Incidental Mutation 'R1371:Sall4'
| ID |
157302 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sall4
|
| Ensembl Gene |
ENSMUSG00000027547 |
| Gene Name |
spalt like transcription factor 4 |
| Synonyms |
Tex20, 5730441M18Rik, C330011P20Rik |
| MMRRC Submission |
039435-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1371 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
168590252-168609121 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 168598394 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Histidine
at position 149
(Y149H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000099363
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029061]
[ENSMUST00000075044]
[ENSMUST00000103074]
[ENSMUST00000137536]
[ENSMUST00000150588]
|
| AlphaFold |
Q8BX22 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029061
AA Change: Y149H
PolyPhen 2
Score 0.096 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000029061
Gene: ENSMUSG00000027547
AA Change: Y149H
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
15 |
24 |
N/A |
INTRINSIC |
|
low complexity region
|
25 |
42 |
N/A |
INTRINSIC |
|
ZnF_C2H2
|
68 |
88 |
1.31e2 |
SMART |
|
low complexity region
|
193 |
203 |
N/A |
INTRINSIC |
|
low complexity region
|
210 |
230 |
N/A |
INTRINSIC |
|
low complexity region
|
254 |
278 |
N/A |
INTRINSIC |
|
low complexity region
|
295 |
313 |
N/A |
INTRINSIC |
|
ZnF_C2H2
|
387 |
409 |
1.04e-3 |
SMART |
|
ZnF_C2H2
|
415 |
437 |
2.15e-5 |
SMART |
|
ZnF_C2H2
|
573 |
595 |
5.34e0 |
SMART |
|
ZnF_C2H2
|
601 |
623 |
1.22e-4 |
SMART |
|
ZnF_C2H2
|
633 |
655 |
1.84e-4 |
SMART |
|
low complexity region
|
855 |
867 |
N/A |
INTRINSIC |
|
ZnF_C2H2
|
880 |
902 |
2.53e-2 |
SMART |
|
ZnF_C2H2
|
908 |
930 |
1.13e-4 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000075044
|
| SMART Domains |
Protein: ENSMUSP00000074556
Gene: ENSMUSG00000027547
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
15 |
24 |
N/A |
INTRINSIC |
|
low complexity region
|
30 |
38 |
N/A |
INTRINSIC |
|
low complexity region
|
66 |
78 |
N/A |
INTRINSIC |
|
ZnF_C2H2
|
91 |
113 |
2.53e-2 |
SMART |
|
ZnF_C2H2
|
119 |
141 |
1.13e-4 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000103074
AA Change: Y149H
PolyPhen 2
Score 0.096 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000099363
Gene: ENSMUSG00000027547
AA Change: Y149H
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
15 |
24 |
N/A |
INTRINSIC |
|
low complexity region
|
25 |
42 |
N/A |
INTRINSIC |
|
ZnF_C2H2
|
68 |
88 |
1.31e2 |
SMART |
|
low complexity region
|
193 |
203 |
N/A |
INTRINSIC |
|
low complexity region
|
210 |
230 |
N/A |
INTRINSIC |
|
low complexity region
|
254 |
278 |
N/A |
INTRINSIC |
|
low complexity region
|
295 |
313 |
N/A |
INTRINSIC |
|
low complexity region
|
411 |
423 |
N/A |
INTRINSIC |
|
ZnF_C2H2
|
436 |
458 |
2.53e-2 |
SMART |
|
ZnF_C2H2
|
464 |
486 |
1.13e-4 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000125138
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130640
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000137536
AA Change: Y118H
PolyPhen 2
Score 0.043 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000115646
Gene: ENSMUSG00000027547
AA Change: Y118H
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:ZnF_C2H2
|
37 |
61 |
6e-9 |
BLAST |
|
low complexity region
|
162 |
172 |
N/A |
INTRINSIC |
|
low complexity region
|
179 |
199 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000150588
|
| SMART Domains |
Protein: ENSMUSP00000119628
Gene: ENSMUSG00000027547
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_C2H2
|
64 |
86 |
1.22e-4 |
SMART |
|
ZnF_C2H2
|
96 |
118 |
1.84e-4 |
SMART |
|
| Meta Mutation Damage Score |
0.0734 |
| Coding Region Coverage |
- 1x: 98.8%
- 3x: 97.7%
- 10x: 94.7%
- 20x: 89.0%
|
| Validation Efficiency |
100% (55/55) |
| MGI Phenotype |
FUNCTION: This gene belongs to the spalt family of zinc finger transcription factors. In mouse, functions for this gene have been described in many embryonic developmental processes, including brain, heart, and limb development. In addition, this gene is an important pluripotency factor that is required for stem cell maintenance. Homozygous mutant mice display embryonic lethality, while conditional knock-out in embryonic germ cells results in failure to establish a robust stem cell population. A pseudogene of this gene is found on chromosome 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
PHENOTYPE: Homozygous mutation of this gene results in early embryonic lethality before somite formation. Heterozygous mutation of this locus causes variable phenotypes, from heart and digit defects to deafness, anogenital tract defects, cranial and carpal bone defects and renal agenesis or hypoplasia. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 49 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca8b |
T |
A |
11: 109,844,379 (GRCm39) |
D884V |
probably damaging |
Het |
| Acvr2a |
C |
T |
2: 48,789,628 (GRCm39) |
T457M |
probably damaging |
Het |
| Akr1b10 |
C |
T |
6: 34,369,394 (GRCm39) |
T208I |
probably benign |
Het |
| Aldh16a1 |
G |
T |
7: 44,796,674 (GRCm39) |
T275K |
possibly damaging |
Het |
| Alkbh2 |
C |
T |
5: 114,262,287 (GRCm39) |
E148K |
probably damaging |
Het |
| Asgr1 |
T |
G |
11: 69,946,923 (GRCm39) |
C56W |
probably benign |
Het |
| Atp11b |
T |
C |
3: 35,860,918 (GRCm39) |
I335T |
probably damaging |
Het |
| BC061237 |
A |
G |
14: 44,741,762 (GRCm39) |
|
probably benign |
Het |
| Bdh1 |
G |
T |
16: 31,275,720 (GRCm39) |
K280N |
probably benign |
Het |
| Bmp1 |
C |
T |
14: 70,729,906 (GRCm39) |
C466Y |
probably damaging |
Het |
| Ccdc181 |
A |
G |
1: 164,108,172 (GRCm39) |
E285G |
probably benign |
Het |
| Ces1f |
C |
T |
8: 94,006,277 (GRCm39) |
G18R |
probably damaging |
Het |
| Cfap43 |
T |
A |
19: 47,824,045 (GRCm39) |
I109L |
possibly damaging |
Het |
| Cma2 |
T |
C |
14: 56,210,283 (GRCm39) |
L56S |
probably damaging |
Het |
| Edc4 |
A |
G |
8: 106,617,382 (GRCm39) |
|
probably benign |
Het |
| F3 |
T |
C |
3: 121,526,159 (GRCm39) |
C241R |
probably damaging |
Het |
| Fhdc1 |
T |
A |
3: 84,352,310 (GRCm39) |
S972C |
probably damaging |
Het |
| Heatr1 |
T |
G |
13: 12,432,513 (GRCm39) |
I1086R |
possibly damaging |
Het |
| Hsh2d |
A |
T |
8: 72,950,738 (GRCm39) |
|
probably benign |
Het |
| Ice1 |
T |
C |
13: 70,744,340 (GRCm39) |
Y2081C |
probably damaging |
Het |
| Il1rl1 |
A |
G |
1: 40,481,873 (GRCm39) |
N194D |
probably damaging |
Het |
| Ip6k1 |
G |
A |
9: 107,923,022 (GRCm39) |
V385M |
probably damaging |
Het |
| Lig1 |
G |
A |
7: 13,022,611 (GRCm39) |
R147Q |
probably damaging |
Het |
| Lrp1b |
C |
T |
2: 40,537,165 (GRCm39) |
V41I |
probably damaging |
Het |
| Macroh2a2 |
A |
T |
10: 61,585,112 (GRCm39) |
D177E |
possibly damaging |
Het |
| Mst1r |
T |
A |
9: 107,794,424 (GRCm39) |
V1201E |
probably damaging |
Het |
| Myof |
T |
C |
19: 37,892,116 (GRCm39) |
|
probably benign |
Het |
| Nbas |
G |
T |
12: 13,532,379 (GRCm39) |
|
probably benign |
Het |
| Ndst1 |
A |
G |
18: 60,840,719 (GRCm39) |
I321T |
possibly damaging |
Het |
| Nek10 |
G |
A |
14: 14,850,983 (GRCm38) |
G343R |
probably damaging |
Het |
| Or2a7 |
A |
T |
6: 43,151,234 (GRCm39) |
T105S |
probably benign |
Het |
| Or2y1 |
T |
A |
11: 49,385,650 (GRCm39) |
C97S |
probably damaging |
Het |
| Or4d2b |
A |
T |
11: 87,780,122 (GRCm39) |
I200N |
probably damaging |
Het |
| Pde4d |
T |
C |
13: 109,253,595 (GRCm39) |
S141P |
probably benign |
Het |
| Pigm |
A |
T |
1: 172,204,381 (GRCm39) |
Q39L |
probably damaging |
Het |
| Prl7a2 |
T |
A |
13: 27,846,750 (GRCm39) |
I88F |
probably benign |
Het |
| Prss16 |
T |
A |
13: 22,192,856 (GRCm39) |
|
probably benign |
Het |
| Psmc4 |
G |
A |
7: 27,742,222 (GRCm39) |
|
probably benign |
Het |
| Ptger3 |
T |
A |
3: 157,273,365 (GRCm39) |
C237* |
probably null |
Het |
| Recql |
G |
A |
6: 142,318,601 (GRCm39) |
T214M |
probably damaging |
Het |
| Rfx7 |
T |
A |
9: 72,526,857 (GRCm39) |
V1349D |
probably damaging |
Het |
| Ros1 |
A |
G |
10: 51,964,041 (GRCm39) |
S1740P |
probably damaging |
Het |
| Rrm2b |
A |
T |
15: 37,947,053 (GRCm39) |
S83T |
probably benign |
Het |
| Smad1 |
A |
G |
8: 80,076,207 (GRCm39) |
|
probably benign |
Het |
| Snrnp70 |
T |
C |
7: 45,030,129 (GRCm39) |
|
probably benign |
Het |
| Spef2 |
C |
A |
15: 9,725,194 (GRCm39) |
|
probably benign |
Het |
| Sptlc1 |
T |
C |
13: 53,505,660 (GRCm39) |
T253A |
probably benign |
Het |
| Zbbx |
T |
C |
3: 74,959,784 (GRCm39) |
Y595C |
possibly damaging |
Het |
| Zfp382 |
T |
C |
7: 29,833,114 (GRCm39) |
V255A |
probably benign |
Het |
|
| Other mutations in Sall4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00569:Sall4
|
APN |
2 |
168,597,232 (GRCm39) |
missense |
probably benign |
0.02 |
|
IGL00592:Sall4
|
APN |
2 |
168,597,883 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL00674:Sall4
|
APN |
2 |
168,597,700 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL01308:Sall4
|
APN |
2 |
168,592,164 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL01538:Sall4
|
APN |
2 |
168,597,776 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01552:Sall4
|
APN |
2 |
168,598,043 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02614:Sall4
|
APN |
2 |
168,597,805 (GRCm39) |
missense |
probably null |
0.79 |
|
R0514:Sall4
|
UTSW |
2 |
168,597,625 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0531:Sall4
|
UTSW |
2 |
168,598,256 (GRCm39) |
missense |
probably benign |
0.10 |
|
R0747:Sall4
|
UTSW |
2 |
168,596,886 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1736:Sall4
|
UTSW |
2 |
168,594,555 (GRCm39) |
missense |
probably benign |
0.10 |
|
R2067:Sall4
|
UTSW |
2 |
168,598,465 (GRCm39) |
missense |
probably benign |
0.00 |
|
R3766:Sall4
|
UTSW |
2 |
168,597,964 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R3783:Sall4
|
UTSW |
2 |
168,598,043 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3784:Sall4
|
UTSW |
2 |
168,598,043 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3785:Sall4
|
UTSW |
2 |
168,598,043 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3787:Sall4
|
UTSW |
2 |
168,598,043 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3877:Sall4
|
UTSW |
2 |
168,598,162 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4356:Sall4
|
UTSW |
2 |
168,597,400 (GRCm39) |
missense |
probably benign |
0.37 |
|
R4358:Sall4
|
UTSW |
2 |
168,597,400 (GRCm39) |
missense |
probably benign |
0.37 |
|
R4760:Sall4
|
UTSW |
2 |
168,592,347 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4869:Sall4
|
UTSW |
2 |
168,597,637 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5979:Sall4
|
UTSW |
2 |
168,592,263 (GRCm39) |
missense |
probably benign |
0.28 |
|
R6089:Sall4
|
UTSW |
2 |
168,597,406 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R6502:Sall4
|
UTSW |
2 |
168,597,628 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6990:Sall4
|
UTSW |
2 |
168,596,990 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7999:Sall4
|
UTSW |
2 |
168,594,561 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8436:Sall4
|
UTSW |
2 |
168,597,830 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9069:Sall4
|
UTSW |
2 |
168,596,773 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9375:Sall4
|
UTSW |
2 |
168,597,781 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9630:Sall4
|
UTSW |
2 |
168,596,408 (GRCm39) |
missense |
probably benign |
|
|
R9720:Sall4
|
UTSW |
2 |
168,592,160 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1177:Sall4
|
UTSW |
2 |
168,594,495 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- ACGCGAATCTGTTCCGTAAGCTG -3'
(R):5'- AAGTTGCACTAAAACCCCTCCTGTC -3'
Sequencing Primer
(F):5'- ACAGGATCTGCTCCAGGAC -3'
(R):5'- TGTCCTCATCATGAATGACAGC -3'
|
| Posted On |
2014-02-18 |
Incidental Mutation