Incidental Mutation 'R2159:Sema4d'
| ID |
235069 |
| 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 |
040162-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2159 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
13 |
| Chromosomal Location |
51839565-51947783 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 51874571 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Aspartic acid
at position 129
(N129D)
|
| 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: N129D
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451
AA Change: N129D
| 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: N129D
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451
AA Change: N129D
| 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: N129D
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451
AA Change: N129D
| 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: ENSMUST00000138228
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139018
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139858
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139865
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146238
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150662
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143396
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146922
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155896
|
| 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: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam21 |
G |
A |
12: 81,607,241 (GRCm39) |
P174S |
probably benign |
Het |
| Aida |
C |
T |
1: 183,103,234 (GRCm39) |
P185S |
probably benign |
Het |
| Alg11 |
T |
G |
8: 22,555,861 (GRCm39) |
I374R |
probably benign |
Het |
| Ano9 |
T |
C |
7: 140,688,030 (GRCm39) |
I229V |
probably benign |
Het |
| Apob |
A |
T |
12: 8,060,081 (GRCm39) |
L2821F |
probably benign |
Het |
| Atp10b |
C |
T |
11: 43,042,680 (GRCm39) |
T80I |
possibly damaging |
Het |
| BC024139 |
T |
C |
15: 76,005,688 (GRCm39) |
H478R |
probably damaging |
Het |
| Btbd1 |
A |
T |
7: 81,450,804 (GRCm39) |
D325E |
possibly damaging |
Het |
| Camk2a |
G |
A |
18: 61,090,257 (GRCm39) |
C199Y |
probably damaging |
Het |
| Casp3 |
A |
G |
8: 47,087,323 (GRCm39) |
D90G |
probably damaging |
Het |
| Ccnt2 |
A |
G |
1: 127,702,891 (GRCm39) |
H71R |
probably benign |
Het |
| Cdk2ap1 |
G |
A |
5: 124,486,667 (GRCm39) |
R65* |
probably null |
Het |
| Cebpb |
G |
T |
2: 167,531,173 (GRCm39) |
A78S |
probably benign |
Het |
| Col5a3 |
A |
G |
9: 20,682,606 (GRCm39) |
F1613L |
unknown |
Het |
| Cpd |
T |
C |
11: 76,688,467 (GRCm39) |
D935G |
probably damaging |
Het |
| Csmd3 |
CCTTTGCGCTT |
CCTT |
15: 47,604,632 (GRCm39) |
|
probably null |
Het |
| Cwc27 |
A |
G |
13: 104,940,837 (GRCm39) |
I174T |
probably damaging |
Het |
| Cyp21a1 |
C |
A |
17: 35,021,378 (GRCm39) |
R331L |
probably benign |
Het |
| Dnah5 |
A |
G |
15: 28,252,691 (GRCm39) |
T795A |
probably benign |
Het |
| Eif2ak2 |
A |
G |
17: 79,181,447 (GRCm39) |
V100A |
possibly damaging |
Het |
| Foxa3 |
A |
G |
7: 18,748,109 (GRCm39) |
V339A |
probably benign |
Het |
| Gp2 |
T |
C |
7: 119,051,507 (GRCm39) |
D236G |
probably benign |
Het |
| Gprc6a |
CAAA |
CA |
10: 51,491,776 (GRCm39) |
|
probably null |
Het |
| Gzmd |
T |
A |
14: 56,368,153 (GRCm39) |
H102L |
probably damaging |
Het |
| Klk1b1 |
A |
T |
7: 43,619,857 (GRCm39) |
I139F |
probably damaging |
Het |
| Lcmt2 |
G |
A |
2: 120,969,766 (GRCm39) |
P439L |
probably damaging |
Het |
| Loxl4 |
C |
T |
19: 42,588,446 (GRCm39) |
A570T |
probably damaging |
Het |
| Mga |
T |
A |
2: 119,750,124 (GRCm39) |
H674Q |
probably damaging |
Het |
| Mybpc3 |
A |
T |
2: 90,955,715 (GRCm39) |
K583M |
probably damaging |
Het |
| Ncoa6 |
G |
T |
2: 155,249,633 (GRCm39) |
P1224T |
probably damaging |
Het |
| Nostrin |
A |
G |
2: 69,011,266 (GRCm39) |
|
probably null |
Het |
| Or13e8 |
T |
C |
4: 43,697,110 (GRCm39) |
H21R |
probably benign |
Het |
| Or4c3 |
A |
T |
2: 89,851,882 (GRCm39) |
V176E |
probably damaging |
Het |
| Oxsr1 |
A |
C |
9: 119,133,880 (GRCm39) |
D58E |
possibly damaging |
Het |
| Parm1 |
A |
G |
5: 91,760,923 (GRCm39) |
Y265C |
probably damaging |
Het |
| Phf10 |
C |
T |
17: 15,172,926 (GRCm39) |
E304K |
probably damaging |
Het |
| Prmt5 |
T |
C |
14: 54,752,795 (GRCm39) |
T139A |
probably benign |
Het |
| Ptgir |
A |
G |
7: 16,640,794 (GRCm39) |
M29V |
possibly damaging |
Het |
| Ptp4a3 |
A |
G |
15: 73,623,865 (GRCm39) |
T32A |
probably benign |
Het |
| Pwwp2b |
A |
T |
7: 138,834,844 (GRCm39) |
D95V |
possibly damaging |
Het |
| Rad51ap2 |
T |
C |
12: 11,507,752 (GRCm39) |
L558S |
possibly damaging |
Het |
| Rapgef4 |
A |
G |
2: 72,005,225 (GRCm39) |
D80G |
probably damaging |
Het |
| Sec24a |
T |
G |
11: 51,603,177 (GRCm39) |
H757P |
probably damaging |
Het |
| Serpini1 |
A |
G |
3: 75,531,251 (GRCm39) |
T323A |
probably benign |
Het |
| Setd1a |
G |
A |
7: 127,384,661 (GRCm39) |
R504H |
possibly damaging |
Het |
| Sftpb |
T |
C |
6: 72,286,770 (GRCm39) |
C226R |
probably damaging |
Het |
| Sp8 |
T |
C |
12: 118,812,441 (GRCm39) |
S99P |
possibly damaging |
Het |
| Srgap3 |
A |
G |
6: 112,748,339 (GRCm39) |
F438L |
probably damaging |
Het |
| Stim2 |
T |
C |
5: 54,267,156 (GRCm39) |
Y365H |
probably damaging |
Het |
| Stk36 |
A |
G |
1: 74,673,896 (GRCm39) |
Q1263R |
probably benign |
Het |
| Tectb |
C |
G |
19: 55,169,431 (GRCm39) |
|
probably benign |
Het |
| Troap |
G |
T |
15: 98,975,467 (GRCm39) |
A184S |
probably damaging |
Het |
| Ttn |
G |
A |
2: 76,729,671 (GRCm39) |
|
probably benign |
Het |
| Vmn2r108 |
C |
A |
17: 20,689,363 (GRCm39) |
A531S |
probably benign |
Het |
| Vmn2r12 |
T |
A |
5: 109,239,340 (GRCm39) |
I408F |
probably benign |
Het |
| Vmn2r8 |
T |
A |
5: 108,950,169 (GRCm39) |
E226V |
probably benign |
Het |
| Vmo1 |
A |
G |
11: 70,404,608 (GRCm39) |
F131S |
probably benign |
Het |
| Vwf |
T |
C |
6: 125,603,304 (GRCm39) |
F885L |
probably damaging |
Het |
| Wdpcp |
A |
T |
11: 21,807,476 (GRCm39) |
M618L |
probably benign |
Het |
| Wdr90 |
T |
C |
17: 26,070,715 (GRCm39) |
E1072G |
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 |
|
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'- TTGCTGTCAGAAATCCGACTG -3'
(R):5'- TGGGCATAGACAGACCAAAC -3'
Sequencing Primer
(F):5'- CAGTAAGCAGCATTCCTTCATGG -3'
(R):5'- GGCATAGACAGACCAAACCTGAG -3'
|
| Posted On |
2014-10-01 |
Incidental Mutation