Incidental Mutation 'R4436:Sdf4'
| ID |
329519 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sdf4
|
| Ensembl Gene |
ENSMUSG00000029076 |
| Gene Name |
stromal cell derived factor 4 |
| Synonyms |
Cab45 |
| MMRRC Submission |
041702-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.143)
|
| Stock # |
R4436 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
156077329-156098067 bp(+) (GRCm39) |
| Type of Mutation |
critical splice donor site (2 bp from exon) |
| DNA Base Change (assembly) |
T to G
at 156093404 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000101204
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030952]
[ENSMUST00000050078]
[ENSMUST00000050078]
[ENSMUST00000050078]
[ENSMUST00000105578]
[ENSMUST00000105578]
[ENSMUST00000105578]
[ENSMUST00000105579]
[ENSMUST00000105579]
[ENSMUST00000105579]
|
| AlphaFold |
Q61112 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030952
|
| SMART Domains |
Protein: ENSMUSP00000030952
Gene: ENSMUSG00000029075
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
22 |
N/A |
INTRINSIC |
|
TNFR
|
27 |
60 |
6.24e-6 |
SMART |
|
TNFR
|
63 |
103 |
1.33e-9 |
SMART |
|
TNFR
|
126 |
164 |
2.59e-3 |
SMART |
|
transmembrane domain
|
213 |
235 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000050078
|
| SMART Domains |
Protein: ENSMUSP00000053175
Gene: ENSMUSG00000029076
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
35 |
N/A |
INTRINSIC |
|
low complexity region
|
44 |
54 |
N/A |
INTRINSIC |
|
EFh
|
101 |
129 |
7.93e-1 |
SMART |
|
EFh
|
140 |
168 |
3.34e1 |
SMART |
|
EFh
|
236 |
264 |
3.48e-1 |
SMART |
|
EFh
|
284 |
309 |
4.08e1 |
SMART |
|
EFh
|
317 |
345 |
2.9e1 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000050078
|
| SMART Domains |
Protein: ENSMUSP00000053175
Gene: ENSMUSG00000029076
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
35 |
N/A |
INTRINSIC |
|
low complexity region
|
44 |
54 |
N/A |
INTRINSIC |
|
EFh
|
101 |
129 |
7.93e-1 |
SMART |
|
EFh
|
140 |
168 |
3.34e1 |
SMART |
|
EFh
|
236 |
264 |
3.48e-1 |
SMART |
|
EFh
|
284 |
309 |
4.08e1 |
SMART |
|
EFh
|
317 |
345 |
2.9e1 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000050078
|
| SMART Domains |
Protein: ENSMUSP00000053175
Gene: ENSMUSG00000029076
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
35 |
N/A |
INTRINSIC |
|
low complexity region
|
44 |
54 |
N/A |
INTRINSIC |
|
EFh
|
101 |
129 |
7.93e-1 |
SMART |
|
EFh
|
140 |
168 |
3.34e1 |
SMART |
|
EFh
|
236 |
264 |
3.48e-1 |
SMART |
|
EFh
|
284 |
309 |
4.08e1 |
SMART |
|
EFh
|
317 |
345 |
2.9e1 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000105578
|
| SMART Domains |
Protein: ENSMUSP00000101203
Gene: ENSMUSG00000029076
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
35 |
N/A |
INTRINSIC |
|
low complexity region
|
44 |
54 |
N/A |
INTRINSIC |
|
EFh
|
101 |
129 |
7.93e-1 |
SMART |
|
EFh
|
140 |
168 |
3.34e1 |
SMART |
|
EFh
|
236 |
264 |
3.48e-1 |
SMART |
|
EFh
|
284 |
309 |
4.08e1 |
SMART |
|
EFh
|
317 |
345 |
2.9e1 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000105578
|
| SMART Domains |
Protein: ENSMUSP00000101203
Gene: ENSMUSG00000029076
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
35 |
N/A |
INTRINSIC |
|
low complexity region
|
44 |
54 |
N/A |
INTRINSIC |
|
EFh
|
101 |
129 |
7.93e-1 |
SMART |
|
EFh
|
140 |
168 |
3.34e1 |
SMART |
|
EFh
|
236 |
264 |
3.48e-1 |
SMART |
|
EFh
|
284 |
309 |
4.08e1 |
SMART |
|
EFh
|
317 |
345 |
2.9e1 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000105578
|
| SMART Domains |
Protein: ENSMUSP00000101203
Gene: ENSMUSG00000029076
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
35 |
N/A |
INTRINSIC |
|
low complexity region
|
44 |
54 |
N/A |
INTRINSIC |
|
EFh
|
101 |
129 |
7.93e-1 |
SMART |
|
EFh
|
140 |
168 |
3.34e1 |
SMART |
|
EFh
|
236 |
264 |
3.48e-1 |
SMART |
|
EFh
|
284 |
309 |
4.08e1 |
SMART |
|
EFh
|
317 |
345 |
2.9e1 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000105579
|
| SMART Domains |
Protein: ENSMUSP00000101204
Gene: ENSMUSG00000029076
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
35 |
N/A |
INTRINSIC |
|
low complexity region
|
44 |
54 |
N/A |
INTRINSIC |
|
EFh
|
101 |
129 |
7.93e-1 |
SMART |
|
EFh
|
140 |
168 |
3.34e1 |
SMART |
|
EFh
|
236 |
264 |
3.48e-1 |
SMART |
|
EFh
|
284 |
309 |
4.08e1 |
SMART |
|
EFh
|
317 |
345 |
2.9e1 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000105579
|
| SMART Domains |
Protein: ENSMUSP00000101204
Gene: ENSMUSG00000029076
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
35 |
N/A |
INTRINSIC |
|
low complexity region
|
44 |
54 |
N/A |
INTRINSIC |
|
EFh
|
101 |
129 |
7.93e-1 |
SMART |
|
EFh
|
140 |
168 |
3.34e1 |
SMART |
|
EFh
|
236 |
264 |
3.48e-1 |
SMART |
|
EFh
|
284 |
309 |
4.08e1 |
SMART |
|
EFh
|
317 |
345 |
2.9e1 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000105579
|
| SMART Domains |
Protein: ENSMUSP00000101204
Gene: ENSMUSG00000029076
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
35 |
N/A |
INTRINSIC |
|
low complexity region
|
44 |
54 |
N/A |
INTRINSIC |
|
EFh
|
101 |
129 |
7.93e-1 |
SMART |
|
EFh
|
140 |
168 |
3.34e1 |
SMART |
|
EFh
|
236 |
264 |
3.48e-1 |
SMART |
|
EFh
|
284 |
309 |
4.08e1 |
SMART |
|
EFh
|
317 |
345 |
2.9e1 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143576
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149971
|
| Meta Mutation Damage Score |
0.9655 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.3%
|
| Validation Efficiency |
96% (54/56) |
| MGI Phenotype |
FUNCTION: This gene encodes a member of the CREC family. The encoded protein contains multiple calcium-binding EF-hand motifs. This protein localizes to the Golgi lumen and may be involved in regulating calcium dependent cellular activities. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adamts16 |
G |
A |
13: 70,927,637 (GRCm39) |
|
probably benign |
Het |
| Aff3 |
T |
C |
1: 38,248,768 (GRCm39) |
I779V |
possibly damaging |
Het |
| Asap1 |
T |
G |
15: 64,221,692 (GRCm39) |
D15A |
probably benign |
Het |
| Ascc2 |
A |
G |
11: 4,606,305 (GRCm39) |
D193G |
probably damaging |
Het |
| Bcl2a1d |
A |
T |
9: 88,613,753 (GRCm39) |
M7K |
probably benign |
Het |
| Ccdc168 |
T |
C |
1: 44,095,276 (GRCm39) |
I1941V |
probably benign |
Het |
| Ccdc85a |
T |
C |
11: 28,526,457 (GRCm39) |
T384A |
probably benign |
Het |
| Cd86 |
T |
C |
16: 36,441,194 (GRCm39) |
N91S |
probably benign |
Het |
| Cdk17 |
T |
A |
10: 93,047,758 (GRCm39) |
|
probably null |
Het |
| Cemip |
T |
C |
7: 83,636,637 (GRCm39) |
D332G |
probably null |
Het |
| Ces2f |
G |
A |
8: 105,679,788 (GRCm39) |
R427H |
probably benign |
Het |
| Clec4a2 |
G |
A |
6: 123,105,013 (GRCm39) |
|
probably null |
Het |
| Coa8 |
T |
A |
12: 111,717,642 (GRCm39) |
D167E |
probably benign |
Het |
| Coq9 |
T |
C |
8: 95,579,743 (GRCm39) |
F198L |
probably benign |
Het |
| Ddx24 |
C |
A |
12: 103,390,233 (GRCm39) |
A253S |
probably damaging |
Het |
| Esyt3 |
A |
T |
9: 99,240,078 (GRCm39) |
|
probably benign |
Het |
| Fat2 |
C |
A |
11: 55,187,024 (GRCm39) |
G1274V |
probably damaging |
Het |
| Ggn |
A |
T |
7: 28,870,976 (GRCm39) |
T132S |
probably damaging |
Het |
| Gm11568 |
T |
A |
11: 99,749,421 (GRCm39) |
C209S |
unknown |
Het |
| Gm6931 |
T |
A |
16: 49,245,225 (GRCm39) |
|
noncoding transcript |
Het |
| Gpr20 |
C |
T |
15: 73,567,649 (GRCm39) |
V247I |
probably benign |
Het |
| Grm8 |
A |
T |
6: 27,761,237 (GRCm39) |
V329E |
possibly damaging |
Het |
| Gtf2ird2 |
T |
C |
5: 134,223,808 (GRCm39) |
L114P |
possibly damaging |
Het |
| Hivep2 |
C |
A |
10: 14,004,713 (GRCm39) |
T437K |
probably benign |
Het |
| Hivep3 |
C |
T |
4: 119,953,120 (GRCm39) |
P479S |
probably benign |
Het |
| Igkv6-20 |
A |
G |
6: 70,313,104 (GRCm39) |
V23A |
probably damaging |
Het |
| Ikbip |
T |
A |
10: 90,937,751 (GRCm39) |
N141K |
probably damaging |
Het |
| Irag1 |
T |
C |
7: 110,476,124 (GRCm39) |
E815G |
probably damaging |
Het |
| Krt77 |
A |
T |
15: 101,773,904 (GRCm39) |
V250E |
probably damaging |
Het |
| Ltn1 |
A |
T |
16: 87,202,502 (GRCm39) |
C1050S |
probably benign |
Het |
| Macf1 |
T |
C |
4: 123,421,135 (GRCm39) |
I40V |
probably benign |
Het |
| Or2h2b-ps1 |
A |
G |
17: 37,480,727 (GRCm39) |
F271L |
probably benign |
Het |
| Or4k15b |
T |
C |
14: 50,272,287 (GRCm39) |
D191G |
probably damaging |
Het |
| Pi4ka |
T |
C |
16: 17,100,246 (GRCm39) |
M1885V |
probably damaging |
Het |
| Plek |
A |
G |
11: 16,942,972 (GRCm39) |
Y107H |
probably damaging |
Het |
| Ppp1r15a |
C |
T |
7: 45,174,203 (GRCm39) |
V202M |
probably damaging |
Het |
| Ppp1r3e |
C |
A |
14: 55,114,007 (GRCm39) |
A222S |
probably benign |
Het |
| Rac2 |
G |
T |
15: 78,454,943 (GRCm39) |
Y32* |
probably null |
Het |
| Siah1b |
G |
A |
X: 162,854,688 (GRCm39) |
P131S |
probably damaging |
Het |
| Spic |
T |
A |
10: 88,512,817 (GRCm39) |
R111S |
probably benign |
Het |
| Ssh3 |
A |
G |
19: 4,315,394 (GRCm39) |
F315L |
probably damaging |
Het |
| Ttn |
T |
C |
2: 76,595,253 (GRCm39) |
K11972R |
probably damaging |
Het |
| Tubd1 |
C |
T |
11: 86,439,745 (GRCm39) |
S30F |
probably benign |
Het |
| Vmn1r17 |
G |
C |
6: 57,337,719 (GRCm39) |
I166M |
possibly damaging |
Het |
| Vmn2r94 |
T |
C |
17: 18,478,645 (GRCm39) |
Y34C |
probably damaging |
Het |
| Xpo7 |
G |
A |
14: 70,906,869 (GRCm39) |
T945M |
probably damaging |
Het |
| Zfp316 |
C |
A |
5: 143,239,803 (GRCm39) |
A739S |
probably damaging |
Het |
| Zswim3 |
T |
A |
2: 164,662,563 (GRCm39) |
C348S |
probably benign |
Het |
|
| Other mutations in Sdf4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01161:Sdf4
|
APN |
4 |
156,093,763 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02283:Sdf4
|
APN |
4 |
156,093,293 (GRCm39) |
missense |
probably benign |
|
|
IGL02666:Sdf4
|
APN |
4 |
156,093,281 (GRCm39) |
nonsense |
probably null |
|
|
IGL02893:Sdf4
|
APN |
4 |
156,080,985 (GRCm39) |
splice site |
probably benign |
|
|
IGL03246:Sdf4
|
APN |
4 |
156,085,154 (GRCm39) |
missense |
probably benign |
0.01 |
|
soap
|
UTSW |
4 |
156,086,916 (GRCm39) |
splice site |
probably null |
|
|
R1648:Sdf4
|
UTSW |
4 |
156,083,886 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R1879:Sdf4
|
UTSW |
4 |
156,094,304 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1893:Sdf4
|
UTSW |
4 |
156,085,205 (GRCm39) |
missense |
probably benign |
0.22 |
|
R3793:Sdf4
|
UTSW |
4 |
156,086,916 (GRCm39) |
splice site |
probably null |
|
|
R4255:Sdf4
|
UTSW |
4 |
156,085,214 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4801:Sdf4
|
UTSW |
4 |
156,085,178 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
R4802:Sdf4
|
UTSW |
4 |
156,085,178 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
R4868:Sdf4
|
UTSW |
4 |
156,093,642 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5752:Sdf4
|
UTSW |
4 |
156,080,761 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5813:Sdf4
|
UTSW |
4 |
156,083,856 (GRCm39) |
missense |
probably benign |
0.03 |
|
R7501:Sdf4
|
UTSW |
4 |
156,080,977 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8109:Sdf4
|
UTSW |
4 |
156,094,295 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8167:Sdf4
|
UTSW |
4 |
156,093,379 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R8867:Sdf4
|
UTSW |
4 |
156,093,759 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGTGCCTGGATAGTCACAGATG -3'
(R):5'- ATCACCATCCTGATCTGCAG -3'
Sequencing Primer
(F):5'- CTGGATAGTCACAGATGTGCCTC -3'
(R):5'- TTGAAGAGAGGTAAGTGTTCAGCTG -3'
|
| Posted On |
2015-07-21 |
Incidental Mutation