Mutagenetix > Incidental Mutation

Incidental Mutation 'R0426:Sema5b'

38687

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

038628-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0426 (G1)

Quality Score

159

Status

Validated

Chromosome

Chromosomal Location

35361517-35485103 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 35466725 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Aspartic acid at position 209 (G209D)

Ref Sequence

ENSEMBL: ENSMUSP00000112536 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000050625] [ENSMUST00000120756]

AlphaFold

Q60519

Predicted Effect

probably damaging
Transcript: ENSMUST00000050625
AA Change: G209D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000057494
Gene: ENSMUSG00000052133
AA Change: G209D

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: G209D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000112536
Gene: ENSMUSG00000052133
AA Change: G209D

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: ENSMUST00000133554

Meta Mutation Damage Score

0.7967

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.9%

Validation Efficiency

96% (86/90)

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: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8b	G	T	11: 109,845,853 (GRCm39)		probably benign	Het
Acadl	A	T	1: 66,880,805 (GRCm39)	F320L	probably damaging	Het
Acsbg1	T	C	9: 54,530,030 (GRCm39)	D222G	probably benign	Het
Anapc15	A	G	7: 101,547,240 (GRCm39)	T39A	probably benign	Het
Ano3	A	T	2: 110,491,519 (GRCm39)	V919E	probably damaging	Het
Arhgef12	T	C	9: 42,882,286 (GRCm39)		probably null	Het
Atad5	T	A	11: 80,003,658 (GRCm39)	I1091N	probably benign	Het
Atf1	A	T	15: 100,130,708 (GRCm39)	H26L	possibly damaging	Het
Atp10a	T	C	7: 58,434,482 (GRCm39)	M252T	probably benign	Het
Btbd8	C	T	5: 107,658,239 (GRCm39)	T1603I	probably damaging	Het
Cd55	C	T	1: 130,376,109 (GRCm39)	R347H	probably benign	Het
Cdc27	A	C	11: 104,403,853 (GRCm39)		probably null	Het
Cdh9	G	A	15: 16,823,540 (GRCm39)		probably null	Het
Cdk11b	T	C	4: 155,726,969 (GRCm39)		probably benign	Het
Cep70	A	G	9: 99,179,737 (GRCm39)	D567G	probably benign	Het
Cep78	A	T	19: 15,948,334 (GRCm39)	Y382*	probably null	Het
Cgas	G	A	9: 78,343,020 (GRCm39)		probably benign	Het
Col9a2	T	C	4: 120,901,857 (GRCm39)		probably benign	Het
Cyp2d12	G	A	15: 82,443,164 (GRCm39)	D409N	probably benign	Het
Ddx39a	A	G	8: 84,448,398 (GRCm39)	T217A	probably benign	Het
Dennd1b	T	A	1: 139,097,934 (GRCm39)	D733E	probably benign	Het
Dicer1	A	G	12: 104,668,801 (GRCm39)	S1294P	probably damaging	Het
Dnah3	T	C	7: 119,542,795 (GRCm39)	E3539G	probably benign	Het
Dnmbp	A	G	19: 43,840,875 (GRCm39)		probably benign	Het
Dysf	T	C	6: 84,126,739 (GRCm39)	L1332P	probably damaging	Het
F5	A	G	1: 164,010,409 (GRCm39)	D380G	probably damaging	Het
Fam171a1	T	C	2: 3,226,433 (GRCm39)	V522A	probably benign	Het
Fhip1b	A	C	7: 105,038,680 (GRCm39)	C186W	probably damaging	Het
Galr2	C	A	11: 116,172,517 (GRCm39)	A69D	probably damaging	Het
Grk2	T	C	19: 4,340,628 (GRCm39)		probably null	Het
Gtf3c1	A	T	7: 125,262,188 (GRCm39)	Y1119*	probably null	Het
Hgd	A	T	16: 37,409,047 (GRCm39)		probably benign	Het
Ildr2	G	T	1: 166,136,468 (GRCm39)	V436L	probably benign	Het
Intu	G	A	3: 40,629,735 (GRCm39)	C355Y	probably damaging	Het
Irf2bpl	G	T	12: 86,929,870 (GRCm39)	P268T	probably benign	Het
Jarid2	T	C	13: 44,994,358 (GRCm39)		probably null	Het
Jup	A	T	11: 100,263,227 (GRCm39)	M716K	probably benign	Het
Kank1	G	A	19: 25,388,837 (GRCm39)	V809I	probably damaging	Het
Kdm1b	T	A	13: 47,217,720 (GRCm39)		probably benign	Het
Kdm3a	C	T	6: 71,577,739 (GRCm39)	C687Y	probably damaging	Het
Kdm5d	T	A	Y: 942,437 (GRCm39)		probably benign	Het
Kifap3	T	A	1: 163,693,121 (GRCm39)		probably benign	Het
Macf1	T	A	4: 123,377,453 (GRCm39)	K1400*	probably null	Het
Majin	A	G	19: 6,262,147 (GRCm39)		probably benign	Het
Mctp1	A	G	13: 77,168,940 (GRCm39)	I846V	probably benign	Het
Mrgpra2b	T	A	7: 47,113,875 (GRCm39)	I286F	possibly damaging	Het
Neil3	T	G	8: 54,062,431 (GRCm39)		probably benign	Het
Nox3	G	T	17: 3,745,838 (GRCm39)	N23K	probably damaging	Het
Nt5c3	T	C	6: 56,860,797 (GRCm39)	K219E	probably benign	Het
Or1e29	T	A	11: 73,667,263 (GRCm39)	M297L	probably benign	Het
Or52b4i	T	A	7: 102,191,893 (GRCm39)	I250N	probably damaging	Het
Or5b105	G	A	19: 13,080,642 (GRCm39)	R3C	possibly damaging	Het
Or6b13	A	C	7: 139,782,029 (GRCm39)	F218C	possibly damaging	Het
Or6d13	A	T	6: 116,517,446 (GRCm39)	N11Y	probably damaging	Het
Or8g34	T	C	9: 39,372,889 (GRCm39)	L54P	probably damaging	Het
Pacsin2	A	G	15: 83,263,996 (GRCm39)	V347A	possibly damaging	Het
Pcdhb7	A	T	18: 37,475,857 (GRCm39)	E331V	probably damaging	Het
Pcid2	A	C	8: 13,131,262 (GRCm39)		probably null	Het
Pcsk9	T	C	4: 106,307,274 (GRCm39)	D323G	possibly damaging	Het
Pdhb	T	C	14: 8,169,801 (GRCm38)	E203G	probably damaging	Het
Phlpp2	A	G	8: 110,655,095 (GRCm39)	Y630C	probably benign	Het
Pidd1	C	T	7: 141,019,046 (GRCm39)	A812T	probably damaging	Het
Plau	G	A	14: 20,892,382 (GRCm39)	R389H	probably benign	Het
Plekhg6	G	A	6: 125,341,592 (GRCm39)		probably null	Het
Ppox	T	C	1: 171,105,322 (GRCm39)	Y321C	probably damaging	Het
Pxdn	A	G	12: 30,037,065 (GRCm39)	N281S	possibly damaging	Het
Pycr3	A	T	15: 75,790,237 (GRCm39)	M138K	probably benign	Het
Radil	T	C	5: 142,483,628 (GRCm39)	Y526C	probably damaging	Het
Ranbp3	C	A	17: 57,014,169 (GRCm39)	D233E	probably benign	Het
Rhpn1	A	G	15: 75,583,721 (GRCm39)	Q402R	possibly damaging	Het
Sec23b	T	A	2: 144,410,532 (GRCm39)		probably benign	Het
Sel1l2	A	T	2: 140,082,832 (GRCm39)	L602*	probably null	Het
Svep1	T	C	4: 58,073,333 (GRCm39)	Y1992C	possibly damaging	Het
Syncrip	T	A	9: 88,338,312 (GRCm39)		probably benign	Het
Synj1	G	T	16: 90,764,242 (GRCm39)	A65E	probably damaging	Het
Taar2	G	A	10: 23,817,393 (GRCm39)	R311H	probably benign	Het
Tecrl	T	C	5: 83,502,610 (GRCm39)		probably benign	Het
Tenm4	G	T	7: 96,427,058 (GRCm39)	G698C	probably damaging	Het
Tmem209	G	A	6: 30,491,181 (GRCm39)	L259F	probably damaging	Het
Tmem247	G	A	17: 87,225,931 (GRCm39)	E124K	possibly damaging	Het
Tnks2	C	A	19: 36,830,221 (GRCm39)	A218E	probably damaging	Het
Tppp	T	A	13: 74,169,430 (GRCm39)	F57I	probably damaging	Het
Trim36	A	G	18: 46,305,592 (GRCm39)	W452R	probably damaging	Het
Vars2	A	T	17: 35,975,476 (GRCm39)	V262E	probably damaging	Het
Vmn2r92	C	T	17: 18,388,219 (GRCm39)	A408V	probably damaging	Het
Zfp516	G	T	18: 82,973,897 (GRCm39)	A32S	probably benign	Het
Zfy2	G	T	Y: 2,107,348 (GRCm39)	L429I	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
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
R2215:Sema5b	UTSW	16	35,480,585 (GRCm39)	missense	probably damaging	1.00
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'- GACCTCACCCTTTGTAATGACCACG -3'
(R):5'- TCTTGGTCTTTGGGCAAACACCTTC -3'

Sequencing Primer
(F):5'- CCCTTTGTAATGACCACGAGATTG -3'
(R):5'- GCAAACACCTTCCCTGTCC -3'

Posted On

2013-05-23