Incidental Mutation 'R1550:Sema5a'
| ID |
169871 |
| 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 |
039589-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1550 (G1)
|
| Quality Score |
176 |
|
Status
|
Not validated
|
| Chromosome |
15 |
| Chromosomal Location |
32244959-32696487 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 32618995 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Threonine
at position 508
(A508T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000069024
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000067458]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000067458
AA Change: A508T
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000069024
Gene: ENSMUSG00000022231
AA Change: A508T
| 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: ENSMUST00000227429
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000227802
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000227807
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000227976
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000228015
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000228442
|
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.1%
- 10x: 95.4%
- 20x: 89.2%
|
| Validation Efficiency |
|
| 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: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc6 |
A |
G |
7: 45,654,668 (GRCm39) |
V551A |
probably benign |
Het |
| Acss1 |
A |
T |
2: 150,484,715 (GRCm39) |
L176Q |
probably damaging |
Het |
| Aldh7a1 |
A |
G |
18: 56,683,454 (GRCm39) |
I117T |
possibly damaging |
Het |
| Arf5 |
C |
T |
6: 28,426,152 (GRCm39) |
R180C |
probably damaging |
Het |
| Arhgap21 |
A |
T |
2: 20,886,576 (GRCm39) |
Y39* |
probably null |
Het |
| Arrdc1 |
A |
G |
2: 24,816,351 (GRCm39) |
L206P |
probably damaging |
Het |
| Cby3 |
A |
T |
11: 50,250,313 (GRCm39) |
Y173F |
probably damaging |
Het |
| Cdh18 |
T |
A |
15: 23,436,634 (GRCm39) |
C497S |
probably damaging |
Het |
| Cyp11b2 |
T |
C |
15: 74,725,442 (GRCm39) |
I226V |
probably benign |
Het |
| Ddit4l |
T |
A |
3: 137,330,036 (GRCm39) |
|
probably null |
Het |
| Ddx11 |
C |
T |
17: 66,445,215 (GRCm39) |
T405I |
probably benign |
Het |
| Dhx40 |
A |
T |
11: 86,667,565 (GRCm39) |
|
probably null |
Het |
| Dlgap2 |
A |
G |
8: 14,872,499 (GRCm39) |
D659G |
probably damaging |
Het |
| Eef2 |
A |
G |
10: 81,016,681 (GRCm39) |
E586G |
probably benign |
Het |
| Fam161a |
A |
G |
11: 22,970,470 (GRCm39) |
Q216R |
possibly damaging |
Het |
| Fbxw24 |
G |
T |
9: 109,436,112 (GRCm39) |
R307S |
probably benign |
Het |
| Gbp2b |
G |
T |
3: 142,312,591 (GRCm39) |
A325S |
probably damaging |
Het |
| Gli1 |
A |
T |
10: 127,174,385 (GRCm39) |
F2Y |
probably damaging |
Het |
| Gnl2 |
T |
C |
4: 124,938,027 (GRCm39) |
V269A |
probably damaging |
Het |
| Grin1 |
A |
G |
2: 25,195,143 (GRCm39) |
V292A |
probably benign |
Het |
| Heg1 |
T |
A |
16: 33,555,923 (GRCm39) |
V1001E |
probably damaging |
Het |
| Herc2 |
T |
A |
7: 55,785,406 (GRCm39) |
I1552N |
probably damaging |
Het |
| Htr1a |
A |
G |
13: 105,581,788 (GRCm39) |
T343A |
probably benign |
Het |
| Itk |
G |
T |
11: 46,280,153 (GRCm39) |
R29S |
probably damaging |
Het |
| Ivns1abp |
G |
T |
1: 151,237,242 (GRCm39) |
G469C |
probably damaging |
Het |
| Jph3 |
A |
T |
8: 122,511,598 (GRCm39) |
N529Y |
possibly damaging |
Het |
| Kdm2b |
A |
G |
5: 123,019,120 (GRCm39) |
L829P |
probably damaging |
Het |
| Kprp |
T |
A |
3: 92,732,033 (GRCm39) |
Y339F |
probably damaging |
Het |
| Lrp2 |
A |
G |
2: 69,333,005 (GRCm39) |
V1504A |
possibly damaging |
Het |
| Lypd6b |
A |
G |
2: 49,833,615 (GRCm39) |
D85G |
probably damaging |
Het |
| Mansc4 |
T |
C |
6: 146,977,136 (GRCm39) |
Y160C |
probably damaging |
Het |
| Mgll |
C |
A |
6: 88,790,871 (GRCm39) |
H164N |
probably benign |
Het |
| Mtmr4 |
A |
T |
11: 87,504,342 (GRCm39) |
D1097V |
probably damaging |
Het |
| Nfasc |
T |
C |
1: 132,536,241 (GRCm39) |
K571E |
probably damaging |
Het |
| Nfat5 |
A |
T |
8: 108,097,205 (GRCm39) |
N1527Y |
probably damaging |
Het |
| Nlgn1 |
A |
G |
3: 25,966,808 (GRCm39) |
L215P |
probably damaging |
Het |
| Or6b9 |
T |
A |
7: 106,555,235 (GRCm39) |
I303L |
probably benign |
Het |
| Pde4dip |
T |
C |
3: 97,627,020 (GRCm39) |
S1173G |
probably damaging |
Het |
| Prrt3 |
A |
T |
6: 113,472,468 (GRCm39) |
V568E |
probably damaging |
Het |
| Ptpra |
G |
A |
2: 130,383,313 (GRCm39) |
R503Q |
possibly damaging |
Het |
| Pttg1ip2 |
C |
A |
5: 5,502,019 (GRCm39) |
W144C |
probably benign |
Het |
| Rnf7l |
A |
G |
10: 63,257,427 (GRCm39) |
L31P |
probably damaging |
Het |
| Serpinb11 |
T |
C |
1: 107,307,418 (GRCm39) |
I283T |
possibly damaging |
Het |
| Setbp1 |
A |
T |
18: 78,901,807 (GRCm39) |
L620Q |
probably damaging |
Het |
| Sipa1l3 |
A |
T |
7: 29,082,628 (GRCm39) |
C756S |
probably benign |
Het |
| Sirpa |
A |
T |
2: 129,471,961 (GRCm39) |
I463F |
probably damaging |
Het |
| Slc13a2 |
G |
T |
11: 78,293,990 (GRCm39) |
N257K |
probably damaging |
Het |
| Slc4a5 |
C |
A |
6: 83,248,039 (GRCm39) |
T530N |
probably damaging |
Het |
| Stab2 |
A |
T |
10: 86,714,790 (GRCm39) |
F125L |
probably benign |
Het |
| Tet2 |
G |
T |
3: 133,175,280 (GRCm39) |
Q1356K |
probably benign |
Het |
| Tet3 |
A |
T |
6: 83,363,010 (GRCm39) |
S856T |
probably damaging |
Het |
| Tg |
C |
T |
15: 66,565,279 (GRCm39) |
T1207I |
possibly damaging |
Het |
| Tkt |
A |
G |
14: 30,287,525 (GRCm39) |
Y173C |
probably damaging |
Het |
| Tlr6 |
T |
A |
5: 65,110,754 (GRCm39) |
I718F |
probably damaging |
Het |
| Tnfrsf11b |
A |
G |
15: 54,117,454 (GRCm39) |
V267A |
possibly damaging |
Het |
| Ubqln3 |
T |
A |
7: 103,790,753 (GRCm39) |
N446Y |
probably damaging |
Het |
| Vmn2r118 |
C |
T |
17: 55,915,083 (GRCm39) |
C521Y |
probably damaging |
Het |
| Vps16 |
A |
G |
2: 130,282,260 (GRCm39) |
D394G |
probably benign |
Het |
| Zfp236 |
A |
T |
18: 82,692,549 (GRCm39) |
M142K |
possibly damaging |
Het |
| Zfp780b |
T |
C |
7: 27,664,282 (GRCm39) |
D91G |
probably benign |
Het |
| Zfp97 |
T |
A |
17: 17,365,468 (GRCm39) |
Y322* |
probably null |
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 |
|
R1484:Sema5a
|
UTSW |
15 |
32,460,431 (GRCm39) |
missense |
probably damaging |
1.00 |
|
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'- TCAGTGAACAATGACTCCTTGCCC -3'
(R):5'- TGGTCCTCCTACAAGCCAGGAATAG -3'
Sequencing Primer
(F):5'- CAGTTCCAGTGTTATCACAGCAAG -3'
(R):5'- TCCTACAAGCCAGGAATAGATCAAG -3'
|
| Posted On |
2014-04-13 |
Incidental Mutation