Incidental Mutation 'R6220:Sema5a'
| ID |
503974 |
| 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 |
044352-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6220 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
15 |
| Chromosomal Location |
32244959-32696487 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 32686875 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Asparagine
at position 996
(Y996N)
|
| 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: Y996N
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000069024
Gene: ENSMUSG00000022231
AA Change: Y996N
| 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
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.5%
- 20x: 98.3%
|
| Validation Efficiency |
100% (65/65) |
| 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: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abhd16b |
A |
G |
2: 181,135,578 (GRCm39) |
D160G |
probably damaging |
Het |
| Acap1 |
A |
G |
11: 69,780,505 (GRCm39) |
F15S |
probably damaging |
Het |
| Adam30 |
A |
T |
3: 98,068,625 (GRCm39) |
S153C |
probably damaging |
Het |
| Afp |
A |
T |
5: 90,652,269 (GRCm39) |
D420V |
possibly damaging |
Het |
| Ak9 |
T |
A |
10: 41,246,095 (GRCm39) |
H729Q |
unknown |
Het |
| Armh3 |
T |
C |
19: 45,834,554 (GRCm39) |
E618G |
possibly damaging |
Het |
| Arsi |
G |
A |
18: 61,049,723 (GRCm39) |
G202E |
probably benign |
Het |
| Bcr |
A |
G |
10: 74,898,124 (GRCm39) |
T423A |
probably benign |
Het |
| Cc2d1b |
C |
T |
4: 108,490,422 (GRCm39) |
R825W |
probably damaging |
Het |
| Ctns |
T |
C |
11: 73,083,954 (GRCm39) |
T23A |
probably benign |
Het |
| Ddx54 |
T |
A |
5: 120,758,754 (GRCm39) |
N332K |
probably benign |
Het |
| Dysf |
T |
A |
6: 84,126,727 (GRCm39) |
I1344N |
probably damaging |
Het |
| Elovl3 |
A |
T |
19: 46,122,939 (GRCm39) |
M172L |
probably benign |
Het |
| Fbxo6 |
A |
T |
4: 148,233,979 (GRCm39) |
I39N |
probably damaging |
Het |
| Filip1l |
T |
A |
16: 57,390,352 (GRCm39) |
N313K |
probably benign |
Het |
| Foxp2 |
C |
A |
6: 15,437,947 (GRCm39) |
T716K |
probably damaging |
Het |
| Gm10549 |
C |
A |
18: 33,597,358 (GRCm39) |
|
probably benign |
Het |
| Gm10645 |
A |
G |
8: 83,892,386 (GRCm39) |
|
probably benign |
Het |
| Gm10735 |
T |
C |
13: 113,178,030 (GRCm39) |
|
probably benign |
Het |
| Gm4847 |
A |
T |
1: 166,462,541 (GRCm39) |
D316E |
probably damaging |
Het |
| Gorasp2 |
T |
C |
2: 70,521,134 (GRCm39) |
L388P |
probably damaging |
Het |
| Heatr5b |
A |
G |
17: 79,081,106 (GRCm39) |
L1382P |
probably damaging |
Het |
| Herc1 |
A |
G |
9: 66,341,070 (GRCm39) |
Y1729C |
probably damaging |
Het |
| Ifi207 |
A |
T |
1: 173,557,112 (GRCm39) |
L542H |
probably damaging |
Het |
| Ighv3-5 |
T |
A |
12: 114,226,338 (GRCm39) |
N96I |
probably damaging |
Het |
| Isl1 |
T |
C |
13: 116,439,803 (GRCm39) |
T182A |
probably benign |
Het |
| Jph4 |
T |
C |
14: 55,347,542 (GRCm39) |
E421G |
probably benign |
Het |
| Lrrc45 |
T |
C |
11: 120,610,353 (GRCm39) |
I488T |
probably benign |
Het |
| Mroh8 |
A |
G |
2: 157,075,083 (GRCm39) |
I471T |
probably benign |
Het |
| Ms4a2 |
A |
T |
19: 11,594,927 (GRCm39) |
D96E |
probably damaging |
Het |
| Mst1r |
T |
A |
9: 107,784,547 (GRCm39) |
N68K |
probably benign |
Het |
| Myo18b |
A |
G |
5: 112,905,373 (GRCm39) |
M2075T |
possibly damaging |
Het |
| Neb |
T |
C |
2: 52,160,984 (GRCm39) |
K2229R |
probably null |
Het |
| Nkx6-3 |
T |
A |
8: 23,643,987 (GRCm39) |
|
probably null |
Het |
| Nlrp1a |
C |
A |
11: 71,033,164 (GRCm39) |
S10I |
probably benign |
Het |
| Npas2 |
A |
T |
1: 39,375,142 (GRCm39) |
T487S |
probably benign |
Het |
| Nrxn1 |
G |
C |
17: 91,395,904 (GRCm39) |
T84R |
probably benign |
Het |
| Or4k2 |
C |
A |
14: 50,424,135 (GRCm39) |
D180Y |
probably damaging |
Het |
| Otx1 |
C |
A |
11: 21,947,037 (GRCm39) |
A91S |
probably damaging |
Het |
| Pcdh18 |
A |
G |
3: 49,699,700 (GRCm39) |
C921R |
probably damaging |
Het |
| Pcdha9 |
A |
G |
18: 37,131,531 (GRCm39) |
Y200C |
probably damaging |
Het |
| Pknox1 |
A |
T |
17: 31,822,177 (GRCm39) |
R315* |
probably null |
Het |
| Rasgrp1 |
C |
T |
2: 117,115,410 (GRCm39) |
W726* |
probably null |
Het |
| Rassf8 |
G |
A |
6: 145,762,859 (GRCm39) |
R402H |
probably damaging |
Het |
| Rev3l |
T |
A |
10: 39,698,775 (GRCm39) |
Y1091N |
probably damaging |
Het |
| Riok3 |
T |
G |
18: 12,282,608 (GRCm39) |
V349G |
probably damaging |
Het |
| Rps18 |
A |
T |
17: 34,174,110 (GRCm39) |
V15E |
probably damaging |
Het |
| Rptor |
A |
T |
11: 119,788,268 (GRCm39) |
Y1323F |
possibly damaging |
Het |
| Rspry1 |
T |
C |
8: 95,385,378 (GRCm39) |
C437R |
probably damaging |
Het |
| Smarcad1 |
A |
G |
6: 65,091,313 (GRCm39) |
I1011M |
probably benign |
Het |
| Supv3l1 |
A |
T |
10: 62,274,800 (GRCm39) |
M295K |
possibly damaging |
Het |
| Sv2c |
T |
C |
13: 96,113,134 (GRCm39) |
D605G |
probably damaging |
Het |
| Teddm1b |
G |
A |
1: 153,750,947 (GRCm39) |
W252* |
probably null |
Het |
| Tes |
T |
A |
6: 17,086,195 (GRCm39) |
C29* |
probably null |
Het |
| Thsd4 |
A |
G |
9: 59,890,030 (GRCm39) |
W856R |
probably damaging |
Het |
| Treml4 |
A |
T |
17: 48,571,876 (GRCm39) |
D93V |
possibly damaging |
Het |
| Trim66 |
T |
C |
7: 109,082,300 (GRCm39) |
T218A |
probably damaging |
Het |
| Tssk5 |
T |
C |
15: 76,257,973 (GRCm39) |
D128G |
probably damaging |
Het |
| Ubr3 |
T |
A |
2: 69,850,819 (GRCm39) |
W1746R |
probably damaging |
Het |
| Vmn2r11 |
T |
C |
5: 109,201,434 (GRCm39) |
I357V |
probably benign |
Het |
| Vmn2r87 |
A |
T |
10: 130,315,807 (GRCm39) |
D86E |
probably benign |
Het |
| Zfp184 |
T |
G |
13: 22,144,377 (GRCm39) |
H694Q |
probably damaging |
Het |
| Zranb3 |
A |
C |
1: 127,927,141 (GRCm39) |
F341L |
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 |
|
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 |
|
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 |
|
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'- TTTCTAGACCCTGACATTCCCAAG -3'
(R):5'- AGTGTCACCTGCCTTTGTGG -3'
Sequencing Primer
(F):5'- GACATCTATACCTTGGGATACGCAG -3'
(R):5'- TGTGGCCTCCCTAGCTG -3'
|
| Posted On |
2018-02-27 |
Incidental Mutation