Incidental Mutation 'R1760:Sema5a'
ID |
192727 |
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 |
039792-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R1760 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
15 |
Chromosomal Location |
32244959-32696487 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to G
at 32641252 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Cysteine to Glycine
at position 689
(C689G)
|
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: C689G
PolyPhen 2
Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000069024 Gene: ENSMUSG00000022231 AA Change: C689G
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: ENSMUST00000227976
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000228015
|
Meta Mutation Damage Score |
0.5443 |
Coding Region Coverage |
- 1x: 97.5%
- 3x: 96.9%
- 10x: 95.3%
- 20x: 92.6%
|
Validation Efficiency |
97% (95/98) |
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: 92 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca2 |
T |
C |
2: 25,333,055 (GRCm39) |
S1585P |
probably benign |
Het |
Abhd16b |
T |
C |
2: 181,135,197 (GRCm39) |
F33S |
probably damaging |
Het |
Adgra2 |
G |
A |
8: 27,609,795 (GRCm39) |
R856Q |
probably damaging |
Het |
Aff3 |
A |
T |
1: 38,368,945 (GRCm39) |
|
probably benign |
Het |
Anxa2 |
A |
T |
9: 69,397,049 (GRCm39) |
Y251F |
probably benign |
Het |
Arid1b |
A |
G |
17: 5,392,088 (GRCm39) |
T1873A |
probably damaging |
Het |
Baz1b |
C |
A |
5: 135,271,378 (GRCm39) |
D1320E |
probably benign |
Het |
Bbs1 |
A |
T |
19: 4,944,350 (GRCm39) |
S426R |
probably benign |
Het |
Bid |
A |
G |
6: 120,877,209 (GRCm39) |
V44A |
possibly damaging |
Het |
Ccdc60 |
T |
A |
5: 116,310,532 (GRCm39) |
M177L |
probably damaging |
Het |
Cdh23 |
G |
A |
10: 60,161,855 (GRCm39) |
T1997M |
probably damaging |
Het |
Cdh5 |
T |
A |
8: 104,854,801 (GRCm39) |
M243K |
probably benign |
Het |
Clpb |
T |
A |
7: 101,435,905 (GRCm39) |
V578E |
possibly damaging |
Het |
Cngb1 |
C |
A |
8: 96,026,328 (GRCm39) |
C151F |
probably benign |
Het |
Cntnap5b |
T |
C |
1: 99,700,535 (GRCm39) |
S16P |
probably benign |
Het |
Cr1l |
T |
A |
1: 194,797,123 (GRCm39) |
M305L |
probably benign |
Het |
Ctnnal1 |
A |
T |
4: 56,838,988 (GRCm39) |
M235K |
probably damaging |
Het |
Ddx55 |
A |
T |
5: 124,706,176 (GRCm39) |
R534W |
probably damaging |
Het |
Dip2b |
T |
A |
15: 100,109,910 (GRCm39) |
L1465Q |
probably damaging |
Het |
Dnah9 |
G |
T |
11: 65,872,048 (GRCm39) |
D2727E |
probably benign |
Het |
Dph3b-ps |
A |
C |
13: 106,683,497 (GRCm39) |
|
noncoding transcript |
Het |
Dst |
T |
A |
1: 34,267,684 (GRCm39) |
L2702Q |
probably damaging |
Het |
Efnb2 |
T |
C |
8: 8,673,184 (GRCm39) |
T158A |
possibly damaging |
Het |
Exosc10 |
A |
T |
4: 148,662,926 (GRCm39) |
K712* |
probably null |
Het |
Fgr |
T |
C |
4: 132,725,653 (GRCm39) |
V354A |
possibly damaging |
Het |
Fsip2 |
A |
G |
2: 82,830,185 (GRCm39) |
D6893G |
possibly damaging |
Het |
Fsip2 |
G |
A |
2: 82,815,240 (GRCm39) |
V3658M |
probably benign |
Het |
Fsip2 |
A |
T |
2: 82,818,055 (GRCm39) |
H4596L |
possibly damaging |
Het |
Gm1527 |
G |
A |
3: 28,949,699 (GRCm39) |
|
probably benign |
Het |
Gm5150 |
G |
T |
3: 16,060,468 (GRCm39) |
Q7K |
probably benign |
Het |
Gpr155 |
C |
T |
2: 73,212,279 (GRCm39) |
V115M |
probably damaging |
Het |
Gpr75 |
T |
C |
11: 30,841,527 (GRCm39) |
L144P |
probably damaging |
Het |
Gsn |
T |
A |
2: 35,174,835 (GRCm39) |
Y127N |
probably damaging |
Het |
Hk1 |
A |
G |
10: 62,117,678 (GRCm39) |
L615S |
probably damaging |
Het |
Igsf9b |
A |
G |
9: 27,229,123 (GRCm39) |
T194A |
possibly damaging |
Het |
Il17rd |
C |
T |
14: 26,813,763 (GRCm39) |
Q46* |
probably null |
Het |
Jak1 |
T |
A |
4: 101,020,126 (GRCm39) |
M678L |
probably benign |
Het |
Kif6 |
T |
C |
17: 49,922,311 (GRCm39) |
V16A |
probably benign |
Het |
Kpna3 |
T |
C |
14: 61,607,990 (GRCm39) |
E405G |
probably benign |
Het |
Lmtk2 |
C |
A |
5: 144,110,993 (GRCm39) |
T571K |
probably damaging |
Het |
Mucl2 |
T |
C |
15: 103,927,838 (GRCm39) |
T40A |
possibly damaging |
Het |
Myh11 |
G |
A |
16: 14,051,559 (GRCm39) |
|
probably benign |
Het |
Myh7 |
C |
T |
14: 55,210,170 (GRCm39) |
R1845Q |
probably damaging |
Het |
Myo1f |
T |
A |
17: 33,805,172 (GRCm39) |
L480Q |
probably benign |
Het |
Nek9 |
T |
G |
12: 85,352,364 (GRCm39) |
D833A |
possibly damaging |
Het |
Nek9 |
T |
C |
12: 85,357,184 (GRCm39) |
E660G |
probably benign |
Het |
Or10z1 |
C |
T |
1: 174,077,926 (GRCm39) |
C189Y |
probably damaging |
Het |
Or2a12 |
A |
G |
6: 42,904,431 (GRCm39) |
I89V |
possibly damaging |
Het |
Or2t45 |
A |
G |
11: 58,669,195 (GRCm39) |
M81V |
possibly damaging |
Het |
Or5h18 |
T |
C |
16: 58,847,350 (GRCm39) |
R307G |
probably benign |
Het |
Or6c65 |
T |
A |
10: 129,603,417 (GRCm39) |
D17E |
probably benign |
Het |
Or6f2 |
G |
A |
7: 139,756,188 (GRCm39) |
V52M |
probably damaging |
Het |
Or7s1a-ps1 |
T |
A |
9: 18,843,791 (GRCm39) |
|
probably benign |
Het |
Otud3 |
G |
T |
4: 138,623,092 (GRCm39) |
T383K |
possibly damaging |
Het |
Pkp4 |
T |
C |
2: 59,142,185 (GRCm39) |
L496P |
probably damaging |
Het |
Pla2g4e |
C |
A |
2: 120,000,527 (GRCm39) |
A737S |
possibly damaging |
Het |
Pla2g4f |
T |
C |
2: 120,144,547 (GRCm39) |
|
probably benign |
Het |
Plxnd1 |
A |
T |
6: 115,944,740 (GRCm39) |
V1018E |
possibly damaging |
Het |
Ppp1r21 |
T |
G |
17: 88,869,653 (GRCm39) |
V402G |
possibly damaging |
Het |
Prkcq |
T |
G |
2: 11,304,881 (GRCm39) |
M690R |
probably damaging |
Het |
Ptpra |
T |
C |
2: 130,391,747 (GRCm39) |
I719T |
probably damaging |
Het |
Rab3ip |
C |
T |
10: 116,773,415 (GRCm39) |
D133N |
probably damaging |
Het |
Relch |
T |
G |
1: 105,647,169 (GRCm39) |
|
probably benign |
Het |
Rsbn1 |
T |
A |
3: 103,867,347 (GRCm39) |
Y563N |
probably damaging |
Het |
Rtf1 |
A |
C |
2: 119,558,889 (GRCm39) |
D530A |
probably benign |
Het |
Rybp |
G |
T |
6: 100,209,224 (GRCm39) |
S199R |
probably benign |
Het |
Senp6 |
T |
A |
9: 80,025,911 (GRCm39) |
V314E |
probably benign |
Het |
Setd1a |
T |
A |
7: 127,385,062 (GRCm39) |
C47S |
possibly damaging |
Het |
Slamf1 |
C |
A |
1: 171,604,734 (GRCm39) |
T168K |
probably benign |
Het |
Slc12a5 |
T |
C |
2: 164,838,048 (GRCm39) |
S937P |
probably damaging |
Het |
Slc38a11 |
C |
T |
2: 65,185,663 (GRCm39) |
|
probably null |
Het |
Slc6a2 |
C |
T |
8: 93,687,846 (GRCm39) |
|
probably benign |
Het |
Snw1 |
A |
T |
12: 87,511,459 (GRCm39) |
F64Y |
probably benign |
Het |
Spata9 |
A |
C |
13: 76,146,643 (GRCm39) |
I172L |
probably benign |
Het |
Sphkap |
T |
C |
1: 83,255,265 (GRCm39) |
H828R |
probably benign |
Het |
Spmip6 |
T |
A |
4: 41,507,330 (GRCm39) |
|
probably null |
Het |
Tmem94 |
A |
T |
11: 115,687,580 (GRCm39) |
K1146N |
probably damaging |
Het |
Trdn |
A |
G |
10: 33,109,883 (GRCm39) |
T294A |
possibly damaging |
Het |
Tsc22d1 |
T |
C |
14: 76,654,388 (GRCm39) |
V289A |
possibly damaging |
Het |
Tti1 |
C |
A |
2: 157,834,955 (GRCm39) |
V1002L |
possibly damaging |
Het |
Tubgcp4 |
T |
A |
2: 121,019,952 (GRCm39) |
|
probably null |
Het |
Ush2a |
G |
A |
1: 188,643,180 (GRCm39) |
E4181K |
possibly damaging |
Het |
Uvrag |
A |
G |
7: 98,537,555 (GRCm39) |
S547P |
probably benign |
Het |
Vav3 |
T |
C |
3: 109,248,443 (GRCm39) |
V30A |
possibly damaging |
Het |
Vegfa |
A |
G |
17: 46,336,395 (GRCm39) |
Y242H |
probably damaging |
Het |
Vmn2r75 |
G |
T |
7: 85,798,019 (GRCm39) |
T598K |
probably damaging |
Het |
Vps13b |
C |
T |
15: 35,884,765 (GRCm39) |
S3146L |
possibly damaging |
Het |
Vrk3 |
A |
G |
7: 44,417,895 (GRCm39) |
Y310C |
probably damaging |
Het |
Zfhx4 |
A |
G |
3: 5,447,676 (GRCm39) |
K1100R |
probably benign |
Het |
Zfp748 |
T |
A |
13: 67,693,540 (GRCm39) |
|
probably null |
Het |
Zfp760 |
A |
T |
17: 21,941,311 (GRCm39) |
D162V |
probably damaging |
Het |
Znfx1 |
T |
A |
2: 166,881,786 (GRCm39) |
M1068L |
probably damaging |
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 |
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 |
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'- TTCAACATCTGGCACAGGGATGG -3'
(R):5'- CAGTGGATCAAGTGTGAGCACAGTC -3'
Sequencing Primer
(F):5'- GTGGCCTCTTGAGCACTAAAC -3'
(R):5'- TGAGCACAGTCCCTGGTG -3'
|
Posted On |
2014-05-23 |