Incidental Mutation 'R2096:Sema4d'
| ID |
232127 |
| 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 |
040100-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2096 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
13 |
| Chromosomal Location |
51839565-51947783 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 51864037 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Asparagine
at position 414
(I414N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000105667
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021900]
[ENSMUST00000110039]
[ENSMUST00000110040]
|
| AlphaFold |
O09126 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000021900
AA Change: I414N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451
AA Change: I414N
| 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: I414N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451
AA Change: I414N
| 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: I414N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451
AA Change: I414N
| 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 |
noncoding transcript
Transcript: ENSMUST00000125511
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.3%
|
| Validation Efficiency |
|
| 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 |
|---|
| Abcb10 |
A |
G |
8: 124,709,195 (GRCm39) |
S120P |
probably benign |
Het |
| Actr3b |
T |
A |
5: 26,036,743 (GRCm39) |
Y185* |
probably null |
Het |
| Atg101 |
T |
A |
15: 101,188,382 (GRCm39) |
H162Q |
possibly damaging |
Het |
| Btf3 |
T |
A |
13: 98,449,659 (GRCm39) |
Q109L |
possibly damaging |
Het |
| Camk2d |
G |
A |
3: 126,574,091 (GRCm39) |
G166D |
probably damaging |
Het |
| Capn7 |
T |
G |
14: 31,071,844 (GRCm39) |
|
probably null |
Het |
| Cd209f |
A |
G |
8: 4,155,537 (GRCm39) |
V17A |
probably benign |
Het |
| Cenpf |
A |
G |
1: 189,385,656 (GRCm39) |
V2208A |
possibly damaging |
Het |
| Cnga1 |
C |
T |
5: 72,776,404 (GRCm39) |
V20I |
possibly damaging |
Het |
| Comp |
T |
C |
8: 70,828,713 (GRCm39) |
C182R |
probably damaging |
Het |
| Ctsl |
A |
G |
13: 64,516,840 (GRCm39) |
|
probably null |
Het |
| Cyp3a44 |
G |
T |
5: 145,725,215 (GRCm39) |
Q329K |
probably damaging |
Het |
| Dcpp1 |
A |
T |
17: 24,099,971 (GRCm39) |
|
probably null |
Het |
| Dhx38 |
A |
G |
8: 110,280,891 (GRCm39) |
V831A |
probably damaging |
Het |
| Dkk2 |
T |
C |
3: 131,791,858 (GRCm39) |
M22T |
probably benign |
Het |
| Dnah2 |
C |
T |
11: 69,346,742 (GRCm39) |
E2615K |
probably damaging |
Het |
| Dpy19l3 |
A |
G |
7: 35,426,713 (GRCm39) |
|
probably null |
Het |
| Gm12888 |
T |
G |
4: 121,176,655 (GRCm39) |
I49L |
probably benign |
Het |
| Insyn2b |
C |
A |
11: 34,352,936 (GRCm39) |
S326Y |
probably benign |
Het |
| Kif15 |
T |
A |
9: 122,815,252 (GRCm39) |
M194K |
probably damaging |
Het |
| Mael |
G |
T |
1: 166,053,244 (GRCm39) |
Q254K |
probably benign |
Het |
| Nek9 |
T |
C |
12: 85,361,322 (GRCm39) |
D461G |
probably benign |
Het |
| Nlrp12 |
T |
C |
7: 3,281,825 (GRCm39) |
N819S |
probably benign |
Het |
| Ntng1 |
T |
A |
3: 109,739,871 (GRCm39) |
N390Y |
probably damaging |
Het |
| Or5g25 |
A |
G |
2: 85,478,434 (GRCm39) |
I77T |
probably benign |
Het |
| P2ry14 |
C |
T |
3: 59,022,738 (GRCm39) |
V250I |
probably damaging |
Het |
| Pcnx2 |
A |
T |
8: 126,485,987 (GRCm39) |
D1870E |
probably benign |
Het |
| Phf2 |
T |
A |
13: 48,985,589 (GRCm39) |
K64* |
probably null |
Het |
| Phip |
T |
C |
9: 82,797,392 (GRCm39) |
H537R |
possibly damaging |
Het |
| Ppa2 |
A |
G |
3: 133,032,445 (GRCm39) |
T97A |
probably damaging |
Het |
| Psd |
G |
A |
19: 46,313,088 (GRCm39) |
|
probably null |
Het |
| Psg23 |
T |
A |
7: 18,348,668 (GRCm39) |
E46D |
probably damaging |
Het |
| Ptch1 |
T |
G |
13: 63,672,773 (GRCm39) |
E944A |
probably benign |
Het |
| Rab11b |
A |
G |
17: 33,967,976 (GRCm39) |
Y74H |
probably damaging |
Het |
| Rfc3 |
A |
T |
5: 151,568,383 (GRCm39) |
S194R |
probably benign |
Het |
| Serpinb1a |
A |
T |
13: 33,031,437 (GRCm39) |
D120E |
probably damaging |
Het |
| Snai2 |
T |
A |
16: 14,524,861 (GRCm39) |
H122Q |
possibly damaging |
Het |
| Spats2l |
T |
C |
1: 57,985,458 (GRCm39) |
S504P |
probably benign |
Het |
| Sprr2j-ps |
T |
C |
3: 92,326,412 (GRCm39) |
S96P |
unknown |
Het |
| Sspo |
G |
T |
6: 48,438,608 (GRCm39) |
V1559L |
probably benign |
Het |
| Tas2r118 |
T |
G |
6: 23,969,912 (GRCm39) |
I50L |
possibly damaging |
Het |
| Tdrd3 |
C |
T |
14: 87,743,788 (GRCm39) |
Q573* |
probably null |
Het |
| Thoc2l |
T |
C |
5: 104,667,835 (GRCm39) |
S786P |
possibly damaging |
Het |
| Tlnrd1 |
G |
A |
7: 83,532,062 (GRCm39) |
T123I |
probably benign |
Het |
| Tmem214 |
T |
A |
5: 31,033,714 (GRCm39) |
L555H |
probably damaging |
Het |
| Tmprss12 |
T |
A |
15: 100,183,117 (GRCm39) |
M153K |
probably benign |
Het |
| Tmprss9 |
G |
A |
10: 80,725,268 (GRCm39) |
G410S |
probably damaging |
Het |
| Trpm6 |
T |
A |
19: 18,803,116 (GRCm39) |
M853K |
probably damaging |
Het |
| Vmn1r35 |
A |
G |
6: 66,655,929 (GRCm39) |
I247T |
possibly damaging |
Het |
| Zcchc7 |
C |
A |
4: 44,931,059 (GRCm39) |
P404T |
probably damaging |
Het |
| Zzef1 |
T |
C |
11: 72,763,465 (GRCm39) |
F1371L |
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 |
|
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 |
|
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'- CAGAGACTCATAATCCCAGGTGC -3'
(R):5'- AGCTAAGTGGGCATGTGACC -3'
Sequencing Primer
(F):5'- AATCCCAGGTGCTGTGATAC -3'
(R):5'- CATGTGACCGCGGTGCTTTTAC -3'
|
| Posted On |
2014-09-18 |
Incidental Mutation