Incidental Mutation 'R0060:Sema4d'
| ID |
201412 |
| 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 |
038353-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R0060 (G1)
|
| Quality Score |
73 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
51839565-51947783 bp(-) (GRCm39) |
| Type of Mutation |
unclassified |
| DNA Base Change (assembly) |
A to G
at 51859293 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000105669
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021900]
[ENSMUST00000110039]
[ENSMUST00000110040]
[ENSMUST00000110042]
|
| AlphaFold |
O09126 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000021900
|
| SMART Domains |
Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451
| 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
|
| SMART Domains |
Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451
| 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
|
| SMART Domains |
Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451
| 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 |
0.0898 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.0%
|
| Validation Efficiency |
98% (60/61) |
| 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: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1810065E05Rik |
A |
C |
11: 58,313,008 (GRCm39) |
|
probably benign |
Het |
| A630091E08Rik |
A |
G |
7: 98,192,875 (GRCm39) |
|
noncoding transcript |
Het |
| Abca8a |
T |
C |
11: 109,961,306 (GRCm39) |
T539A |
probably damaging |
Het |
| Ankrd60 |
A |
T |
2: 173,414,406 (GRCm39) |
M1K |
probably null |
Het |
| Arnt2 |
G |
A |
7: 83,996,738 (GRCm39) |
R63C |
probably damaging |
Het |
| Cabcoco1 |
A |
T |
10: 68,369,692 (GRCm39) |
|
probably null |
Het |
| Capn7 |
T |
C |
14: 31,087,561 (GRCm39) |
|
probably benign |
Het |
| Cd109 |
G |
A |
9: 78,610,389 (GRCm39) |
E1145K |
probably damaging |
Het |
| Celsr1 |
A |
T |
15: 85,806,399 (GRCm39) |
V2353D |
probably damaging |
Het |
| Cep350 |
C |
T |
1: 155,804,372 (GRCm39) |
D904N |
probably damaging |
Het |
| Chl1 |
T |
A |
6: 103,688,019 (GRCm39) |
|
probably benign |
Het |
| Colec10 |
G |
A |
15: 54,302,542 (GRCm39) |
|
probably benign |
Het |
| Cst11 |
T |
A |
2: 148,612,322 (GRCm39) |
Q105L |
probably damaging |
Het |
| Eps8l3 |
T |
C |
3: 107,786,857 (GRCm39) |
L11S |
probably damaging |
Het |
| Gsdme |
A |
G |
6: 50,198,009 (GRCm39) |
I317T |
possibly damaging |
Het |
| Itgad |
T |
C |
7: 127,802,158 (GRCm39) |
S979P |
probably damaging |
Het |
| Mga |
T |
C |
2: 119,791,442 (GRCm39) |
|
probably null |
Het |
| Nubpl |
T |
C |
12: 52,357,470 (GRCm39) |
|
probably benign |
Het |
| Or2b4 |
T |
C |
17: 38,116,891 (GRCm39) |
L285P |
probably damaging |
Het |
| Or5be3 |
T |
C |
2: 86,864,118 (GRCm39) |
Y149C |
probably damaging |
Het |
| Pard3b |
G |
A |
1: 61,678,474 (GRCm39) |
E25K |
probably damaging |
Het |
| Phactr1 |
T |
A |
13: 42,836,197 (GRCm39) |
Y8* |
probably null |
Het |
| Phf14 |
T |
C |
6: 11,953,316 (GRCm39) |
S352P |
probably damaging |
Het |
| Ppp1r16a |
C |
T |
15: 76,574,999 (GRCm39) |
|
probably benign |
Het |
| Prap1 |
G |
T |
7: 139,673,390 (GRCm39) |
|
probably benign |
Het |
| Prdm8 |
T |
A |
5: 98,333,119 (GRCm39) |
F229I |
probably benign |
Het |
| Rfx6 |
T |
C |
10: 51,553,936 (GRCm39) |
F11L |
probably benign |
Het |
| Rfx8 |
T |
A |
1: 39,757,565 (GRCm39) |
|
probably benign |
Het |
| Rif1 |
C |
T |
2: 52,001,129 (GRCm39) |
R1528C |
probably damaging |
Het |
| Ripk4 |
G |
A |
16: 97,564,718 (GRCm39) |
|
probably benign |
Het |
| Satb1 |
T |
A |
17: 52,047,231 (GRCm39) |
I695F |
probably damaging |
Het |
| Slc30a4 |
T |
A |
2: 122,527,104 (GRCm39) |
T381S |
probably benign |
Het |
| Suv39h2 |
T |
C |
2: 3,465,953 (GRCm39) |
Y134C |
probably damaging |
Het |
| Tcerg1 |
C |
T |
18: 42,657,073 (GRCm39) |
A185V |
unknown |
Het |
| Tep1 |
T |
A |
14: 51,103,486 (GRCm39) |
D268V |
probably damaging |
Het |
| Tmem89 |
T |
A |
9: 108,744,485 (GRCm39) |
V126D |
probably damaging |
Het |
| Trf |
T |
C |
9: 103,098,121 (GRCm39) |
T46A |
probably benign |
Het |
| Trmt6 |
C |
T |
2: 132,648,689 (GRCm39) |
R415Q |
possibly damaging |
Het |
| Trp53bp1 |
T |
C |
2: 121,035,006 (GRCm39) |
K1625E |
probably damaging |
Het |
| Zcchc4 |
T |
A |
5: 52,964,420 (GRCm39) |
I292N |
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 |
|
|
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 |
|
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'- CCTAGAAGACAGCAGGCGCACA -3'
(R):5'- AGGTCTTAGCGGTCGGGCCTT -3'
Sequencing Primer
(F):5'- AGGCGCACATTACTCTATGGC -3'
(R):5'- GCCTTGTGGCCTATTCTGAG -3'
|
| Posted On |
2014-06-06 |
Incidental Mutation