Incidental Mutation 'R7606:Sema4d'
| ID |
588320 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema4d
|
| Ensembl Gene |
ENSMUSG00000021451 |
| Gene Name |
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D |
| Synonyms |
Semacl2, Semcl2, Semaj, M-sema G, coll-4, CD100, semaphorin H |
| MMRRC Submission |
045676-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R7606 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
51839565-51947783 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 51877658 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 58
(D58G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000021900
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021900]
[ENSMUST00000110039]
[ENSMUST00000110040]
|
| AlphaFold |
O09126 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000021900
AA Change: D58G
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451
AA Change: D58G
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
Sema
|
50 |
482 |
7.68e-192 |
SMART |
|
PSI
|
502 |
554 |
1.41e-12 |
SMART |
|
IG
|
561 |
647 |
4.78e-1 |
SMART |
|
transmembrane domain
|
733 |
755 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000110039
AA Change: D58G
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451
AA Change: D58G
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
Sema
|
50 |
482 |
7.68e-192 |
SMART |
|
PSI
|
502 |
554 |
1.41e-12 |
SMART |
|
IG
|
561 |
647 |
4.78e-1 |
SMART |
|
transmembrane domain
|
733 |
755 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000110040
AA Change: D58G
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451
AA Change: D58G
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
Sema
|
50 |
482 |
7.68e-192 |
SMART |
|
PSI
|
502 |
554 |
1.41e-12 |
SMART |
|
IG
|
561 |
647 |
4.78e-1 |
SMART |
|
transmembrane domain
|
733 |
755 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.0%
|
| Validation Efficiency |
100% (59/59) |
| MGI Phenotype |
PHENOTYPE: Mice homozygous for disruptions in this gene display functional defects in their immune system but are normal in other systems of the body. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aadac |
T |
A |
3: 59,943,456 (GRCm39) |
|
probably null |
Het |
| Adat1 |
T |
C |
8: 112,709,236 (GRCm39) |
K196E |
possibly damaging |
Het |
| Aire |
T |
C |
10: 77,873,767 (GRCm39) |
D314G |
probably damaging |
Het |
| Atp11a |
C |
T |
8: 12,894,427 (GRCm39) |
T674I |
probably damaging |
Het |
| Atp8b1 |
T |
C |
18: 64,688,186 (GRCm39) |
D644G |
probably damaging |
Het |
| Bag4 |
A |
G |
8: 26,259,333 (GRCm39) |
S289P |
probably damaging |
Het |
| Bcat1 |
G |
T |
6: 144,994,358 (GRCm39) |
H46Q |
probably benign |
Het |
| Btg4 |
A |
G |
9: 51,029,307 (GRCm39) |
N164S |
probably damaging |
Het |
| Ccz1 |
G |
A |
5: 143,951,626 (GRCm39) |
A2V |
probably benign |
Het |
| Cd209g |
T |
C |
8: 4,186,839 (GRCm39) |
L128P |
probably damaging |
Het |
| Col4a2 |
T |
A |
8: 11,493,571 (GRCm39) |
M1380K |
probably benign |
Het |
| Cpox |
T |
C |
16: 58,494,812 (GRCm39) |
V283A |
probably benign |
Het |
| Dnah10 |
A |
T |
5: 124,894,776 (GRCm39) |
D3504V |
probably benign |
Het |
| Eml1 |
A |
T |
12: 108,503,625 (GRCm39) |
I741F |
probably benign |
Het |
| Fam171a2 |
A |
G |
11: 102,335,002 (GRCm39) |
V45A |
possibly damaging |
Het |
| Fem1a |
A |
G |
17: 56,563,946 (GRCm39) |
D13G |
probably damaging |
Het |
| Fkbp14 |
A |
G |
6: 54,570,003 (GRCm39) |
I9T |
probably benign |
Het |
| Golt1b |
G |
A |
6: 142,338,068 (GRCm39) |
G13D |
probably damaging |
Het |
| Heatr5b |
T |
C |
17: 79,070,455 (GRCm39) |
N1653D |
probably benign |
Het |
| Hrg |
A |
G |
16: 22,769,873 (GRCm39) |
M1V |
probably null |
Het |
| Itgb2 |
T |
A |
10: 77,391,995 (GRCm39) |
I356N |
probably damaging |
Het |
| Kcnb2 |
A |
G |
1: 15,383,064 (GRCm39) |
E130G |
probably damaging |
Het |
| Kpna2 |
A |
T |
11: 106,882,884 (GRCm39) |
F124Y |
probably damaging |
Het |
| Lyst |
T |
C |
13: 13,812,060 (GRCm39) |
I824T |
probably damaging |
Het |
| Meis2 |
T |
C |
2: 115,893,801 (GRCm39) |
H38R |
possibly damaging |
Het |
| Mknk1 |
T |
G |
4: 115,735,191 (GRCm39) |
I353S |
probably damaging |
Het |
| Mrc1 |
T |
A |
2: 14,242,955 (GRCm39) |
I27N |
probably damaging |
Het |
| Mup4 |
T |
C |
4: 59,958,568 (GRCm39) |
T111A |
probably damaging |
Het |
| Myo1f |
T |
C |
17: 33,795,424 (GRCm39) |
V53A |
probably damaging |
Het |
| Neb |
T |
G |
2: 52,116,456 (GRCm39) |
E994A |
|
Het |
| Nlrc5 |
T |
C |
8: 95,203,745 (GRCm39) |
M615T |
possibly damaging |
Het |
| Nup88 |
T |
C |
11: 70,852,441 (GRCm39) |
E218G |
possibly damaging |
Het |
| Or10g3b |
A |
T |
14: 52,587,420 (GRCm39) |
F28I |
probably benign |
Het |
| Or4c114 |
A |
G |
2: 88,905,641 (GRCm39) |
|
probably benign |
Het |
| Parp11 |
A |
G |
6: 127,447,723 (GRCm39) |
D19G |
probably benign |
Het |
| Parp2 |
A |
T |
14: 51,057,487 (GRCm39) |
T429S |
probably damaging |
Het |
| Pcdhb6 |
G |
A |
18: 37,468,659 (GRCm39) |
E527K |
probably damaging |
Het |
| Pde8a |
A |
G |
7: 80,982,715 (GRCm39) |
Y778C |
probably damaging |
Het |
| Pea15a |
T |
C |
1: 172,028,150 (GRCm39) |
|
probably null |
Het |
| Plcd3 |
A |
G |
11: 102,967,683 (GRCm39) |
Y420H |
probably damaging |
Het |
| Ppp1ca |
C |
A |
19: 4,243,088 (GRCm39) |
S85R |
possibly damaging |
Het |
| Pth |
A |
C |
7: 112,985,450 (GRCm39) |
I13S |
probably benign |
Het |
| Rbm27 |
A |
G |
18: 42,460,578 (GRCm39) |
T842A |
probably damaging |
Het |
| Rcbtb2 |
T |
A |
14: 73,419,806 (GRCm39) |
|
probably null |
Het |
| Rubcnl |
C |
T |
14: 75,276,314 (GRCm39) |
L323F |
probably benign |
Het |
| Ryr3 |
A |
T |
2: 112,475,590 (GRCm39) |
Y4539* |
probably null |
Het |
| Scamp3 |
T |
A |
3: 89,088,525 (GRCm39) |
F244I |
probably damaging |
Het |
| Skor1 |
G |
T |
9: 63,052,664 (GRCm39) |
A435E |
probably damaging |
Het |
| Slc35a4 |
A |
G |
18: 36,815,638 (GRCm39) |
Y156C |
probably benign |
Het |
| Spryd7 |
T |
C |
14: 61,777,607 (GRCm39) |
T158A |
possibly damaging |
Het |
| Srgap3 |
A |
C |
6: 112,716,337 (GRCm39) |
I621S |
probably benign |
Het |
| Tbc1d31 |
A |
G |
15: 57,815,066 (GRCm39) |
E581G |
probably damaging |
Het |
| Tcf4 |
C |
T |
18: 69,776,054 (GRCm39) |
T318I |
probably damaging |
Het |
| Usf3 |
C |
T |
16: 44,039,306 (GRCm39) |
T1262M |
probably damaging |
Het |
| Vcam1 |
T |
C |
3: 115,914,704 (GRCm39) |
D316G |
possibly damaging |
Het |
| Vmn2r72 |
T |
A |
7: 85,400,362 (GRCm39) |
E229V |
possibly damaging |
Het |
| Zfhx2 |
T |
C |
14: 55,304,120 (GRCm39) |
E1288G |
probably benign |
Het |
|
| Other mutations in Sema4d |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02131:Sema4d
|
APN |
13 |
51,856,973 (GRCm39) |
splice site |
probably null |
|
|
IGL02155:Sema4d
|
APN |
13 |
51,857,303 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL02422:Sema4d
|
APN |
13 |
51,857,124 (GRCm39) |
missense |
probably benign |
|
|
IGL02795:Sema4d
|
APN |
13 |
51,857,447 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL03068:Sema4d
|
APN |
13 |
51,862,922 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03164:Sema4d
|
APN |
13 |
51,862,958 (GRCm39) |
missense |
possibly damaging |
0.58 |
|
R0060:Sema4d
|
UTSW |
13 |
51,859,293 (GRCm39) |
unclassified |
probably benign |
|
|
R0060:Sema4d
|
UTSW |
13 |
51,859,293 (GRCm39) |
unclassified |
probably benign |
|
|
R0305:Sema4d
|
UTSW |
13 |
51,866,764 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0309:Sema4d
|
UTSW |
13 |
51,879,347 (GRCm39) |
missense |
probably benign |
0.14 |
|
R0708:Sema4d
|
UTSW |
13 |
51,866,755 (GRCm39) |
missense |
probably benign |
0.17 |
|
R1809:Sema4d
|
UTSW |
13 |
51,867,727 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1851:Sema4d
|
UTSW |
13 |
51,865,258 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R2096:Sema4d
|
UTSW |
13 |
51,864,037 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2159:Sema4d
|
UTSW |
13 |
51,874,571 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2367:Sema4d
|
UTSW |
13 |
51,857,176 (GRCm39) |
intron |
probably benign |
|
|
R4329:Sema4d
|
UTSW |
13 |
51,857,340 (GRCm39) |
missense |
probably benign |
|
|
R4372:Sema4d
|
UTSW |
13 |
51,866,767 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4384:Sema4d
|
UTSW |
13 |
51,856,919 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4590:Sema4d
|
UTSW |
13 |
51,877,654 (GRCm39) |
missense |
probably benign |
0.29 |
|
R4980:Sema4d
|
UTSW |
13 |
51,865,270 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5523:Sema4d
|
UTSW |
13 |
51,865,390 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R6086:Sema4d
|
UTSW |
13 |
51,867,781 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7197:Sema4d
|
UTSW |
13 |
51,856,872 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7340:Sema4d
|
UTSW |
13 |
51,877,598 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7859:Sema4d
|
UTSW |
13 |
51,876,387 (GRCm39) |
missense |
probably benign |
0.30 |
|
R8193:Sema4d
|
UTSW |
13 |
51,859,192 (GRCm39) |
nonsense |
probably null |
|
|
R8703:Sema4d
|
UTSW |
13 |
51,854,959 (GRCm39) |
missense |
|
|
|
R8796:Sema4d
|
UTSW |
13 |
51,865,546 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8842:Sema4d
|
UTSW |
13 |
51,863,018 (GRCm39) |
missense |
probably benign |
0.04 |
|
R8904:Sema4d
|
UTSW |
13 |
51,854,935 (GRCm39) |
nonsense |
probably null |
|
|
R9016:Sema4d
|
UTSW |
13 |
51,867,794 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9115:Sema4d
|
UTSW |
13 |
51,877,596 (GRCm39) |
missense |
probably benign |
|
|
Z1176:Sema4d
|
UTSW |
13 |
51,857,111 (GRCm39) |
missense |
probably damaging |
0.99 |
|
| Predicted Primers |
PCR Primer
(F):5'- CCTTTTAAAGGTGACCACACGG -3'
(R):5'- CTGCATTGAGGTTACCTGGG -3'
Sequencing Primer
(F):5'- CTTTTAAAGGTGACCACACGGAATAC -3'
(R):5'- GTCTGGTGCAGTTTCACAA -3'
|
| Posted On |
2019-10-24 |
Incidental Mutation