Mutagenetix > Incidental Mutation

Incidental Mutation 'R1775:Sema5b'

258040

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

039806-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1775 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

35361517-35485103 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 35480694 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Arginine at position 787 (K787R)

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: K758R

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000057494
Gene: ENSMUSG00000052133
AA Change: K758R

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: K787R

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000112536
Gene: ENSMUSG00000052133
AA Change: K787R

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

0.0898

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.5%
20x: 92.9%

Validation Efficiency

98% (95/97)

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: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700034J04Rik	A	G	12: 11,272,143 (GRCm39)	S20P	unknown	Het
4921528I07Rik	G	A	9: 114,108,386 (GRCm39)		noncoding transcript	Het
4930562C15Rik	G	A	16: 4,669,422 (GRCm39)		probably null	Het
4933427I04Rik	A	G	4: 123,754,286 (GRCm39)	T67A	possibly damaging	Het
Abcc2	A	T	19: 43,786,858 (GRCm39)	N160Y	possibly damaging	Het
Acaca	A	G	11: 84,191,248 (GRCm39)	D155G	possibly damaging	Het
Afg3l1	G	A	8: 124,219,639 (GRCm39)	R389Q	possibly damaging	Het
Ank2	G	A	3: 126,728,196 (GRCm39)	T799M	probably benign	Het
Anxa2	T	C	9: 69,395,363 (GRCm39)	Y202H	possibly damaging	Het
Arhgef33	A	G	17: 80,681,172 (GRCm39)	T771A	probably benign	Het
Atp12a	T	C	14: 56,610,046 (GRCm39)	V182A	probably benign	Het
Birc6	T	C	17: 74,919,281 (GRCm39)	L210S	probably damaging	Het
Car3	A	G	3: 14,929,492 (GRCm39)	T73A	probably benign	Het
Cd5l	T	C	3: 87,275,966 (GRCm39)	L312P	probably damaging	Het
Celf5	A	G	10: 81,303,138 (GRCm39)		probably benign	Het
Cep290	T	A	10: 100,332,672 (GRCm39)	V257E	probably damaging	Het
Cntrob	T	C	11: 69,211,693 (GRCm39)	D177G	possibly damaging	Het
Copg2	A	T	6: 30,787,271 (GRCm39)	F658I	probably damaging	Het
Csmd3	T	C	15: 47,763,135 (GRCm39)	T1234A	probably damaging	Het
Dhx35	A	G	2: 158,648,357 (GRCm39)	T72A	probably damaging	Het
Dmrtc2	A	T	7: 24,573,792 (GRCm39)	H209L	possibly damaging	Het
Eml5	G	T	12: 98,818,963 (GRCm39)		probably null	Het
Evpl	T	C	11: 116,114,486 (GRCm39)	E1068G	possibly damaging	Het
Ezh2	A	G	6: 47,553,594 (GRCm39)	M41T	probably damaging	Het
Fmo3	A	G	1: 162,796,294 (GRCm39)	S93P	possibly damaging	Het
Gdi2	A	G	13: 3,610,018 (GRCm39)	Y213C	possibly damaging	Het
Gpr15	A	T	16: 58,538,921 (GRCm39)	I56K	probably benign	Het
Gria2	G	T	3: 80,598,645 (GRCm39)	S796R	probably benign	Het
Hectd4	T	A	5: 121,429,254 (GRCm39)		probably benign	Het
Hgfac	T	C	5: 35,200,194 (GRCm39)		probably benign	Het
Hspg2	C	T	4: 137,247,467 (GRCm39)	R1200W	probably damaging	Het
Ift52	G	A	2: 162,867,275 (GRCm39)	D78N	possibly damaging	Het
Iqca1	C	A	1: 90,009,138 (GRCm39)	W415L	probably damaging	Het
Ism1	A	T	2: 139,587,963 (GRCm39)	K236N	probably damaging	Het
Itgb6	C	T	2: 60,502,988 (GRCm39)	W43*	probably null	Het
Kcnk18	T	A	19: 59,223,773 (GRCm39)	I306N	probably damaging	Het
Kctd8	T	C	5: 69,497,903 (GRCm39)	K248E	probably damaging	Het
Layn	T	A	9: 50,970,833 (GRCm39)	I237F	probably benign	Het
Lce3f	C	T	3: 92,900,248 (GRCm39)	P23L	unknown	Het
Lct	A	G	1: 128,228,038 (GRCm39)	F1152L	probably damaging	Het
Mettl25b	A	G	3: 87,831,124 (GRCm39)	S404P	probably damaging	Het
Mxra8	T	C	4: 155,927,531 (GRCm39)	I413T	probably damaging	Het
Nedd9	A	G	13: 41,471,438 (GRCm39)	V187A	probably benign	Het
Net1	A	G	13: 3,937,642 (GRCm39)	L207P	probably damaging	Het
Neurod1	G	T	2: 79,284,781 (GRCm39)	P201T	probably benign	Het
Nlrp1b	A	G	11: 71,052,647 (GRCm39)	F927S	probably damaging	Het
Ntrk3	T	A	7: 78,005,789 (GRCm39)	H524L	possibly damaging	Het
Nup98	A	C	7: 101,784,144 (GRCm39)	S1063A	probably benign	Het
Or10ak11	T	A	4: 118,687,065 (GRCm39)	M191L	probably benign	Het
Or11h4b	G	T	14: 50,918,623 (GRCm39)	P156Q	possibly damaging	Het
Or56b1	G	A	7: 104,285,366 (GRCm39)	V162I	probably benign	Het
Or5b97	C	A	19: 12,878,599 (GRCm39)	V182F	probably benign	Het
Or5m9b	G	A	2: 85,905,104 (GRCm39)	V7I	possibly damaging	Het
Or6d15	T	C	6: 116,559,925 (GRCm39)		probably benign	Het
Pdzd2	G	A	15: 12,592,546 (GRCm39)	R33W	probably damaging	Het
Phf21a	G	A	2: 92,160,860 (GRCm39)	V243I	probably damaging	Het
Ppp1r12b	A	G	1: 134,821,086 (GRCm39)		probably null	Het
Rexo5	T	C	7: 119,444,634 (GRCm39)	V703A	probably benign	Het
Rgs4	A	G	1: 169,572,847 (GRCm39)	S30P	probably benign	Het
Rxra	C	A	2: 27,646,256 (GRCm39)	D340E	probably damaging	Het
Samhd1	A	G	2: 156,949,467 (GRCm39)	V473A	probably benign	Het
Scn3a	T	A	2: 65,302,686 (GRCm39)	K1253N	probably damaging	Het
Scn7a	T	C	2: 66,511,299 (GRCm39)	N1207S	probably benign	Het
Sec24d	T	A	3: 123,130,166 (GRCm39)	I443N	probably damaging	Het
Sema4g	T	A	19: 44,987,681 (GRCm39)		probably null	Het
Serpinc1	A	G	1: 160,817,217 (GRCm39)	N104D	probably benign	Het
Sfn	T	C	4: 133,328,542 (GRCm39)	H180R	probably damaging	Het
Slc22a6	G	T	19: 8,596,471 (GRCm39)		probably null	Het
Slc9a8	T	C	2: 167,299,278 (GRCm39)	S217P	probably benign	Het
Smc6	A	G	12: 11,359,270 (GRCm39)	N965D	probably benign	Het
Sod2	T	A	17: 13,233,919 (GRCm39)	I177N	probably damaging	Het
Sp4	A	T	12: 118,263,335 (GRCm39)	I237K	probably damaging	Het
Sulf2	T	C	2: 165,921,532 (GRCm39)	K697R	probably benign	Het
Svs4	A	T	2: 164,119,005 (GRCm39)	D110E	unknown	Het
Tas1r1	T	A	4: 152,122,675 (GRCm39)	R57*	probably null	Het
Tlr5	T	C	1: 182,801,287 (GRCm39)	I197T	probably damaging	Het
Tmc3	T	C	7: 83,261,740 (GRCm39)	V606A	probably benign	Het
Tmem241	T	A	18: 12,251,469 (GRCm39)	L37F	probably damaging	Het
Tmem59l	A	T	8: 70,938,903 (GRCm39)	N90K	probably damaging	Het
Tram1	A	C	1: 13,646,680 (GRCm39)		probably benign	Het
Trim15	T	A	17: 37,176,061 (GRCm39)	H162L	probably benign	Het
Ttc28	T	A	5: 111,424,677 (GRCm39)	Y1501N	probably benign	Het
Ttc34	T	C	4: 154,946,671 (GRCm39)	V857A	probably benign	Het
Tulp4	A	G	17: 6,189,321 (GRCm39)	T48A	probably damaging	Het
Usp9y	T	C	Y: 1,368,089 (GRCm39)	E939G	probably damaging	Het
Utp20	A	G	10: 88,606,670 (GRCm39)	I1634T	probably benign	Het
Vmn2r72	T	C	7: 85,387,378 (GRCm39)	M729V	probably benign	Het
Vps13c	C	T	9: 67,788,729 (GRCm39)	T334M	probably damaging	Het
Wnk4	C	G	11: 101,167,166 (GRCm39)		probably benign	Het
Xpo1	A	G	11: 23,221,193 (GRCm39)	N97D	probably benign	Het
Xpo4	A	T	14: 57,841,129 (GRCm39)	F518Y	probably benign	Het
Zfp668	C	T	7: 127,465,778 (GRCm39)	V469I	possibly damaging	Het
Zfp85	C	A	13: 67,897,823 (GRCm39)	C83F	probably 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
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'- AGGAGTTCAAGACCTGCAACC -3'
(R):5'- TTGCAGTCTTGGTACTCCG -3'

Sequencing Primer
(F):5'- TGCAACCCCGAGGCTTG -3'
(R):5'- AAGTTCTCTTGCGGACGC -3'

Posted On

2015-01-22