Mutagenetix > Incidental Mutation

Incidental Mutation 'R1666:Sema5b'

187231

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

039702-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1666 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

35361517-35485103 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 35478852 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 559 (P559S)

Ref Sequence

ENSEMBL: ENSMUSP00000112536 (fasta)

Gene Model

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

AlphaFold

Q60519

Predicted Effect

probably benign
Transcript: ENSMUST00000050625
AA Change: P559S

PolyPhen 2 Score 0.028 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000057494
Gene: ENSMUSG00000052133
AA Change: P559S

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 benign
Transcript: ENSMUST00000120756
AA Change: P559S

PolyPhen 2 Score 0.028 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000112536
Gene: ENSMUSG00000052133
AA Change: P559S

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

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.6%

Validation Efficiency

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acvrl1	G	A	15: 101,035,458 (GRCm39)	R328H	probably damaging	Het
Afp	T	C	5: 90,652,927 (GRCm39)	S466P	probably damaging	Het
Arhgap45	A	G	10: 79,864,584 (GRCm39)	S879G	possibly damaging	Het
Asic1	A	G	15: 99,597,006 (GRCm39)	D556G	probably damaging	Het
Atp2a3	T	A	11: 72,869,633 (GRCm39)		probably null	Het
Brinp2	C	A	1: 158,074,128 (GRCm39)	E664D	probably damaging	Het
Cap2	C	A	13: 46,768,799 (GRCm39)	H147N	probably damaging	Het
Cd209f	G	A	8: 4,154,862 (GRCm39)	Q79*	probably null	Het
Chrna7	T	C	7: 62,861,890 (GRCm39)	Y54C	possibly damaging	Het
Clec1a	T	C	6: 129,413,967 (GRCm39)	D40G	probably benign	Het
Col11a1	A	G	3: 113,855,184 (GRCm39)	E148G	unknown	Het
Comp	A	T	8: 70,831,607 (GRCm39)		probably null	Het
Cpz	A	G	5: 35,665,460 (GRCm39)		probably null	Het
Cyfip1	T	A	7: 55,521,646 (GRCm39)	N13K	probably damaging	Het
Cyp2c50	A	T	19: 40,079,499 (GRCm39)	M198L	probably benign	Het
Deup1	A	T	9: 15,486,487 (GRCm39)	Y398N	possibly damaging	Het
Elapor1	A	G	3: 108,377,313 (GRCm39)	S434P	probably benign	Het
Epb41l4a	A	G	18: 34,054,962 (GRCm39)	L42P	probably damaging	Het
Exo1	T	C	1: 175,736,052 (GRCm39)	I812T	possibly damaging	Het
Fbxl17	A	T	17: 63,692,060 (GRCm39)		probably null	Het
Fxn	A	G	19: 24,239,377 (GRCm39)	Y172H	probably damaging	Het
Gabra6	A	G	11: 42,208,461 (GRCm39)	S124P	probably damaging	Het
Gje1	C	A	10: 14,592,551 (GRCm39)	W77L	possibly damaging	Het
Glra1	A	G	11: 55,465,225 (GRCm39)	S23P	probably damaging	Het
Gm6811	T	C	17: 21,314,529 (GRCm39)		noncoding transcript	Het
Greb1l	T	A	18: 10,501,080 (GRCm39)		probably null	Het
Greb1l	T	C	18: 10,529,708 (GRCm39)		probably null	Het
Grm6	A	T	11: 50,750,711 (GRCm39)	I625F	probably damaging	Het
Guca1a	A	G	17: 47,711,167 (GRCm39)	F60L	probably damaging	Het
Hectd1	T	A	12: 51,800,607 (GRCm39)	E2070D	possibly damaging	Het
Itga5	G	A	15: 103,256,329 (GRCm39)	T910I	probably benign	Het
Kctd10	A	G	5: 114,507,051 (GRCm39)	V142A	probably benign	Het
Kif1c	C	T	11: 70,619,223 (GRCm39)	L953F	probably damaging	Het
Lmtk3	A	T	7: 45,443,588 (GRCm39)	D757V	probably benign	Het
Lpcat1	T	C	13: 73,658,242 (GRCm39)		probably null	Het
Lrrc30	A	T	17: 67,939,200 (GRCm39)	C127S	probably benign	Het
Mc4r	A	G	18: 66,992,480 (GRCm39)	L211P	probably damaging	Het
Mgat5b	T	A	11: 116,874,474 (GRCm39)	N635K	probably benign	Het
Mms19	A	T	19: 41,940,995 (GRCm39)	M443K	possibly damaging	Het
Mroh5	T	C	15: 73,659,754 (GRCm39)	N359S	probably benign	Het
Nlrc4	G	A	17: 74,752,901 (GRCm39)	T494M	probably damaging	Het
Ntf3	T	C	6: 126,079,401 (GRCm39)	D35G	possibly damaging	Het
Or5g25	A	T	2: 85,478,157 (GRCm39)	C169*	probably null	Het
Osbpl5	T	C	7: 143,262,776 (GRCm39)	H192R	probably damaging	Het
Parp4	A	T	14: 56,861,620 (GRCm39)	K984N	possibly damaging	Het
Pdgfra	G	A	5: 75,349,681 (GRCm39)	G892D	possibly damaging	Het
Pik3c2g	A	T	6: 139,612,634 (GRCm39)		probably benign	Het
Ppcdc	T	A	9: 57,321,998 (GRCm39)	M181L	possibly damaging	Het
Pramel7	G	A	2: 87,322,747 (GRCm39)	P6S	probably damaging	Het
Prkcz	G	T	4: 155,374,208 (GRCm39)	F69L	probably damaging	Het
Prkd1	G	A	12: 50,441,709 (GRCm39)	H277Y	probably damaging	Het
Ptgs2	A	G	1: 149,977,021 (GRCm39)	Y44C	probably damaging	Het
Rbck1	T	A	2: 152,158,819 (GRCm39)	S488C	probably damaging	Het
Rbl1	T	C	2: 157,001,654 (GRCm39)	Y878C	probably damaging	Het
Rbm6	G	A	9: 107,669,055 (GRCm39)	T619I	probably benign	Het
Rp1	A	G	1: 4,420,086 (GRCm39)	I342T	probably damaging	Het
Rpn2	C	T	2: 157,136,075 (GRCm39)	T161M	possibly damaging	Het
Rufy4	G	A	1: 74,186,837 (GRCm39)	V542I	probably benign	Het
Serpinb3d	A	G	1: 107,008,481 (GRCm39)	V128A	probably benign	Het
Slc35f3	T	A	8: 127,115,960 (GRCm39)	S296T	probably damaging	Het
Slco1a8	T	A	6: 141,927,775 (GRCm39)		probably null	Het
Smarca2	A	G	19: 26,624,434 (GRCm39)	I365V	possibly damaging	Het
Spdya	T	A	17: 71,885,235 (GRCm39)	C230S	probably damaging	Het
Sv2b	G	A	7: 74,856,089 (GRCm39)	A67V	probably benign	Het
Tapbpl	A	G	6: 125,207,164 (GRCm39)	V175A	probably benign	Het
Tmt1a3	A	G	15: 100,233,099 (GRCm39)	I97V	probably benign	Het
Ttn	T	C	2: 76,642,095 (GRCm39)	T13373A	probably damaging	Het
Tubb5	A	T	17: 36,147,530 (GRCm39)	N52K	probably benign	Het
Tyr	T	A	7: 87,142,149 (GRCm39)	Y137F	probably damaging	Het
Unc45b	T	A	11: 82,808,565 (GRCm39)	I217N	probably benign	Het
Vmn1r202	A	T	13: 22,685,540 (GRCm39)	D292E	possibly damaging	Het
Vmn1r22	A	G	6: 57,877,704 (GRCm39)	M91T	probably benign	Het
Washc2	T	A	6: 116,200,215 (GRCm39)		probably null	Het
Zfp566	A	T	7: 29,777,901 (GRCm39)	H93Q	probably benign	Het
Zfp740	A	G	15: 102,116,753 (GRCm39)	D56G	probably damaging	Het
Zfp804b	A	C	5: 6,821,323 (GRCm39)	L580R	possibly damaging	Het
Zmiz2	T	G	11: 6,346,836 (GRCm39)	S148R	probably benign	Het
Zmym6	T	A	4: 127,016,652 (GRCm39)	I719N	probably damaging	Het
Zyx	T	A	6: 42,332,966 (GRCm39)	V372E	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
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'- AACTTTGCAGCACGCTTGAAGAC -3'
(R):5'- CTTGGATGAGATGCCCCATTTCCC -3'

Sequencing Primer
(F):5'- AGTTCCAACATGAGCCTGTG -3'
(R):5'- CAGTTCTCACTGTACAAGTCCTAAG -3'

Posted On

2014-05-09