Incidental Mutation 'R2215:Sema5b'
| ID |
241118 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Sema5b
|
| Ensembl Gene |
ENSMUSG00000052133 |
| Gene Name |
sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B |
| Synonyms |
SemG, SemG, Semag |
| MMRRC Submission |
040217-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2215 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
16 |
| Chromosomal Location |
35361517-35485103 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 35480585 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 751
(T751A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000112536
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000050625]
[ENSMUST00000120756]
|
| AlphaFold |
Q60519 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000050625
AA Change: T722A
PolyPhen 2
Score 0.859 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000057494
Gene: ENSMUSG00000052133
AA Change: T722A
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
Sema
|
68 |
479 |
1.68e-174 |
SMART |
|
PSI
|
497 |
544 |
9.18e-12 |
SMART |
|
TSP1
|
609 |
662 |
3.34e-15 |
SMART |
|
TSP1
|
667 |
713 |
3.42e-12 |
SMART |
|
TSP1
|
798 |
850 |
1.58e-16 |
SMART |
|
TSP1
|
855 |
907 |
2.45e-13 |
SMART |
|
TSP1
|
910 |
957 |
1.02e-1 |
SMART |
|
transmembrane domain
|
977 |
999 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000120756
AA Change: T751A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000112536
Gene: ENSMUSG00000052133
AA Change: T751A
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
Sema
|
68 |
479 |
1.68e-174 |
SMART |
|
PSI
|
497 |
544 |
9.18e-12 |
SMART |
|
TSP1
|
609 |
662 |
3.34e-15 |
SMART |
|
TSP1
|
667 |
742 |
7.61e-10 |
SMART |
|
TSP1
|
827 |
879 |
1.58e-16 |
SMART |
|
TSP1
|
884 |
936 |
2.45e-13 |
SMART |
|
TSP1
|
939 |
986 |
1.02e-1 |
SMART |
|
transmembrane domain
|
1006 |
1028 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128347
|
| SMART Domains |
Protein: ENSMUSP00000121703
Gene: ENSMUSG00000052133
| Domain | Start | End | E-Value | Type |
|---|
|
TSP1
|
1 |
32 |
8.81e-1 |
SMART |
|
TSP1
|
35 |
82 |
1.02e-1 |
SMART |
|
transmembrane domain
|
102 |
124 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128966
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139805
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149097
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149855
|
| SMART Domains |
Protein: ENSMUSP00000115969
Gene: ENSMUSG00000052133
| Domain | Start | End | E-Value | Type |
|---|
|
TSP1
|
17 |
70 |
3.34e-15 |
SMART |
|
TSP1
|
75 |
121 |
3.42e-12 |
SMART |
|
TSP1
|
206 |
258 |
1.58e-16 |
SMART |
|
TSP1
|
263 |
315 |
2.45e-13 |
SMART |
|
TSP1
|
317 |
364 |
1.02e-1 |
SMART |
|
transmembrane domain
|
384 |
406 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.4663 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.3%
|
| Validation Efficiency |
100% (68/68) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the semaphorin protein family which regulates axon growth during development of the nervous system. The encoded protein has a characteristic Sema domain near the N-terminus, through which semaphorins bind to plexin, and five thrombospondin type 1 repeats in the C-terminal region of the protein. The protein product may be cleaved and exist as a secreted molecule (PMID: 19463192). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
PHENOTYPE: Mice homozygous for a null mutation display defects in neurite arborization of multiple retinal cell types. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 66 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acaca |
T |
A |
11: 84,254,619 (GRCm39) |
S1899T |
probably damaging |
Het |
| Accs |
G |
T |
2: 93,672,243 (GRCm39) |
N208K |
probably benign |
Het |
| Actn4 |
C |
A |
7: 28,618,178 (GRCm39) |
V22L |
possibly damaging |
Het |
| Adam21 |
A |
G |
12: 81,607,064 (GRCm39) |
S233P |
probably damaging |
Het |
| Adrm1b |
G |
A |
3: 92,335,730 (GRCm39) |
A324V |
probably damaging |
Het |
| Agmat |
C |
T |
4: 141,476,899 (GRCm39) |
R102C |
probably benign |
Het |
| Akap8l |
T |
C |
17: 32,540,569 (GRCm39) |
E608G |
possibly damaging |
Het |
| Arap2 |
T |
C |
5: 62,834,519 (GRCm39) |
I788V |
probably damaging |
Het |
| Arhgef12 |
G |
T |
9: 42,917,167 (GRCm39) |
H391N |
probably damaging |
Het |
| Arhgef28 |
G |
T |
13: 98,187,529 (GRCm39) |
H255Q |
possibly damaging |
Het |
| Baz1a |
G |
A |
12: 55,022,154 (GRCm39) |
R43* |
probably null |
Het |
| Bcas3 |
T |
C |
11: 85,692,769 (GRCm39) |
S862P |
probably damaging |
Het |
| Blm |
A |
T |
7: 80,149,595 (GRCm39) |
H671Q |
possibly damaging |
Het |
| Bmp8a |
C |
T |
4: 123,218,911 (GRCm39) |
V166I |
probably benign |
Het |
| Cep120 |
G |
T |
18: 53,860,707 (GRCm39) |
P241Q |
probably damaging |
Het |
| Col14a1 |
G |
A |
15: 55,244,238 (GRCm39) |
G437E |
unknown |
Het |
| Cyp2a5 |
T |
C |
7: 26,539,900 (GRCm39) |
L3S |
probably damaging |
Het |
| D16Ertd472e |
T |
C |
16: 78,342,155 (GRCm39) |
T242A |
probably benign |
Het |
| Dach1 |
A |
G |
14: 98,405,917 (GRCm39) |
|
probably null |
Het |
| Ddx20 |
A |
T |
3: 105,587,656 (GRCm39) |
|
probably benign |
Het |
| Eif4enif1 |
A |
G |
11: 3,177,476 (GRCm39) |
S185G |
probably damaging |
Het |
| Ep400 |
A |
T |
5: 110,841,421 (GRCm39) |
|
probably benign |
Het |
| Fam117b |
T |
A |
1: 60,008,219 (GRCm39) |
I351K |
probably damaging |
Het |
| Fbxo31 |
T |
C |
8: 122,293,050 (GRCm39) |
I112V |
probably benign |
Het |
| Galntl5 |
A |
T |
5: 25,403,476 (GRCm39) |
N149I |
probably damaging |
Het |
| Gja8 |
A |
T |
3: 96,827,218 (GRCm39) |
F148Y |
probably damaging |
Het |
| Gpatch1 |
A |
T |
7: 34,993,252 (GRCm39) |
L531Q |
possibly damaging |
Het |
| Gprin1 |
G |
A |
13: 54,888,046 (GRCm39) |
T76M |
probably damaging |
Het |
| Htr4 |
T |
A |
18: 62,546,787 (GRCm39) |
C113* |
probably null |
Het |
| Igf1r |
T |
A |
7: 67,814,982 (GRCm39) |
D294E |
probably benign |
Het |
| Kdm6b |
G |
A |
11: 69,295,870 (GRCm39) |
P799L |
unknown |
Het |
| Lat |
A |
T |
7: 125,967,137 (GRCm39) |
V139E |
probably damaging |
Het |
| Lrrc34 |
G |
A |
3: 30,697,678 (GRCm39) |
R51C |
probably benign |
Het |
| Map3k1 |
A |
G |
13: 111,892,322 (GRCm39) |
S978P |
probably benign |
Het |
| Masp1 |
T |
A |
16: 23,271,271 (GRCm39) |
D659V |
possibly damaging |
Het |
| Mcam |
A |
T |
9: 44,051,250 (GRCm39) |
R415* |
probably null |
Het |
| Mtmr10 |
A |
G |
7: 63,987,403 (GRCm39) |
T648A |
probably benign |
Het |
| Myh2 |
T |
C |
11: 67,082,563 (GRCm39) |
W1378R |
probably benign |
Het |
| Nipsnap2 |
A |
G |
5: 129,816,649 (GRCm39) |
E64G |
probably damaging |
Het |
| Or4a68 |
T |
C |
2: 89,270,381 (GRCm39) |
M81V |
probably benign |
Het |
| Or52n4b |
T |
C |
7: 108,144,095 (GRCm39) |
L119P |
probably damaging |
Het |
| Or6c3 |
A |
T |
10: 129,309,289 (GRCm39) |
I243F |
probably damaging |
Het |
| Or9s27 |
G |
A |
1: 92,516,708 (GRCm39) |
V219I |
probably benign |
Het |
| Pcdhb8 |
T |
G |
18: 37,490,127 (GRCm39) |
S602A |
probably damaging |
Het |
| Peg10 |
A |
T |
6: 4,756,918 (GRCm39) |
|
probably benign |
Het |
| Pld1 |
A |
T |
3: 28,132,542 (GRCm39) |
I577F |
probably benign |
Het |
| Plekhm1 |
A |
T |
11: 103,267,811 (GRCm39) |
I720N |
probably damaging |
Het |
| Ppp2r1a |
A |
G |
17: 21,182,005 (GRCm39) |
|
probably null |
Het |
| Retreg3 |
G |
T |
11: 101,010,459 (GRCm39) |
Y49* |
probably null |
Het |
| Rrp36 |
T |
C |
17: 46,983,746 (GRCm39) |
E22G |
possibly damaging |
Het |
| Sec14l2 |
C |
A |
11: 4,059,169 (GRCm39) |
A167S |
probably damaging |
Het |
| Smarcc1 |
C |
A |
9: 110,066,907 (GRCm39) |
|
probably benign |
Het |
| Smox |
T |
C |
2: 131,362,190 (GRCm39) |
|
probably null |
Het |
| Spats2l |
A |
T |
1: 57,985,575 (GRCm39) |
T543S |
possibly damaging |
Het |
| Sppl2a |
G |
T |
2: 126,769,754 (GRCm39) |
T34K |
probably benign |
Het |
| Svep1 |
T |
C |
4: 58,138,602 (GRCm39) |
|
probably benign |
Het |
| Tet2 |
T |
A |
3: 133,192,362 (GRCm39) |
I691F |
probably benign |
Het |
| Tnxb |
T |
C |
17: 34,923,114 (GRCm39) |
Y2566H |
possibly damaging |
Het |
| Ttn |
T |
C |
2: 76,570,853 (GRCm39) |
E26680G |
probably damaging |
Het |
| Txlna |
T |
C |
4: 129,533,111 (GRCm39) |
E139G |
possibly damaging |
Het |
| Ubap2 |
T |
C |
4: 41,196,483 (GRCm39) |
|
probably null |
Het |
| Ubr3 |
A |
T |
2: 69,809,661 (GRCm39) |
|
probably null |
Het |
| Usp37 |
A |
C |
1: 74,483,685 (GRCm39) |
F844V |
probably damaging |
Het |
| Usp6nl |
A |
G |
2: 6,429,150 (GRCm39) |
D204G |
probably damaging |
Het |
| Vmn1r230 |
T |
C |
17: 21,067,684 (GRCm39) |
I291T |
probably benign |
Het |
| Zfp229 |
T |
G |
17: 21,965,258 (GRCm39) |
V496G |
possibly damaging |
Het |
|
| Other mutations in Sema5b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00901:Sema5b
|
APN |
16 |
35,471,685 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01584:Sema5b
|
APN |
16 |
35,465,793 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01859:Sema5b
|
APN |
16 |
35,467,479 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
IGL02195:Sema5b
|
APN |
16 |
35,480,849 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
IGL02346:Sema5b
|
APN |
16 |
35,470,125 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02850:Sema5b
|
APN |
16 |
35,480,885 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL03277:Sema5b
|
APN |
16 |
35,471,682 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R0101:Sema5b
|
UTSW |
16 |
35,483,472 (GRCm39) |
splice site |
probably benign |
|
|
R0368:Sema5b
|
UTSW |
16 |
35,448,470 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0426:Sema5b
|
UTSW |
16 |
35,466,725 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0675:Sema5b
|
UTSW |
16 |
35,480,703 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0905:Sema5b
|
UTSW |
16 |
35,443,001 (GRCm39) |
missense |
probably benign |
0.33 |
|
R1163:Sema5b
|
UTSW |
16 |
35,448,466 (GRCm39) |
missense |
probably benign |
0.19 |
|
R1195:Sema5b
|
UTSW |
16 |
35,472,030 (GRCm39) |
missense |
probably null |
0.94 |
|
R1195:Sema5b
|
UTSW |
16 |
35,472,030 (GRCm39) |
missense |
probably null |
0.94 |
|
R1666:Sema5b
|
UTSW |
16 |
35,478,852 (GRCm39) |
missense |
probably benign |
0.03 |
|
R1706:Sema5b
|
UTSW |
16 |
35,470,125 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1733:Sema5b
|
UTSW |
16 |
35,466,737 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1775:Sema5b
|
UTSW |
16 |
35,480,694 (GRCm39) |
missense |
probably benign |
|
|
R2844:Sema5b
|
UTSW |
16 |
35,480,301 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3086:Sema5b
|
UTSW |
16 |
35,443,093 (GRCm39) |
missense |
probably benign |
|
|
R3613:Sema5b
|
UTSW |
16 |
35,480,520 (GRCm39) |
missense |
probably benign |
|
|
R4774:Sema5b
|
UTSW |
16 |
35,483,552 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5743:Sema5b
|
UTSW |
16 |
35,478,846 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5856:Sema5b
|
UTSW |
16 |
35,466,756 (GRCm39) |
nonsense |
probably null |
|
|
R5993:Sema5b
|
UTSW |
16 |
35,466,572 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6248:Sema5b
|
UTSW |
16 |
35,448,377 (GRCm39) |
splice site |
probably null |
|
|
R6420:Sema5b
|
UTSW |
16 |
35,483,516 (GRCm39) |
missense |
probably benign |
0.08 |
|
R6795:Sema5b
|
UTSW |
16 |
35,478,941 (GRCm39) |
nonsense |
probably null |
|
|
R6825:Sema5b
|
UTSW |
16 |
35,448,377 (GRCm39) |
splice site |
probably null |
|
|
R7066:Sema5b
|
UTSW |
16 |
35,471,682 (GRCm39) |
missense |
probably benign |
0.26 |
|
R7244:Sema5b
|
UTSW |
16 |
35,480,915 (GRCm39) |
missense |
probably benign |
|
|
R7446:Sema5b
|
UTSW |
16 |
35,467,573 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7497:Sema5b
|
UTSW |
16 |
35,481,700 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7516:Sema5b
|
UTSW |
16 |
35,471,540 (GRCm39) |
missense |
probably benign |
0.05 |
|
R7878:Sema5b
|
UTSW |
16 |
35,481,996 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7922:Sema5b
|
UTSW |
16 |
35,478,626 (GRCm39) |
frame shift |
probably null |
|
|
R8397:Sema5b
|
UTSW |
16 |
35,471,691 (GRCm39) |
missense |
possibly damaging |
0.59 |
|
R8537:Sema5b
|
UTSW |
16 |
35,471,979 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R8929:Sema5b
|
UTSW |
16 |
35,467,737 (GRCm39) |
intron |
probably benign |
|
|
R9262:Sema5b
|
UTSW |
16 |
35,453,223 (GRCm39) |
missense |
possibly damaging |
0.57 |
|
R9389:Sema5b
|
UTSW |
16 |
35,466,092 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9579:Sema5b
|
UTSW |
16 |
35,467,582 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9623:Sema5b
|
UTSW |
16 |
35,443,121 (GRCm39) |
missense |
possibly damaging |
0.74 |
|
Z1088:Sema5b
|
UTSW |
16 |
35,480,960 (GRCm39) |
missense |
probably damaging |
0.99 |
|
Z1176:Sema5b
|
UTSW |
16 |
35,470,234 (GRCm39) |
missense |
probably benign |
0.01 |
|
Z1176:Sema5b
|
UTSW |
16 |
35,466,643 (GRCm39) |
missense |
probably benign |
0.05 |
|
Z1176:Sema5b
|
UTSW |
16 |
35,448,388 (GRCm39) |
missense |
probably benign |
0.01 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGCAGCAACAACTGTGGAGG -3'
(R):5'- TTGCAGTCTTGGTACTCCGC -3'
Sequencing Primer
(F):5'- TCGCGACGCCGTTCTTG -3'
(R):5'- AAGTTCTCTTGCGGACGC -3'
|
| Posted On |
2014-10-15 |
Incidental Mutation