Incidental Mutation 'R9115:Sema4d'
| ID |
692489 |
| 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 |
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R9115 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
13 |
| Chromosomal Location |
51839565-51947783 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 51877596 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Threonine
at position 79
(S79T)
|
| 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: S79T
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451
AA Change: S79T
| 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: S79T
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451
AA Change: S79T
| 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: S79T
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451
AA Change: S79T
| 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: 99.9%
- 10x: 99.5%
- 20x: 98.1%
|
| 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: 53 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aire |
T |
C |
10: 77,879,309 (GRCm39) |
T17A |
|
Het |
| Ankrd31 |
T |
C |
13: 96,940,773 (GRCm39) |
|
probably null |
Het |
| Brwd1 |
C |
T |
16: 95,848,314 (GRCm39) |
R569K |
probably damaging |
Het |
| Capns1 |
A |
T |
7: 29,889,978 (GRCm39) |
I177K |
probably benign |
Het |
| Ccdc182 |
A |
G |
11: 88,185,343 (GRCm39) |
N141S |
probably benign |
Het |
| Celsr1 |
A |
G |
15: 85,803,217 (GRCm39) |
W2441R |
probably damaging |
Het |
| Cftr |
A |
T |
6: 18,235,310 (GRCm39) |
R516S |
probably damaging |
Het |
| Ckap4 |
C |
T |
10: 84,363,507 (GRCm39) |
V519M |
probably damaging |
Het |
| Col27a1 |
C |
T |
4: 63,231,974 (GRCm39) |
P1277L |
unknown |
Het |
| Cspg4 |
T |
C |
9: 56,797,736 (GRCm39) |
L1400P |
probably damaging |
Het |
| Cyp4f39 |
T |
A |
17: 32,711,296 (GRCm39) |
F481Y |
probably damaging |
Het |
| Dmxl2 |
T |
C |
9: 54,309,011 (GRCm39) |
I1913M |
probably benign |
Het |
| Dock10 |
T |
C |
1: 80,490,156 (GRCm39) |
T1989A |
probably damaging |
Het |
| Eef2 |
CC |
CCC |
10: 81,014,603 (GRCm39) |
|
probably null |
Het |
| Fcgbpl1 |
G |
A |
7: 27,853,754 (GRCm39) |
V1573I |
possibly damaging |
Het |
| Fshr |
T |
A |
17: 89,292,948 (GRCm39) |
I577F |
probably damaging |
Het |
| Gfm2 |
T |
C |
13: 97,301,707 (GRCm39) |
|
probably null |
Het |
| Gm12695 |
T |
C |
4: 96,657,846 (GRCm39) |
N108D |
possibly damaging |
Het |
| Gm3285 |
T |
A |
10: 77,698,007 (GRCm39) |
L52H |
unknown |
Het |
| Gm5930 |
A |
T |
14: 44,575,006 (GRCm39) |
L95* |
probably null |
Het |
| Hjurp |
CTCTGGGAGGGCTTGCTCCGGGGGCAGTGTGTCCTGTTCTTGTGCAGCCCCT |
C |
1: 88,193,999 (GRCm39) |
|
probably benign |
Het |
| Klhl26 |
A |
G |
8: 70,904,896 (GRCm39) |
M338T |
possibly damaging |
Het |
| Lrrc4c |
T |
C |
2: 97,459,686 (GRCm39) |
I104T |
probably benign |
Het |
| Mapk10 |
A |
T |
5: 103,186,532 (GRCm39) |
V60E |
|
Het |
| Mfsd4b3-ps |
T |
A |
10: 39,824,012 (GRCm39) |
K83* |
probably null |
Het |
| Muc15 |
C |
T |
2: 110,562,089 (GRCm39) |
T175I |
probably damaging |
Het |
| Nmu |
G |
A |
5: 76,511,572 (GRCm39) |
|
probably benign |
Het |
| Nol4l |
G |
T |
2: 153,253,638 (GRCm39) |
T645K |
probably damaging |
Het |
| Nr2f1 |
A |
G |
13: 78,337,869 (GRCm39) |
S416P |
probably benign |
Het |
| Ntn4 |
A |
C |
10: 93,569,675 (GRCm39) |
I463L |
probably benign |
Het |
| Nxt2 |
C |
T |
X: 141,020,747 (GRCm39) |
A118V |
possibly damaging |
Het |
| Or12k7 |
T |
C |
2: 36,959,052 (GRCm39) |
L245P |
probably damaging |
Het |
| Or52h2 |
C |
A |
7: 103,838,931 (GRCm39) |
C161F |
possibly damaging |
Het |
| Or8h8 |
T |
A |
2: 86,752,998 (GRCm39) |
R293W |
probably damaging |
Het |
| Pccb |
T |
A |
9: 100,869,908 (GRCm39) |
N341I |
probably damaging |
Het |
| Pgm3 |
G |
A |
9: 86,447,662 (GRCm39) |
L194F |
probably damaging |
Het |
| Prkra |
T |
A |
2: 76,478,193 (GRCm39) |
H3L |
probably benign |
Het |
| Rbm12 |
TATTGCGGGACCGGGCATTGCGGGACCGGGCATTGCGGGACCGGGCATTGCGGGACCGGGCATTGCGGGACCGGGCATTGCGGGACCAGGCATTGCGGGACC |
TATTGCGGGACCGGGCATTGCGGGACCGGGCATTGCGGGACCGGGCATTGCGGGACCAGGCATTGCGGGACC |
2: 155,938,030 (GRCm39) |
|
probably benign |
Het |
| Ryr1 |
T |
A |
7: 28,803,989 (GRCm39) |
K600* |
probably null |
Het |
| Slc37a1 |
T |
C |
17: 31,534,486 (GRCm39) |
C53R |
probably damaging |
Het |
| Sptbn1 |
A |
G |
11: 30,087,526 (GRCm39) |
I971T |
probably damaging |
Het |
| Tcstv1a |
T |
A |
13: 120,355,453 (GRCm39) |
I60F |
possibly damaging |
Het |
| Tdrkh |
G |
T |
3: 94,335,598 (GRCm39) |
C397F |
possibly damaging |
Het |
| Tecrl |
A |
T |
5: 83,427,906 (GRCm39) |
M314K |
possibly damaging |
Het |
| Ttn |
T |
C |
2: 76,780,496 (GRCm39) |
K1131R |
unknown |
Het |
| Uimc1 |
A |
T |
13: 55,198,584 (GRCm39) |
Y531N |
possibly damaging |
Het |
| Usp5 |
A |
G |
6: 124,803,384 (GRCm39) |
S39P |
probably damaging |
Het |
| Virma |
A |
G |
4: 11,498,744 (GRCm39) |
T62A |
probably benign |
Het |
| Vmn2r85 |
A |
G |
10: 130,254,153 (GRCm39) |
Y844H |
probably benign |
Het |
| Yars1 |
T |
C |
4: 129,109,143 (GRCm39) |
V458A |
probably benign |
Het |
| Zfp235 |
G |
A |
7: 23,841,453 (GRCm39) |
C624Y |
probably damaging |
Het |
| Zfp712 |
A |
T |
13: 67,189,241 (GRCm39) |
S429T |
probably damaging |
Het |
| Zmynd11 |
A |
T |
13: 9,743,495 (GRCm39) |
D307E |
probably 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 |
|
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 |
|
Z1176:Sema4d
|
UTSW |
13 |
51,857,111 (GRCm39) |
missense |
probably damaging |
0.99 |
|
| Predicted Primers |
PCR Primer
(F):5'- GAATTTCAGATGTCCTCAGCCTCC -3'
(R):5'- TGAGTTCTGCTCCATGCTGG -3'
Sequencing Primer
(F):5'- AGATGTCCTCAGCCTCCATTAC -3'
(R):5'- ACGCAGGCTCAGCAGTGAC -3'
|
| Posted On |
2021-12-30 |
Incidental Mutation