benign |
Het |
| Nrxn3 |
T |
C |
12: 90,171,515 (GRCm39) |
S276P |
probably damaging |
Het |
| Or8d1 |
T |
C |
9: 38,766,927 (GRCm39) |
S190P |
probably damaging |
Het |
| Patj |
A |
G |
4: 98,423,816 (GRCm39) |
K621E |
probably damaging |
Het |
| Prss2 |
A |
G |
6: 41,499,780 (GRCm39) |
I24V |
probably damaging |
Het |
| R3hcc1l |
T |
C |
19: 42,571,259 (GRCm39) |
|
probably benign |
Het |
| Rest |
T |
C |
5: 77,429,027 (GRCm39) |
V482A |
probably benign |
Het |
| Rexo1 |
A |
T |
10: 80,378,492 (GRCm39) |
S476T |
probably damaging |
Het |
| Rin2 |
C |
T |
2: 145,702,366 (GRCm39) |
T354I |
probably benign |
Het |
| Slc16a3 |
T |
C |
11: 120,846,774 (GRCm39) |
|
probably benign |
Het |
| Slc5a4b |
G |
A |
10: 75,894,725 (GRCm39) |
Q594* |
probably null |
Het |
| Slk |
T |
G |
19: 47,603,862 (GRCm39) |
V202G |
probably damaging |
Het |
| Smarca2 |
T |
A |
19: 26,597,277 (GRCm39) |
V53D |
possibly damaging |
Het |
| Snrnp200 |
T |
A |
2: 127,080,673 (GRCm39) |
V2036E |
probably benign |
Het |
| Syt17 |
A |
G |
7: 118,036,040 (GRCm39) |
|
probably null |
Het |
| Taf2 |
T |
C |
15: 54,922,276 (GRCm39) |
D337G |
possibly damaging |
Het |
| Tcstv2a |
G |
T |
13: 120,725,579 (GRCm39) |
R81L |
probably benign |
Het |
| Tecrl |
A |
G |
5: 83,461,134 (GRCm39) |
Y108H |
probably benign |
Het |
| Tln1 |
A |
T |
4: 43,551,018 (GRCm39) |
F409L |
probably benign |
Het |
| Tmem59l |
A |
G |
8: 70,939,951 (GRCm39) |
L6S |
unknown |
Het |
| Ttc23 |
G |
A |
7: 67,319,904 (GRCm39) |
R187Q |
probably benign |
Het |
| Ttl |
T |
C |
2: 128,923,977 (GRCm39) |
V230A |
probably benign |
Het |
| Ube2u |
G |
A |
4: 100,338,843 (GRCm39) |
W36* |
probably null |
Het |
| Ube4a |
A |
T |
9: 44,857,830 (GRCm39) |
|
probably benign |
Het |
| Ulk1 |
C |
T |
5: 110,937,223 (GRCm39) |
R691Q |
probably benign |
Het |
| Unc45a |
A |
G |
7: 79,982,728 (GRCm39) |
I399T |
possibly damaging |
Het |
| Utp25 |
C |
T |
1: 192,812,445 (GRCm39) |
R5Q |
possibly damaging |
Het |
| Wdr59 |
A |
C |
8: 112,193,419 (GRCm39) |
|
probably null |
Het |
| Zfp24 |
A |
G |
18: 24,151,172 (GRCm39) |
|
probably benign |
Het |
| Zfp777 |
A |
T |
6: 48,019,041 (GRCm39) |
W342R |
probably damaging |
Het |
| Zfp979 |
A |
T |
4: 147,697,913 (GRCm39) |
C265* |
probably null |
Het |
| Zzef1 |
T |
A |
11: 72,804,157 (GRCm39) |
L2633Q |
probably damaging |
Het |
|
| Other mutations in Sox5 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01364:Sox5
|
APN |
6 |
144,062,198 (GRCm39) |
missense |
probably damaging |
0.96 |
|
IGL03217:Sox5
|
APN |
6 |
143,853,223 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Stocking
|
UTSW |
6 |
144,062,169 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0230:Sox5
|
UTSW |
6 |
144,155,064 (GRCm39) |
missense |
probably benign |
0.02 |
|
R0610:Sox5
|
UTSW |
6 |
143,779,165 (GRCm39) |
missense |
possibly damaging |
0.56 |
|
R1162:Sox5
|
UTSW |
6 |
143,906,538 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1857:Sox5
|
UTSW |
6 |
143,906,541 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1959:Sox5
|
UTSW |
6 |
143,819,831 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R4057:Sox5
|
UTSW |
6 |
144,062,248 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4164:Sox5
|
UTSW |
6 |
144,062,206 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4284:Sox5
|
UTSW |
6 |
143,781,055 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4430:Sox5
|
UTSW |
6 |
143,987,000 (GRCm39) |
missense |
possibly damaging |
0.57 |
|
R4470:Sox5
|
UTSW |
6 |
143,790,491 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R4672:Sox5
|
UTSW |
6 |
143,779,075 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4683:Sox5
|
UTSW |
6 |
143,779,193 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4693:Sox5
|
UTSW |
6 |
143,781,042 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4735:Sox5
|
UTSW |
6 |
143,906,561 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4745:Sox5
|
UTSW |
6 |
143,779,214 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
R4762:Sox5
|
UTSW |
6 |
143,807,109 (GRCm39) |
critical splice donor site |
probably null |
|
|
R4996:Sox5
|
UTSW |
6 |
143,974,070 (GRCm39) |
nonsense |
probably null |
|
|
R5218:Sox5
|
UTSW |
6 |
143,906,616 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R5673:Sox5
|
UTSW |
6 |
144,062,206 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5856:Sox5
|
UTSW |
6 |
144,155,088 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6249:Sox5
|
UTSW |
6 |
143,779,009 (GRCm39) |
missense |
probably benign |
0.33 |
|
R6394:Sox5
|
UTSW |
6 |
143,987,039 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6703:Sox5
|
UTSW |
6 |
143,779,191 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6812:Sox5
|
UTSW |
6 |
144,062,169 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7312:Sox5
|
UTSW |
6 |
144,100,759 (GRCm39) |
missense |
probably benign |
|
|
R7543:Sox5
|
UTSW |
6 |
143,786,905 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R8110:Sox5
|
UTSW |
6 |
144,062,200 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R8231:Sox5
|
UTSW |
6 |
143,974,014 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8250:Sox5
|
UTSW |
6 |
144,100,777 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R8705:Sox5
|
UTSW |
6 |
143,987,012 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
R8937:Sox5
|
UTSW |
6 |
143,853,169 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9182:Sox5
|
UTSW |
6 |
143,779,118 (GRCm39) |
missense |
possibly damaging |
0.51 |
|
R9193:Sox5
|
UTSW |
6 |
143,790,570 (GRCm39) |
missense |
probably benign |
0.27 |
|
R9740:Sox5
|
UTSW |
6 |
144,100,947 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R9762:Sox5
|
UTSW |
6 |
143,819,842 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGACTGCGGTAAATGTGAGC -3'
(R):5'- GTCCAAACCCCTGCTGATTAG -3'
Sequencing Primer
(F):5'- TAAATGTGAGCCCCACTGG -3'
(R):5'- GGTGAATACGCCAATATCCCATGG -3'
|
| Posted On |
2015-07-21 |
Incidental Mutation