Incidental Mutation 'R4384:Sema4d'
| ID |
326128 |
| 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 |
042002-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4384 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
51839565-51947783 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 51856919 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Proline
at position 771
(L771P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000105667
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021900]
[ENSMUST00000110039]
[ENSMUST00000110040]
[ENSMUST00000110042]
|
| AlphaFold |
O09126 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000021900
AA Change: L771P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451
AA Change: L771P
| 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 damaging
Transcript: ENSMUST00000110039
AA Change: L771P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451
AA Change: L771P
| 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 damaging
Transcript: ENSMUST00000110040
AA Change: L771P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451
AA Change: L771P
| 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: ENSMUST00000110042
|
| SMART Domains |
Protein: ENSMUSP00000105669
Gene: ENSMUSG00000021451
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:IG
|
2 |
46 |
2e-15 |
BLAST |
|
| Meta Mutation Damage Score |
0.4127 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.4%
|
| Validation Efficiency |
97% (56/58) |
| 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: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acer2 |
T |
A |
4: 86,792,805 (GRCm39) |
V27E |
possibly damaging |
Het |
| Adam23 |
T |
C |
1: 63,605,787 (GRCm39) |
Y624H |
probably damaging |
Het |
| Arhgef10 |
T |
A |
8: 14,980,157 (GRCm39) |
C132* |
probably null |
Het |
| Boc |
A |
T |
16: 44,311,545 (GRCm39) |
L726H |
probably damaging |
Het |
| Brip1 |
A |
T |
11: 86,039,255 (GRCm39) |
D426E |
possibly damaging |
Het |
| Cadps2 |
T |
A |
6: 23,412,987 (GRCm39) |
Q654L |
probably benign |
Het |
| Calr3 |
T |
A |
8: 73,182,008 (GRCm39) |
D120V |
probably damaging |
Het |
| Cntnap3 |
A |
G |
13: 64,896,274 (GRCm39) |
Y1067H |
probably damaging |
Het |
| Csnk1g1 |
T |
C |
9: 65,927,190 (GRCm39) |
V119A |
probably damaging |
Het |
| Ddias |
G |
A |
7: 92,507,431 (GRCm39) |
T828I |
probably damaging |
Het |
| Dennd4c |
A |
G |
4: 86,729,687 (GRCm39) |
Y763C |
probably damaging |
Het |
| Dscam |
T |
A |
16: 96,510,416 (GRCm39) |
I948F |
probably damaging |
Het |
| E030018B13Rik |
A |
G |
7: 63,569,141 (GRCm39) |
|
probably benign |
Het |
| E2f8 |
G |
A |
7: 48,516,847 (GRCm39) |
T844I |
possibly damaging |
Het |
| Eps8 |
T |
A |
6: 137,476,590 (GRCm39) |
H603L |
probably benign |
Het |
| Esrrg |
G |
A |
1: 187,775,908 (GRCm39) |
C122Y |
probably damaging |
Het |
| Frmd4a |
C |
T |
2: 4,599,374 (GRCm39) |
R467* |
probably null |
Het |
| Gad2 |
G |
A |
2: 22,575,422 (GRCm39) |
V509I |
probably benign |
Het |
| Gpat4 |
A |
G |
8: 23,664,602 (GRCm39) |
I446T |
probably benign |
Het |
| Klhl12 |
T |
G |
1: 134,415,392 (GRCm39) |
D435E |
probably damaging |
Het |
| Luc7l |
T |
C |
17: 26,498,936 (GRCm39) |
|
probably benign |
Het |
| Marchf2 |
C |
A |
17: 33,915,167 (GRCm39) |
M142I |
probably benign |
Het |
| Marf1 |
T |
A |
16: 13,960,505 (GRCm39) |
Y513F |
possibly damaging |
Het |
| Mdm2 |
T |
C |
10: 117,532,344 (GRCm39) |
D114G |
possibly damaging |
Het |
| Med1 |
G |
A |
11: 98,043,688 (GRCm39) |
|
probably benign |
Het |
| Meikin |
C |
T |
11: 54,308,613 (GRCm39) |
Q404* |
probably null |
Het |
| Myh9 |
A |
T |
15: 77,675,912 (GRCm39) |
|
probably benign |
Het |
| Mylip |
T |
C |
13: 45,543,434 (GRCm39) |
M1T |
probably null |
Het |
| Ncapg2 |
T |
C |
12: 116,403,497 (GRCm39) |
|
probably null |
Het |
| Nmd3 |
T |
C |
3: 69,631,731 (GRCm39) |
|
probably benign |
Het |
| Nwd2 |
T |
A |
5: 63,963,914 (GRCm39) |
L1166H |
probably damaging |
Het |
| Or1j13 |
A |
G |
2: 36,370,010 (GRCm39) |
L44P |
probably damaging |
Het |
| Or8b48 |
T |
C |
9: 38,493,349 (GRCm39) |
Y259H |
probably damaging |
Het |
| Rubcn |
A |
G |
16: 32,677,272 (GRCm39) |
I71T |
probably damaging |
Het |
| Rwdd3 |
T |
C |
3: 120,952,406 (GRCm39) |
|
probably benign |
Het |
| Ryr2 |
T |
C |
13: 11,620,119 (GRCm39) |
E3826G |
probably damaging |
Het |
| Sdad1 |
T |
C |
5: 92,446,116 (GRCm39) |
Q273R |
probably benign |
Het |
| Sdha |
A |
T |
13: 74,475,104 (GRCm39) |
I579K |
possibly damaging |
Het |
| Shroom3 |
G |
T |
5: 93,090,945 (GRCm39) |
V1151F |
probably damaging |
Het |
| Slc6a11 |
A |
G |
6: 114,224,688 (GRCm39) |
E624G |
possibly damaging |
Het |
| Tada3 |
G |
T |
6: 113,347,340 (GRCm39) |
R117S |
probably damaging |
Het |
| Tm9sf3 |
T |
C |
19: 41,236,372 (GRCm39) |
M130V |
probably damaging |
Het |
| Trpc1 |
C |
A |
9: 95,614,161 (GRCm39) |
M34I |
probably benign |
Het |
| Trpc4ap |
A |
G |
2: 155,482,427 (GRCm39) |
V521A |
possibly damaging |
Het |
| Trpm2 |
A |
G |
10: 77,753,559 (GRCm39) |
V1315A |
probably benign |
Het |
| Tvp23a |
A |
G |
16: 10,246,546 (GRCm39) |
S80P |
probably benign |
Het |
| Usp54 |
A |
T |
14: 20,600,153 (GRCm39) |
|
probably null |
Het |
| Vmn2r27 |
A |
G |
6: 124,201,115 (GRCm39) |
Y281H |
probably benign |
Het |
| Vwf |
T |
A |
6: 125,632,079 (GRCm39) |
I37N |
unknown |
Het |
| Zfp329 |
G |
A |
7: 12,545,584 (GRCm39) |
|
probably benign |
Het |
| Zfp616 |
G |
T |
11: 73,974,005 (GRCm39) |
L91F |
possibly damaging |
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 |
|
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 |
|
R7606:Sema4d
|
UTSW |
13 |
51,877,658 (GRCm39) |
missense |
probably benign |
0.00 |
|
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'- TTGACATCAAACGGTTTGTCC -3'
(R):5'- ATGGTCATCAACACGGTCCC -3'
Sequencing Primer
(F):5'- CAGAGAGTTCATCGATCCGTTGC -3'
(R):5'- GTCCCCCAGCTCCACTCAG -3'
|
| Posted On |
2015-07-06 |
Incidental Mutation