Incidental Mutation 'PIT4305001:Sema5a'
| ID |
554581 |
| 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 |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
PIT4305001 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
15 |
| Chromosomal Location |
32244959-32696487 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 32628345 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 553
(T553A)
|
| 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: T553A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000069024
Gene: ENSMUSG00000022231
AA Change: T553A
| 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 |
|
| Coding Region Coverage |
- 1x: 93.4%
- 3x: 91.3%
- 10x: 86.8%
- 20x: 76.6%
|
| 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: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adamts4 |
A |
G |
1: 171,086,610 (GRCm39) |
N801D |
probably benign |
Het |
| Adcy2 |
T |
C |
13: 68,826,721 (GRCm39) |
K661R |
probably benign |
Het |
| Akap1 |
A |
T |
11: 88,735,204 (GRCm39) |
M486K |
probably benign |
Het |
| Arhgap40 |
T |
A |
2: 158,373,825 (GRCm39) |
I202N |
probably benign |
Het |
| C1qtnf2 |
T |
A |
11: 43,382,022 (GRCm39) |
L248Q |
probably damaging |
Het |
| Casp1 |
A |
T |
9: 5,306,135 (GRCm39) |
H340L |
probably benign |
Het |
| Cd5 |
A |
G |
19: 10,703,750 (GRCm39) |
V104A |
possibly damaging |
Het |
| Celsr1 |
T |
A |
15: 85,785,138 (GRCm39) |
E3032V |
possibly damaging |
Het |
| Cts7 |
A |
G |
13: 61,504,386 (GRCm39) |
I59T |
probably damaging |
Het |
| Cutc |
G |
T |
19: 43,756,708 (GRCm39) |
A267S |
probably damaging |
Het |
| Dmwd |
A |
G |
7: 18,814,643 (GRCm39) |
Q431R |
probably damaging |
Het |
| Dnah6 |
T |
C |
6: 73,042,738 (GRCm39) |
N3280S |
probably benign |
Het |
| Dnah7b |
A |
T |
1: 46,412,508 (GRCm39) |
N4039I |
probably damaging |
Het |
| Dnaja4 |
T |
C |
9: 54,617,918 (GRCm39) |
I260T |
probably benign |
Het |
| Drd5 |
T |
C |
5: 38,477,927 (GRCm39) |
F307L |
probably damaging |
Het |
| Dsc2 |
C |
T |
18: 20,179,300 (GRCm39) |
S256N |
probably damaging |
Het |
| Dstyk |
G |
T |
1: 132,383,634 (GRCm39) |
E617* |
probably null |
Het |
| Dusp15 |
G |
A |
2: 152,787,396 (GRCm39) |
H72Y |
probably benign |
Het |
| Dysf |
C |
T |
6: 84,077,216 (GRCm39) |
R660* |
probably null |
Het |
| Fbxl13 |
T |
A |
5: 21,727,146 (GRCm39) |
I584L |
probably benign |
Het |
| Gsap |
T |
C |
5: 21,391,407 (GRCm39) |
L16P |
probably damaging |
Het |
| Hgsnat |
C |
T |
8: 26,435,227 (GRCm39) |
A636T |
possibly damaging |
Het |
| Hivep1 |
A |
G |
13: 42,335,147 (GRCm39) |
T161A |
|
Het |
| Hspg2 |
T |
C |
4: 137,277,684 (GRCm39) |
S2928P |
possibly damaging |
Het |
| Ifi214 |
G |
A |
1: 173,355,485 (GRCm39) |
P108S |
probably benign |
Het |
| Il17ra |
A |
T |
6: 120,458,367 (GRCm39) |
Y506F |
probably damaging |
Het |
| Il9r |
T |
A |
11: 32,144,734 (GRCm39) |
Q53L |
probably benign |
Het |
| Irf2bp2 |
C |
T |
8: 127,319,398 (GRCm39) |
G260R |
probably damaging |
Het |
| Jdp2 |
T |
A |
12: 85,685,626 (GRCm39) |
I129N |
probably damaging |
Het |
| Kif1b |
T |
C |
4: 149,305,249 (GRCm39) |
|
probably null |
Het |
| Klrd1 |
A |
G |
6: 129,573,670 (GRCm39) |
T120A |
unknown |
Het |
| Lfng |
A |
G |
5: 140,598,283 (GRCm39) |
N202D |
probably damaging |
Het |
| Ltbp3 |
A |
G |
19: 5,802,095 (GRCm39) |
E757G |
probably damaging |
Het |
| Ltn1 |
G |
A |
16: 87,217,211 (GRCm39) |
P342L |
probably damaging |
Het |
| Lum |
A |
C |
10: 97,404,738 (GRCm39) |
Y211S |
probably damaging |
Het |
| Ncapd2 |
G |
A |
6: 125,160,990 (GRCm39) |
R292* |
probably null |
Het |
| Nlrc4 |
T |
C |
17: 74,753,304 (GRCm39) |
T360A |
probably damaging |
Het |
| Or4c1 |
T |
C |
2: 89,133,727 (GRCm39) |
I70V |
probably benign |
Het |
| Or7g32 |
T |
C |
9: 19,389,357 (GRCm39) |
Y63C |
probably damaging |
Het |
| Pakap |
C |
A |
4: 57,638,029 (GRCm39) |
T22K |
possibly damaging |
Het |
| Pde3a |
A |
G |
6: 141,438,036 (GRCm39) |
D1035G |
probably benign |
Het |
| Phf20l1 |
A |
T |
15: 66,484,901 (GRCm39) |
K322I |
possibly damaging |
Het |
| Pik3r3 |
A |
C |
4: 116,149,323 (GRCm39) |
N349T |
probably benign |
Het |
| Poc1a |
A |
G |
9: 106,227,028 (GRCm39) |
Q420R |
|
Het |
| Prl7d1 |
A |
T |
13: 27,898,320 (GRCm39) |
M63K |
possibly damaging |
Het |
| Rap1gds1 |
C |
A |
3: 138,662,061 (GRCm39) |
M398I |
probably benign |
Het |
| Rapgef6 |
T |
A |
11: 54,570,203 (GRCm39) |
V1192D |
probably damaging |
Het |
| Rif1 |
T |
C |
2: 52,001,970 (GRCm39) |
V166A |
|
Het |
| Robo4 |
T |
C |
9: 37,322,687 (GRCm39) |
Y847H |
probably damaging |
Het |
| Sardh |
T |
C |
2: 27,118,326 (GRCm39) |
N468S |
probably damaging |
Het |
| Serpina12 |
A |
G |
12: 104,001,976 (GRCm39) |
Y247H |
probably damaging |
Het |
| Speer4e2 |
T |
C |
5: 15,028,804 (GRCm39) |
D29G |
probably benign |
Het |
| Ston2 |
G |
T |
12: 91,615,276 (GRCm39) |
D377E |
possibly damaging |
Het |
| Syne1 |
A |
G |
10: 5,283,023 (GRCm39) |
S1557P |
probably damaging |
Het |
| Syt6 |
C |
T |
3: 103,482,769 (GRCm39) |
R26W |
possibly damaging |
Het |
| Tep1 |
C |
T |
14: 51,066,684 (GRCm39) |
G2305R |
possibly damaging |
Het |
| Ticrr |
A |
G |
7: 79,328,771 (GRCm39) |
T637A |
possibly damaging |
Het |
| Tnn |
A |
T |
1: 159,913,647 (GRCm39) |
F1546Y |
possibly damaging |
Het |
| Tpr |
A |
G |
1: 150,315,888 (GRCm39) |
D2055G |
possibly damaging |
Het |
| Trim39 |
A |
G |
17: 36,579,862 (GRCm39) |
V31A |
possibly damaging |
Het |
| Trpc7 |
G |
T |
13: 57,035,321 (GRCm39) |
T204K |
probably benign |
Het |
| Urgcp |
T |
C |
11: 5,667,996 (GRCm39) |
Y157C |
probably damaging |
Het |
| Vmn1r81 |
A |
T |
7: 11,994,590 (GRCm39) |
I6K |
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 |
|
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 |
|
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'- AAGAGTTGTGATTGCCACTTG -3'
(R):5'- CCACCTTCATCTACTAAAGGATAGC -3'
Sequencing Primer
(F):5'- CCACTTGAGAGAGATACCTTTTGGC -3'
(R):5'- GTGTTAAGAAGGGCTGCCC -3'
|
| Posted On |
2019-06-07 |
Incidental Mutation