Incidental Mutation 'R1484:Sema5a'
| ID |
163348 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema5a
|
| Ensembl Gene |
ENSMUSG00000022231 |
| Gene Name |
sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A |
| Synonyms |
M-Sema D, semF, Semaf, 9130201M22Rik |
| MMRRC Submission |
039537-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1484 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
15 |
| Chromosomal Location |
32244959-32696487 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 32460431 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 64
(D64G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000069024
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000067458]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000067458
AA Change: D64G
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000069024
Gene: ENSMUSG00000022231
AA Change: D64G
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
22 |
N/A |
INTRINSIC |
|
Sema
|
58 |
468 |
2.18e-173 |
SMART |
|
PSI
|
486 |
533 |
1.78e-9 |
SMART |
|
TSP1
|
543 |
597 |
2.23e-1 |
SMART |
|
TSP1
|
598 |
651 |
2.05e-15 |
SMART |
|
TSP1
|
656 |
702 |
6.94e-13 |
SMART |
|
low complexity region
|
707 |
715 |
N/A |
INTRINSIC |
|
low complexity region
|
755 |
771 |
N/A |
INTRINSIC |
|
TSP1
|
787 |
839 |
4.17e-16 |
SMART |
|
TSP1
|
844 |
896 |
9.08e-17 |
SMART |
|
TSP1
|
899 |
946 |
3.19e-3 |
SMART |
|
low complexity region
|
949 |
960 |
N/A |
INTRINSIC |
|
transmembrane domain
|
971 |
993 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000226876
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000227802
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000227976
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000228015
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000228442
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000228555
|
| Meta Mutation Damage Score |
0.8464 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.4%
- 10x: 96.5%
- 20x: 93.4%
|
| Validation Efficiency |
97% (85/88) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the semaphorin gene family that encodes membrane proteins containing a semaphorin domain and several thrombospondin type-1 repeats. Members of this family are involved in axonal guidance during neural development. This gene has been implicated as an autism susceptibility gene.[provided by RefSeq, Jan 2010]
PHENOTYPE: Mice homozygous for one null mutation die during organogenesis and display defects in branching of cranial vessels. Mice homozygous for another null mutation appear normal. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 85 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930584F24Rik |
A |
T |
5: 26,684,776 (GRCm39) |
|
noncoding transcript |
Het |
| Acvr1 |
A |
T |
2: 58,369,901 (GRCm39) |
V36E |
probably damaging |
Het |
| Aldh4a1 |
A |
G |
4: 139,370,758 (GRCm39) |
I414V |
probably benign |
Het |
| Alox5 |
C |
T |
6: 116,431,128 (GRCm39) |
C100Y |
probably damaging |
Het |
| Ano5 |
T |
A |
7: 51,216,068 (GRCm39) |
D348E |
probably damaging |
Het |
| Arhgap30 |
G |
A |
1: 171,230,839 (GRCm39) |
V199M |
probably damaging |
Het |
| Arl13b |
T |
A |
16: 62,626,999 (GRCm39) |
Q234L |
probably benign |
Het |
| Atxn1 |
C |
A |
13: 45,711,052 (GRCm39) |
E627* |
probably null |
Het |
| Bend3 |
T |
C |
10: 43,386,197 (GRCm39) |
F197L |
probably benign |
Het |
| Brca1 |
A |
T |
11: 101,420,638 (GRCm39) |
V190E |
possibly damaging |
Het |
| Brpf1 |
T |
C |
6: 113,292,096 (GRCm39) |
W381R |
probably damaging |
Het |
| Brwd1 |
A |
C |
16: 95,829,491 (GRCm39) |
|
probably null |
Het |
| C1s2 |
T |
C |
6: 124,602,604 (GRCm39) |
I530V |
possibly damaging |
Het |
| C2cd3 |
C |
T |
7: 100,089,397 (GRCm39) |
R1638W |
probably damaging |
Het |
| Capns1 |
T |
A |
7: 29,893,511 (GRCm39) |
|
probably benign |
Het |
| Cd109 |
CATTTATTTATTTATTTATTTATTTATTTATTTAT |
CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT |
9: 78,619,782 (GRCm39) |
|
probably benign |
Het |
| Cep126 |
G |
A |
9: 8,100,554 (GRCm39) |
T660I |
possibly damaging |
Het |
| Cep295 |
A |
C |
9: 15,246,080 (GRCm39) |
I744R |
probably damaging |
Het |
| Chd3 |
T |
C |
11: 69,250,725 (GRCm39) |
E668G |
probably benign |
Het |
| Chek2 |
A |
G |
5: 110,996,553 (GRCm39) |
T172A |
probably damaging |
Het |
| Col6a4 |
A |
G |
9: 105,890,501 (GRCm39) |
|
probably null |
Het |
| Coq3 |
G |
A |
4: 21,900,291 (GRCm39) |
V173I |
probably benign |
Het |
| Cyp4x1 |
A |
T |
4: 114,970,098 (GRCm39) |
I343N |
probably damaging |
Het |
| Dnah7b |
T |
A |
1: 46,176,703 (GRCm39) |
D774E |
probably benign |
Het |
| Dnai3 |
T |
C |
3: 145,802,996 (GRCm39) |
D65G |
probably benign |
Het |
| Ecm1 |
G |
A |
3: 95,643,275 (GRCm39) |
R342C |
probably damaging |
Het |
| Esrra |
T |
C |
19: 6,890,197 (GRCm39) |
Y209C |
probably damaging |
Het |
| Gpr149 |
A |
T |
3: 62,502,592 (GRCm39) |
D421E |
probably benign |
Het |
| Gpr15 |
T |
C |
16: 58,538,937 (GRCm39) |
N51D |
probably damaging |
Het |
| Gpr156 |
T |
C |
16: 37,812,558 (GRCm39) |
V298A |
probably damaging |
Het |
| Hmcn2 |
G |
A |
2: 31,236,507 (GRCm39) |
G350D |
probably damaging |
Het |
| Ifih1 |
A |
T |
2: 62,440,902 (GRCm39) |
N421K |
probably benign |
Het |
| Ilvbl |
C |
A |
10: 78,412,564 (GRCm39) |
T95K |
probably damaging |
Het |
| Itgb4 |
T |
A |
11: 115,890,625 (GRCm39) |
D1104E |
probably benign |
Het |
| Katnip |
C |
A |
7: 125,415,743 (GRCm39) |
|
probably benign |
Het |
| Lipf |
A |
T |
19: 33,942,180 (GRCm39) |
M37L |
probably benign |
Het |
| Lyst |
T |
A |
13: 13,852,775 (GRCm39) |
N2258K |
probably benign |
Het |
| Moxd1 |
A |
G |
10: 24,099,758 (GRCm39) |
Y86C |
probably damaging |
Het |
| Muc5ac |
T |
C |
7: 141,367,629 (GRCm39) |
|
probably null |
Het |
| Myo16 |
G |
A |
8: 10,610,145 (GRCm39) |
R1162H |
probably damaging |
Het |
| Myo5c |
A |
T |
9: 75,208,092 (GRCm39) |
N1609Y |
probably damaging |
Het |
| Nbeal1 |
T |
C |
1: 60,240,098 (GRCm39) |
F155L |
probably damaging |
Het |
| Nek4 |
A |
T |
14: 30,704,290 (GRCm39) |
M602L |
possibly damaging |
Het |
| Nek9 |
A |
G |
12: 85,348,622 (GRCm39) |
S971P |
probably damaging |
Het |
| Nfya |
A |
T |
17: 48,700,570 (GRCm39) |
|
probably benign |
Het |
| Nrxn3 |
A |
T |
12: 89,221,547 (GRCm39) |
N442I |
probably damaging |
Het |
| Nup42 |
A |
C |
5: 24,383,075 (GRCm39) |
K200N |
probably benign |
Het |
| Or1e26 |
T |
A |
11: 73,480,187 (GRCm39) |
I126L |
possibly damaging |
Het |
| Or4c111 |
G |
A |
2: 88,843,713 (GRCm39) |
R232* |
probably null |
Het |
| Or7g32 |
G |
A |
9: 19,389,423 (GRCm39) |
T38I |
probably damaging |
Het |
| Pcdh15 |
T |
A |
10: 74,126,833 (GRCm39) |
I304N |
probably damaging |
Het |
| Pigo |
G |
C |
4: 43,024,779 (GRCm39) |
P107A |
probably damaging |
Het |
| Plce1 |
C |
T |
19: 38,693,783 (GRCm39) |
Q769* |
probably null |
Het |
| Plin2 |
C |
T |
4: 86,575,481 (GRCm39) |
R356H |
probably benign |
Het |
| Ppp1r9a |
G |
T |
6: 5,113,712 (GRCm39) |
E739* |
probably null |
Het |
| Ppp3cc |
G |
T |
14: 70,478,397 (GRCm39) |
N268K |
probably damaging |
Het |
| Prkag3 |
T |
A |
1: 74,779,919 (GRCm39) |
D472V |
probably damaging |
Het |
| Ptch2 |
A |
T |
4: 116,968,046 (GRCm39) |
D846V |
probably damaging |
Het |
| Rhob |
A |
T |
12: 8,549,388 (GRCm39) |
M82K |
probably damaging |
Het |
| Rps6kc1 |
T |
A |
1: 190,531,672 (GRCm39) |
R777W |
possibly damaging |
Het |
| Sap130 |
T |
A |
18: 31,844,380 (GRCm39) |
V850E |
probably damaging |
Het |
| Sema3a |
T |
G |
5: 13,523,407 (GRCm39) |
N125K |
probably damaging |
Het |
| Sgo2b |
T |
A |
8: 64,384,507 (GRCm39) |
D163V |
possibly damaging |
Het |
| Slc15a1 |
A |
T |
14: 121,728,651 (GRCm39) |
Y31* |
probably null |
Het |
| Smchd1 |
A |
T |
17: 71,685,252 (GRCm39) |
M1392K |
probably benign |
Het |
| Sobp |
T |
A |
10: 43,036,827 (GRCm39) |
N37I |
probably damaging |
Het |
| Spock3 |
G |
T |
8: 63,673,739 (GRCm39) |
C142F |
probably damaging |
Het |
| Stx6 |
A |
C |
1: 155,053,650 (GRCm39) |
S86R |
probably benign |
Het |
| Sult2a4 |
C |
A |
7: 13,643,726 (GRCm39) |
M280I |
probably benign |
Het |
| Synm |
A |
T |
7: 67,386,080 (GRCm39) |
D527E |
probably damaging |
Het |
| Tax1bp1 |
C |
T |
6: 52,710,305 (GRCm39) |
R195W |
probably damaging |
Het |
| Themis2 |
A |
T |
4: 132,519,796 (GRCm39) |
N76K |
possibly damaging |
Het |
| Tmem8b |
A |
G |
4: 43,690,234 (GRCm39) |
T890A |
probably benign |
Het |
| Traf7 |
T |
A |
17: 24,730,785 (GRCm39) |
H366L |
possibly damaging |
Het |
| Trim30c |
A |
T |
7: 104,032,459 (GRCm39) |
V289D |
probably benign |
Het |
| Tsr1 |
T |
A |
11: 74,792,914 (GRCm39) |
D407E |
probably damaging |
Het |
| Ubap2 |
G |
T |
4: 41,235,593 (GRCm39) |
A33E |
probably damaging |
Het |
| Unc13d |
C |
A |
11: 115,964,701 (GRCm39) |
R255L |
possibly damaging |
Het |
| Ush2a |
G |
T |
1: 188,542,534 (GRCm39) |
G3367* |
probably null |
Het |
| Vmn1r229 |
T |
C |
17: 21,034,791 (GRCm39) |
L12P |
probably damaging |
Het |
| Vmn2r27 |
C |
A |
6: 124,177,474 (GRCm39) |
G510V |
probably damaging |
Het |
| Vps4b |
T |
C |
1: 106,707,712 (GRCm39) |
E257G |
probably damaging |
Het |
| Vps72 |
T |
C |
3: 95,026,462 (GRCm39) |
S136P |
probably damaging |
Het |
| Wdr36 |
T |
C |
18: 32,976,938 (GRCm39) |
I181T |
possibly damaging |
Het |
| Wfikkn1 |
C |
T |
17: 26,096,765 (GRCm39) |
A520T |
probably benign |
Het |
|
| Other mutations in Sema5a |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00672:Sema5a
|
APN |
15 |
32,619,026 (GRCm39) |
missense |
probably benign |
0.06 |
|
IGL01148:Sema5a
|
APN |
15 |
32,681,641 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01285:Sema5a
|
APN |
15 |
32,575,143 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
IGL01647:Sema5a
|
APN |
15 |
32,417,587 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
IGL01845:Sema5a
|
APN |
15 |
32,474,514 (GRCm39) |
splice site |
probably benign |
|
|
IGL01970:Sema5a
|
APN |
15 |
32,686,792 (GRCm39) |
missense |
probably benign |
0.02 |
|
IGL01986:Sema5a
|
APN |
15 |
32,682,506 (GRCm39) |
splice site |
probably benign |
|
|
IGL02053:Sema5a
|
APN |
15 |
32,550,413 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02234:Sema5a
|
APN |
15 |
32,679,318 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02325:Sema5a
|
APN |
15 |
32,686,977 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
IGL02370:Sema5a
|
APN |
15 |
32,682,445 (GRCm39) |
splice site |
probably benign |
|
|
IGL02427:Sema5a
|
APN |
15 |
32,673,690 (GRCm39) |
splice site |
probably benign |
|
|
IGL02621:Sema5a
|
APN |
15 |
32,538,802 (GRCm39) |
splice site |
probably benign |
|
|
IGL02656:Sema5a
|
APN |
15 |
32,631,431 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL03091:Sema5a
|
APN |
15 |
32,538,880 (GRCm39) |
splice site |
probably benign |
|
|
IGL03107:Sema5a
|
APN |
15 |
32,669,554 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL03114:Sema5a
|
APN |
15 |
32,673,573 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL03222:Sema5a
|
APN |
15 |
32,628,304 (GRCm39) |
missense |
probably benign |
0.32 |
|
PIT4305001:Sema5a
|
UTSW |
15 |
32,628,345 (GRCm39) |
missense |
probably benign |
|
|
R0190:Sema5a
|
UTSW |
15 |
32,562,920 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R0409:Sema5a
|
UTSW |
15 |
32,681,755 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0413:Sema5a
|
UTSW |
15 |
32,669,590 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0504:Sema5a
|
UTSW |
15 |
32,574,949 (GRCm39) |
splice site |
probably benign |
|
|
R1235:Sema5a
|
UTSW |
15 |
32,609,372 (GRCm39) |
missense |
probably benign |
0.04 |
|
R1550:Sema5a
|
UTSW |
15 |
32,618,995 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1557:Sema5a
|
UTSW |
15 |
32,460,418 (GRCm39) |
missense |
probably benign |
0.04 |
|
R1670:Sema5a
|
UTSW |
15 |
32,548,945 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1688:Sema5a
|
UTSW |
15 |
32,669,570 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1760:Sema5a
|
UTSW |
15 |
32,641,252 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1960:Sema5a
|
UTSW |
15 |
32,562,877 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
R1967:Sema5a
|
UTSW |
15 |
32,681,765 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2062:Sema5a
|
UTSW |
15 |
32,609,363 (GRCm39) |
splice site |
probably benign |
|
|
R2082:Sema5a
|
UTSW |
15 |
32,619,002 (GRCm39) |
missense |
probably benign |
0.04 |
|
R2218:Sema5a
|
UTSW |
15 |
32,631,455 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2267:Sema5a
|
UTSW |
15 |
32,575,065 (GRCm39) |
missense |
probably benign |
0.03 |
|
R2299:Sema5a
|
UTSW |
15 |
32,562,922 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R2438:Sema5a
|
UTSW |
15 |
32,550,399 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R2698:Sema5a
|
UTSW |
15 |
32,673,546 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3950:Sema5a
|
UTSW |
15 |
32,689,484 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4197:Sema5a
|
UTSW |
15 |
32,619,064 (GRCm39) |
missense |
probably benign |
|
|
R4496:Sema5a
|
UTSW |
15 |
32,641,133 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4840:Sema5a
|
UTSW |
15 |
32,550,400 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R4842:Sema5a
|
UTSW |
15 |
32,609,563 (GRCm39) |
missense |
probably benign |
|
|
R4867:Sema5a
|
UTSW |
15 |
32,550,436 (GRCm39) |
missense |
possibly damaging |
0.60 |
|
R4934:Sema5a
|
UTSW |
15 |
32,679,310 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4977:Sema5a
|
UTSW |
15 |
32,679,332 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5204:Sema5a
|
UTSW |
15 |
32,686,793 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5580:Sema5a
|
UTSW |
15 |
32,575,031 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5937:Sema5a
|
UTSW |
15 |
32,574,987 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6220:Sema5a
|
UTSW |
15 |
32,686,875 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6897:Sema5a
|
UTSW |
15 |
32,550,421 (GRCm39) |
missense |
probably benign |
0.05 |
|
R7037:Sema5a
|
UTSW |
15 |
32,686,993 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7072:Sema5a
|
UTSW |
15 |
32,575,105 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R7273:Sema5a
|
UTSW |
15 |
32,417,608 (GRCm39) |
missense |
probably benign |
|
|
R7572:Sema5a
|
UTSW |
15 |
32,673,574 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7621:Sema5a
|
UTSW |
15 |
32,609,378 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
R7642:Sema5a
|
UTSW |
15 |
32,682,471 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R7870:Sema5a
|
UTSW |
15 |
32,609,485 (GRCm39) |
missense |
probably benign |
0.23 |
|
R7880:Sema5a
|
UTSW |
15 |
32,686,954 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8025:Sema5a
|
UTSW |
15 |
32,548,928 (GRCm39) |
missense |
probably benign |
0.37 |
|
R8034:Sema5a
|
UTSW |
15 |
32,574,987 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8241:Sema5a
|
UTSW |
15 |
32,575,064 (GRCm39) |
missense |
probably benign |
|
|
R8539:Sema5a
|
UTSW |
15 |
32,618,989 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8728:Sema5a
|
UTSW |
15 |
32,562,703 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8807:Sema5a
|
UTSW |
15 |
32,562,868 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R8825:Sema5a
|
UTSW |
15 |
32,689,498 (GRCm39) |
missense |
probably benign |
0.02 |
|
R9109:Sema5a
|
UTSW |
15 |
32,619,040 (GRCm39) |
missense |
probably benign |
0.02 |
|
R9235:Sema5a
|
UTSW |
15 |
32,619,034 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9298:Sema5a
|
UTSW |
15 |
32,619,040 (GRCm39) |
missense |
probably benign |
0.02 |
|
R9354:Sema5a
|
UTSW |
15 |
32,562,902 (GRCm39) |
nonsense |
probably null |
|
|
R9515:Sema5a
|
UTSW |
15 |
32,679,373 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9663:Sema5a
|
UTSW |
15 |
32,673,546 (GRCm39) |
nonsense |
probably null |
|
|
X0020:Sema5a
|
UTSW |
15 |
32,417,646 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTGCACTGTCTGCTTCAGGACC -3'
(R):5'- GGCAATGGGCAATTCAATGTCACC -3'
Sequencing Primer
(F):5'- TCAGGACCTGGCCTCTC -3'
(R):5'- tgtttcactggatcagactgc -3'
|
| Posted On |
2014-03-28 |
Incidental Mutation