Mutagenetix > Incidental Mutation

Incidental Mutation 'R8290:Sema6b'

638676

Institutional Source

Beutler Lab

Gene Symbol

Sema6b

Ensembl Gene

ENSMUSG00000001227

Gene Name

sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B

Synonyms

semaZ, Seman, VIb, Sema

MMRRC Submission

067712-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.152) question?

Stock #

R8290 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

56430085-56447343 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 56431803 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glutamic Acid at position 620 (V620E)

Ref Sequence

ENSEMBL: ENSMUSP00000001256 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001256] [ENSMUST00000041357] [ENSMUST00000167545]

AlphaFold

O54951

Predicted Effect

possibly damaging
Transcript: ENSMUST00000001256
AA Change: V620E

PolyPhen 2 Score 0.928 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000001256
Gene: ENSMUSG00000001227
AA Change: V620E

Domain	Start	End	E-Value	Type
low complexity region	13	21	N/A	INTRINSIC
Sema	66	496	2.48e-177	SMART
PSI	527	581	4.09e-1	SMART
transmembrane domain	604	626	N/A	INTRINSIC
low complexity region	655	685	N/A	INTRINSIC
low complexity region	707	718	N/A	INTRINSIC
low complexity region	739	760	N/A	INTRINSIC
low complexity region	855	866	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000041357

SMART Domains

Protein: ENSMUSP00000038048
Gene: ENSMUSG00000037095

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
LRR	84	107	1.86e0	SMART
LRR_TYP	108	131	3.63e-3	SMART
LRR	133	155	5.89e1	SMART
LRR_TYP	156	179	1.45e-2	SMART
LRR_TYP	180	203	8.47e-4	SMART
LRR	205	227	2.08e1	SMART
LRR	229	251	1.91e1	SMART
LRR	252	275	5.34e-1	SMART
LRRCT	292	342	9.69e-9	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000167545
AA Change: V620E

PolyPhen 2 Score 0.928 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000130985
Gene: ENSMUSG00000001227
AA Change: V620E

Domain	Start	End	E-Value	Type
low complexity region	13	21	N/A	INTRINSIC
Sema	66	496	2.48e-177	SMART
PSI	527	581	4.09e-1	SMART
transmembrane domain	604	626	N/A	INTRINSIC
low complexity region	655	685	N/A	INTRINSIC
low complexity region	707	718	N/A	INTRINSIC
low complexity region	739	760	N/A	INTRINSIC
low complexity region	855	866	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

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 family, a group of proteins characterized by the presence of a conserved semaphorin (sema) domain. Whereas some semaphorins are transmembrane proteins, others are secreted. Semaphorins play a major role in axon guidance. The protein encoded by this gene may be involved in both peripheral and central nervous system development. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit abnormal mossy fiber and mossy cell axon projections, thickened suprapyramidal bundles, and elongated infrapyramydal bundles. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc12	A	T	8: 87,238,911 (GRCm39)	Y1100N	probably damaging	Het
Abcf2	CAT	CATAAT	5: 24,781,589 (GRCm39)		probably benign	Het
Adgrv1	T	C	13: 81,630,002 (GRCm39)	T3576A	probably benign	Het
Adnp2	A	T	18: 80,185,948 (GRCm39)	N8K	probably damaging	Het
Aftph	A	T	11: 20,675,712 (GRCm39)	H632Q	probably benign	Het
Arhgef11	A	T	3: 87,633,275 (GRCm39)	I710F	probably damaging	Het
Atp6v1c2	T	C	12: 17,338,153 (GRCm39)	N341S	possibly damaging	Het
Ccsap	T	G	8: 124,585,986 (GRCm39)	D55A	probably benign	Het
Cdh17	A	G	4: 11,817,037 (GRCm39)	N816S	probably benign	Het
Celf3	A	G	3: 94,386,489 (GRCm39)	I26V	probably benign	Het
Celsr1	G	T	15: 85,917,286 (GRCm39)	S229*	probably null	Het
Chek2	A	G	5: 111,008,766 (GRCm39)	E299G	possibly damaging	Het
Clca3a2	A	G	3: 144,793,719 (GRCm39)	V312A	possibly damaging	Het
Cnn1	A	G	9: 22,012,447 (GRCm39)	K25R	probably benign	Het
Cry1	A	T	10: 84,978,977 (GRCm39)	Y516*	probably null	Het
Dcaf4	T	C	12: 83,588,333 (GRCm39)	S498P	probably benign	Het
Dmgdh	T	C	13: 93,843,244 (GRCm39)	V360A	probably benign	Het
Dnajc18	G	A	18: 35,816,324 (GRCm39)	R205*	probably null	Het
Eif4a2	G	T	16: 22,927,372 (GRCm39)	G22C	probably damaging	Het
Elmo2	A	G	2: 165,150,923 (GRCm39)	I196T	probably damaging	Het
Epha3	A	G	16: 63,472,859 (GRCm39)	I342T	possibly damaging	Het
Epha8	G	T	4: 136,665,897 (GRCm39)	L420M	probably damaging	Het
Etf1	G	A	18: 35,064,891 (GRCm39)	P35L	unknown	Het
Etnk2	A	C	1: 133,307,127 (GRCm39)	*386C	probably null	Het
Fgg	A	T	3: 82,920,141 (GRCm39)	I307F	probably benign	Het
Flg2	A	G	3: 93,110,069 (GRCm39)	Q699R	unknown	Het
Foxp4	T	A	17: 48,191,778 (GRCm39)	T120S	unknown	Het
Fzd1	A	G	5: 4,807,060 (GRCm39)	V174A	possibly damaging	Het
Gad1	A	C	2: 70,404,610 (GRCm39)	I167L	probably benign	Het
Gfm2	T	A	13: 97,282,171 (GRCm39)	D55E	probably benign	Het
Grb14	G	T	2: 64,805,929 (GRCm39)	A12E	probably benign	Het
Hnmt	A	C	2: 23,893,896 (GRCm39)	Y199*	probably null	Het
Kit	A	G	5: 75,801,829 (GRCm39)	I615V	probably benign	Het
Kpna6	A	G	4: 129,555,097 (GRCm39)		probably null	Het
Lpxn	C	T	19: 12,810,052 (GRCm39)	R275C	probably damaging	Het
Magi1	C	T	6: 94,260,066 (GRCm39)	G80S	probably damaging	Het
Men1	A	G	19: 6,388,316 (GRCm39)	I312V	probably benign	Het
Msx2	A	G	13: 53,622,528 (GRCm39)	F161L	probably damaging	Het
Mtr	T	C	13: 12,205,139 (GRCm39)	D1107G	probably damaging	Het
Muc4	A	T	16: 32,575,434 (GRCm39)	M1397L	probably benign	Het
Mybpc3	A	G	2: 90,951,473 (GRCm39)	N259S	probably benign	Het
Myo5c	A	G	9: 75,196,178 (GRCm39)	K1242R	probably benign	Het
Myoc	T	C	1: 162,476,601 (GRCm39)	V435A	possibly damaging	Het
Nbea	G	A	3: 55,966,056 (GRCm39)	Q469*	probably null	Het
Ndufa10	A	C	1: 92,390,869 (GRCm39)	M227R	possibly damaging	Het
Obscn	C	T	11: 58,953,536 (GRCm39)	D3831N	probably damaging	Het
Obscn	T	C	11: 59,015,400 (GRCm39)	E1024G	probably damaging	Het
Oma1	T	C	4: 103,176,671 (GRCm39)	L145P	probably damaging	Het
Phf11	T	C	14: 59,485,418 (GRCm39)	Y114C	probably damaging	Het
Phf12	C	A	11: 77,920,465 (GRCm39)	N1000K	probably benign	Het
Plxnb1	G	T	9: 108,938,687 (GRCm39)	A1350S	probably benign	Het
Prkd1	C	T	12: 50,388,799 (GRCm39)	V915I	probably damaging	Het
Prkra	T	A	2: 76,463,982 (GRCm39)	N227Y	probably damaging	Het
Prtg	A	T	9: 72,798,077 (GRCm39)	H681L	probably damaging	Het
Rtn1	T	C	12: 72,355,193 (GRCm39)	K251R	probably benign	Het
Senp7	T	A	16: 55,974,000 (GRCm39)	L407*	probably null	Het
Sh3pxd2a	A	T	19: 47,302,575 (GRCm39)	L168Q	probably damaging	Het
Shtn1	A	G	19: 58,988,326 (GRCm39)	L453P	probably damaging	Het
Slc26a6	G	A	9: 108,733,230 (GRCm39)	R43H	probably benign	Het
Stac3	T	C	10: 127,339,229 (GRCm39)		probably null	Het
Taf2	A	G	15: 54,926,416 (GRCm39)	F178S	probably damaging	Het
Tcp10a	G	A	17: 7,601,716 (GRCm39)	E239K	probably benign	Het
Ubox5	A	G	2: 130,442,333 (GRCm39)	V118A	probably damaging	Het
Unc13d	C	A	11: 115,958,973 (GRCm39)	L729F	probably damaging	Het
Vmn1r228	T	C	17: 20,996,724 (GRCm39)	T265A	probably benign	Het
Vmn2r100	G	A	17: 19,751,612 (GRCm39)	V615I	probably damaging	Het
Vmn2r60	T	G	7: 41,791,690 (GRCm39)	C538G	probably damaging	Het
Vmn2r93	A	T	17: 18,524,291 (GRCm39)	N95I	probably damaging	Het
Vsig2	A	G	9: 37,451,264 (GRCm39)	N55S	probably benign	Het
Zfp472	A	G	17: 33,197,088 (GRCm39)	T388A	probably benign	Het
Zfp853	G	A	5: 143,274,826 (GRCm39)	Q214*	probably null	Het
Zfp949	A	G	9: 88,451,293 (GRCm39)	R288G	probably damaging	Het

Other mutations in Sema6b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00324:Sema6b	APN	17	56,437,048 (GRCm39)	missense	probably damaging	1.00
IGL01102:Sema6b	APN	17	56,439,761 (GRCm39)	missense	possibly damaging	0.91
IGL01533:Sema6b	APN	17	56,436,499 (GRCm39)	splice site	probably benign
IGL01611:Sema6b	APN	17	56,436,969 (GRCm39)	splice site	probably null
IGL01996:Sema6b	APN	17	56,438,157 (GRCm39)	missense	probably damaging	1.00
IGL02118:Sema6b	APN	17	56,439,821 (GRCm39)	missense	probably benign
R0010:Sema6b	UTSW	17	56,431,105 (GRCm39)	missense	probably benign	0.06
R0066:Sema6b	UTSW	17	56,435,271 (GRCm39)	missense	possibly damaging	0.83
R0066:Sema6b	UTSW	17	56,435,271 (GRCm39)	missense	possibly damaging	0.83
R0525:Sema6b	UTSW	17	56,433,630 (GRCm39)	missense	probably damaging	0.96
R0635:Sema6b	UTSW	17	56,436,971 (GRCm39)	critical splice donor site	probably null
R1129:Sema6b	UTSW	17	56,431,347 (GRCm39)	missense	probably benign
R1927:Sema6b	UTSW	17	56,439,797 (GRCm39)	missense	probably benign	0.00
R2211:Sema6b	UTSW	17	56,431,741 (GRCm39)	missense	probably benign	0.00
R4081:Sema6b	UTSW	17	56,435,307 (GRCm39)	missense	probably damaging	0.99
R5013:Sema6b	UTSW	17	56,439,497 (GRCm39)	critical splice donor site	probably null
R5296:Sema6b	UTSW	17	56,434,091 (GRCm39)	critical splice acceptor site	probably null
R5314:Sema6b	UTSW	17	56,435,413 (GRCm39)	nonsense	probably null
R6317:Sema6b	UTSW	17	56,431,047 (GRCm39)	missense	probably benign	0.26
R6419:Sema6b	UTSW	17	56,439,784 (GRCm39)	nonsense	probably null
R7255:Sema6b	UTSW	17	56,432,336 (GRCm39)	missense	probably benign	0.01
R7289:Sema6b	UTSW	17	56,432,573 (GRCm39)	missense	possibly damaging	0.77
R7805:Sema6b	UTSW	17	56,438,555 (GRCm39)	missense	probably damaging	1.00
R8157:Sema6b	UTSW	17	56,435,448 (GRCm39)	missense	probably damaging	1.00
R8305:Sema6b	UTSW	17	56,434,084 (GRCm39)	missense	probably damaging	1.00
R9502:Sema6b	UTSW	17	56,439,500 (GRCm39)	missense	probably benign	0.13

Predicted Primers

PCR Primer
(F):5'- TGTCCAGCCATTCTGCATAAGC -3'
(R):5'- TATCTAGCAGACTTTCAGACTGGTTTC -3'

Sequencing Primer
(F):5'- TGCATAAGCGGGGCCAG -3'
(R):5'- CAGACTTTCAGACTGGTTTCCAAGG -3'

Posted On

2020-07-28