Incidental Mutation 'R0305:Sema4d'
| ID |
24923 |
| 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 |
038516-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R0305 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
51839565-51947783 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 51866764 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 242
(Y242C)
|
| 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: Y242C
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451
AA Change: Y242C
| 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: Y242C
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451
AA Change: Y242C
| 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: Y242C
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451
AA Change: Y242C
| 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
|
| Meta Mutation Damage Score |
0.2716 |
| Coding Region Coverage |
- 1x: 98.9%
- 3x: 98.0%
- 10x: 95.5%
- 20x: 91.2%
|
| Validation Efficiency |
100% (59/59) |
| 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: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2310022A10Rik |
G |
A |
7: 27,274,061 (GRCm39) |
R183Q |
probably damaging |
Het |
| Abca5 |
A |
G |
11: 110,164,137 (GRCm39) |
|
probably benign |
Het |
| Ada |
T |
C |
2: 163,570,077 (GRCm39) |
K312R |
probably benign |
Het |
| Adam21 |
C |
A |
12: 81,607,059 (GRCm39) |
K234N |
possibly damaging |
Het |
| Afdn |
T |
A |
17: 14,108,776 (GRCm39) |
|
probably null |
Het |
| Aimp1 |
T |
G |
3: 132,379,747 (GRCm39) |
K132Q |
possibly damaging |
Het |
| Aldh16a1 |
C |
T |
7: 44,797,403 (GRCm39) |
R135Q |
probably damaging |
Het |
| Alox12b |
A |
T |
11: 69,058,205 (GRCm39) |
Y519F |
probably benign |
Het |
| Alppl2 |
T |
C |
1: 87,017,324 (GRCm39) |
E25G |
probably benign |
Het |
| Apob |
A |
T |
12: 8,062,210 (GRCm39) |
N3531I |
probably damaging |
Het |
| Arhgap23 |
T |
C |
11: 97,391,935 (GRCm39) |
L321P |
probably damaging |
Het |
| Cab39l |
C |
T |
14: 59,757,028 (GRCm39) |
Q137* |
probably null |
Het |
| Cenpo |
A |
T |
12: 4,266,660 (GRCm39) |
H149Q |
possibly damaging |
Het |
| Cpt1a |
A |
G |
19: 3,428,455 (GRCm39) |
T610A |
probably benign |
Het |
| Dcbld2 |
A |
G |
16: 58,269,302 (GRCm39) |
T271A |
probably damaging |
Het |
| Dcps |
A |
G |
9: 35,087,065 (GRCm39) |
|
probably null |
Het |
| Dnai2 |
A |
G |
11: 114,643,720 (GRCm39) |
D462G |
probably benign |
Het |
| Dsg2 |
T |
A |
18: 20,715,752 (GRCm39) |
|
probably benign |
Het |
| Eomes |
A |
T |
9: 118,313,825 (GRCm39) |
E623D |
probably benign |
Het |
| Fras1 |
A |
T |
5: 96,744,747 (GRCm39) |
H594L |
probably benign |
Het |
| Gad1-ps |
T |
G |
10: 99,280,665 (GRCm39) |
|
noncoding transcript |
Het |
| Galk2 |
A |
G |
2: 125,729,808 (GRCm39) |
Y63C |
probably damaging |
Het |
| H2-T10 |
A |
G |
17: 36,430,260 (GRCm39) |
L227P |
probably damaging |
Het |
| Itgb4 |
T |
G |
11: 115,870,238 (GRCm39) |
C73G |
probably damaging |
Het |
| Itpr2 |
T |
C |
6: 146,212,601 (GRCm39) |
H1472R |
possibly damaging |
Het |
| Kcnh5 |
C |
T |
12: 75,161,171 (GRCm39) |
A246T |
probably benign |
Het |
| Kpna6 |
G |
T |
4: 129,543,042 (GRCm39) |
R458S |
probably benign |
Het |
| Lifr |
A |
G |
15: 7,206,982 (GRCm39) |
T498A |
probably damaging |
Het |
| Lrrd1 |
T |
G |
5: 3,915,707 (GRCm39) |
I768S |
probably damaging |
Het |
| Map2 |
T |
C |
1: 66,452,253 (GRCm39) |
V223A |
probably benign |
Het |
| Nod2 |
G |
A |
8: 89,391,951 (GRCm39) |
A731T |
probably damaging |
Het |
| Nrxn2 |
G |
A |
19: 6,569,313 (GRCm39) |
C1403Y |
probably damaging |
Het |
| Nxph1 |
A |
T |
6: 9,247,754 (GRCm39) |
I242F |
probably damaging |
Het |
| Or5p79 |
G |
A |
7: 108,221,792 (GRCm39) |
V258I |
probably benign |
Het |
| Pgr |
A |
G |
9: 8,902,088 (GRCm39) |
|
probably benign |
Het |
| Pik3cb |
A |
G |
9: 98,946,129 (GRCm39) |
S566P |
possibly damaging |
Het |
| Sftpc |
T |
A |
14: 70,761,518 (GRCm39) |
|
probably benign |
Het |
| Sh3tc1 |
T |
G |
5: 35,881,343 (GRCm39) |
E33D |
probably benign |
Het |
| Slc17a5 |
A |
G |
9: 78,464,819 (GRCm39) |
L344P |
probably benign |
Het |
| Slc39a5 |
T |
A |
10: 128,234,265 (GRCm39) |
|
probably benign |
Het |
| Slc7a13 |
C |
A |
4: 19,839,401 (GRCm39) |
H335N |
probably benign |
Het |
| Slco1a4 |
A |
C |
6: 141,763,479 (GRCm39) |
N412K |
possibly damaging |
Het |
| Sox1 |
A |
T |
8: 12,446,736 (GRCm39) |
T126S |
probably damaging |
Het |
| Specc1l |
T |
A |
10: 75,081,663 (GRCm39) |
V353E |
probably damaging |
Het |
| Stat5b |
T |
C |
11: 100,693,329 (GRCm39) |
E104G |
probably benign |
Het |
| Sult4a1 |
A |
G |
15: 83,970,868 (GRCm39) |
V179A |
probably damaging |
Het |
| Tafa5 |
T |
A |
15: 87,604,709 (GRCm39) |
I83N |
probably damaging |
Het |
| Tbl3 |
G |
A |
17: 24,924,435 (GRCm39) |
R134C |
probably damaging |
Het |
| Tmem256 |
T |
A |
11: 69,729,737 (GRCm39) |
|
probably benign |
Het |
| Tmigd1 |
A |
G |
11: 76,797,960 (GRCm39) |
T101A |
probably damaging |
Het |
| Unc5b |
C |
A |
10: 60,615,437 (GRCm39) |
|
probably benign |
Het |
| Unc79 |
T |
A |
12: 103,079,459 (GRCm39) |
S1679T |
probably benign |
Het |
| Vmn2r1 |
T |
G |
3: 63,997,087 (GRCm39) |
C248G |
probably damaging |
Het |
| Vmn2r57 |
T |
C |
7: 41,076,967 (GRCm39) |
I400V |
probably benign |
Het |
| Vwa8 |
T |
A |
14: 79,246,713 (GRCm39) |
L685H |
probably damaging |
Het |
| Yeats4 |
A |
G |
10: 117,051,741 (GRCm39) |
F172S |
probably damaging |
Het |
| Zfpm2 |
T |
G |
15: 40,637,431 (GRCm39) |
|
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 |
|
|
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'- TGGGTCTCAAGAGAAACCATGCAC -3'
(R):5'- AGGAGTCTGGAAATCCTTCGGGTG -3'
Sequencing Primer
(F):5'- ctggtctcttactgtgcctc -3'
(R):5'- TGTGGCATACATACTGTAGACG -3'
|
| Posted On |
2013-04-16 |
Incidental Mutation