Incidental Mutation 'R8842:Sema4d'
| ID |
674492 |
| 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 |
068669-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R8842 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
51839565-51947783 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 51863018 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Threonine
at position 447
(A447T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000021900
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021900]
[ENSMUST00000110039]
[ENSMUST00000110040]
[ENSMUST00000110042]
|
| AlphaFold |
O09126 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000021900
AA Change: A447T
PolyPhen 2
Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451
AA Change: A447T
| 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: A447T
PolyPhen 2
Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451
AA Change: A447T
| 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: A447T
PolyPhen 2
Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451
AA Change: A447T
| 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 |
0.1212 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.1%
- 20x: 96.1%
|
| Validation Efficiency |
100% (50/50) |
| 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: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Arhgap17 |
G |
A |
7: 122,893,750 (GRCm39) |
P557S |
probably benign |
Het |
| Atad5 |
G |
T |
11: 80,000,910 (GRCm39) |
D1014Y |
possibly damaging |
Het |
| Bmp6 |
T |
A |
13: 38,530,359 (GRCm39) |
S151T |
probably benign |
Het |
| Bmp6 |
C |
T |
13: 38,682,795 (GRCm39) |
Q459* |
probably null |
Het |
| Ccdc39 |
A |
G |
3: 33,880,612 (GRCm39) |
Y452H |
probably damaging |
Het |
| Cenpj |
A |
G |
14: 56,780,329 (GRCm39) |
Y961H |
probably damaging |
Het |
| Col6a6 |
A |
T |
9: 105,655,166 (GRCm39) |
Y852N |
probably damaging |
Het |
| Cpne8 |
A |
G |
15: 90,456,218 (GRCm39) |
I156T |
probably benign |
Het |
| Cul1 |
T |
A |
6: 47,492,010 (GRCm39) |
L430Q |
probably damaging |
Het |
| Dhx30 |
A |
G |
9: 109,914,296 (GRCm39) |
S1031P |
probably benign |
Het |
| Dhx9 |
A |
T |
1: 153,338,335 (GRCm39) |
F774I |
possibly damaging |
Het |
| Fezf2 |
A |
C |
14: 12,345,079 (GRCm38) |
M36R |
probably damaging |
Het |
| Gbp2b |
A |
T |
3: 142,312,576 (GRCm39) |
I320L |
probably benign |
Het |
| Gemin6 |
T |
A |
17: 80,533,115 (GRCm39) |
V16D |
possibly damaging |
Het |
| Gpr158 |
T |
A |
2: 21,581,751 (GRCm39) |
V410D |
possibly damaging |
Het |
| H2-DMb2 |
C |
T |
17: 34,366,904 (GRCm39) |
T112M |
probably damaging |
Het |
| Hecw2 |
T |
C |
1: 53,990,033 (GRCm39) |
T114A |
|
Het |
| Herc2 |
G |
T |
7: 55,738,059 (GRCm39) |
R234L |
probably damaging |
Het |
| Igsf11 |
A |
G |
16: 38,829,243 (GRCm39) |
I46V |
probably benign |
Het |
| Izumo1r |
C |
T |
9: 14,813,705 (GRCm39) |
G38S |
possibly damaging |
Het |
| Katna1 |
A |
G |
10: 7,614,600 (GRCm39) |
D36G |
probably benign |
Het |
| Kdm1b |
G |
T |
13: 47,231,832 (GRCm39) |
R697L |
probably damaging |
Het |
| Kif1b |
T |
A |
4: 149,338,196 (GRCm39) |
I483F |
probably damaging |
Het |
| Krt1 |
AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC |
AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC |
15: 101,758,813 (GRCm39) |
|
probably benign |
Het |
| Lrp1b |
G |
A |
2: 41,158,417 (GRCm39) |
T1714I |
|
Het |
| Man2a2 |
A |
G |
7: 80,003,067 (GRCm39) |
L1014P |
probably damaging |
Het |
| Marf1 |
T |
C |
16: 13,935,169 (GRCm39) |
E1533G |
probably damaging |
Het |
| Mfsd2a |
A |
T |
4: 122,845,623 (GRCm39) |
I176N |
probably damaging |
Het |
| Mterf1b |
T |
A |
5: 4,246,961 (GRCm39) |
F201I |
possibly damaging |
Het |
| Neurod2 |
T |
C |
11: 98,218,507 (GRCm39) |
E219G |
probably damaging |
Het |
| Nln |
T |
C |
13: 104,209,486 (GRCm39) |
E29G |
probably benign |
Het |
| Obscn |
G |
A |
11: 58,892,861 (GRCm39) |
T6795M |
possibly damaging |
Het |
| Or1e1c |
G |
T |
11: 73,266,186 (GRCm39) |
V207F |
probably benign |
Het |
| Or1i2 |
A |
G |
10: 78,447,635 (GRCm39) |
V280A |
possibly damaging |
Het |
| Or1n1 |
C |
A |
2: 36,749,539 (GRCm39) |
A274S |
probably benign |
Het |
| Or4c118 |
C |
T |
2: 88,975,074 (GRCm39) |
V98I |
probably benign |
Het |
| Otog |
A |
T |
7: 45,895,948 (GRCm39) |
I138F |
probably damaging |
Het |
| Pdcd2l |
G |
A |
7: 33,884,192 (GRCm39) |
Q337* |
probably null |
Het |
| Ptprk |
A |
T |
10: 28,442,497 (GRCm39) |
N859I |
probably damaging |
Het |
| Pygl |
G |
T |
12: 70,274,368 (GRCm39) |
|
probably benign |
Het |
| Slc27a6 |
A |
T |
18: 58,712,888 (GRCm39) |
S237C |
probably benign |
Het |
| Smarcc1 |
G |
A |
9: 110,051,199 (GRCm39) |
M1006I |
possibly damaging |
Het |
| Sult2a2 |
G |
T |
7: 13,472,192 (GRCm39) |
G130C |
probably damaging |
Het |
| Trpm7 |
T |
A |
2: 126,663,131 (GRCm39) |
H1039L |
probably benign |
Het |
| Wdr64 |
T |
G |
1: 175,599,893 (GRCm39) |
N573K |
probably benign |
Het |
| Zbtb48 |
T |
C |
4: 152,104,496 (GRCm39) |
I611V |
probably benign |
Het |
| Zer1 |
T |
C |
2: 30,001,062 (GRCm39) |
S120G |
possibly damaging |
Het |
| Zswim4 |
C |
T |
8: 84,940,699 (GRCm39) |
R800Q |
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 |
|
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'- AGTCCTAGCCACAGAGAAGC -3'
(R):5'- GCTTGAGTTATCCACGAGTGTG -3'
Sequencing Primer
(F):5'- GTCCTAGCCACAGAGAAGCTACAAG -3'
(R):5'- TTTAATCCCAGCACTCGGGAG -3'
|
| Posted On |
2021-07-15 |
Incidental Mutation