Mutagenetix > Incidental Mutation

Incidental Mutation 'R0010:Sema6b'

50150

Institutional Source

Beutler Lab

Gene Symbol

Sema6b

Ensembl Gene

ENSMUSG00000001227

Gene Name

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

Synonyms

Sema, Seman, semaZ, VIb

MMRRC Submission

038305-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.193) question?

Stock #

R0010 (G1)

Quality Score

Status

Validated (trace)

Chromosome

Chromosomal Location

56123085-56140343 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 56124105 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Lysine at position 853 (E853K)

Ref Sequence

ENSEMBL: ENSMUSP00000130985 (fasta)

Gene Model

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

AlphaFold

O54951

Predicted Effect

probably benign
Transcript: ENSMUST00000001256
AA Change: E853K

PolyPhen 2 Score 0.057 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000001256
Gene: ENSMUSG00000001227
AA Change: E853K

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

probably benign
Transcript: ENSMUST00000167545
AA Change: E853K

PolyPhen 2 Score 0.057 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000130985
Gene: ENSMUSG00000001227
AA Change: E853K

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

Meta Mutation Damage Score

0.1535

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.0%
20x: 94.9%

Validation Efficiency

100% (89/89)

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrf3	T	C	5: 30,205,609		probably benign	Het
Ahrr	G	A	13: 74,283,024		probably benign	Het
Bbs7	T	C	3: 36,607,717		probably null	Het
BC037034	T	C	5: 138,260,293		probably null	Het
Cacna1h	T	C	17: 25,380,844	K1566E	probably damaging	Het
Ccdc73	C	T	2: 104,980,987		probably benign	Het
Cd74	A	T	18: 60,809,071	H124L	probably benign	Het
Cd74	A	T	18: 60,803,896		probably benign	Het
Cdk5rap2	T	C	4: 70,243,459	E270G	probably benign	Het
Ces2a	G	A	8: 104,741,396	D520N	probably benign	Het
Cldnd1	T	A	16: 58,731,259		probably benign	Het
Cox17	T	A	16: 38,347,170	C24S	possibly damaging	Het
Cyp2b9	T	A	7: 26,186,753		probably benign	Het
Dennd4a	T	C	9: 64,896,715	L1112P	probably benign	Het
Dennd4c	T	C	4: 86,781,577	S222P	probably damaging	Het
Dhx37	T	A	5: 125,431,616	Q85L	probably benign	Het
Egfem1	G	T	3: 29,582,919	C192F	probably damaging	Het
Eif3f	A	T	7: 108,941,005	N336Y	possibly damaging	Het
Evc2	T	A	5: 37,417,449	L1016Q	probably damaging	Het
Fam114a2	G	T	11: 57,514,156	T40N	probably damaging	Het
Fam135b	T	C	15: 71,622,032	K16R	probably damaging	Het
Fcho1	A	G	8: 71,709,999	Y725H	probably damaging	Het
Frem1	T	C	4: 83,000,098	I536V	probably benign	Het
Ginm1	T	C	10: 7,775,374		probably benign	Het
Glrb	A	T	3: 80,860,315		probably benign	Het
Glt6d1	C	A	2: 25,794,727		probably null	Het
Gm10320	T	C	13: 98,489,546	Y110C	probably damaging	Het
Gm20388	G	A	8: 122,270,598		probably benign	Het
Gm3985	A	T	8: 32,942,456		noncoding transcript	Het
Gm5422	A	G	10: 31,249,754		noncoding transcript	Het
Igkv6-29	A	T	6: 70,138,770		probably benign	Het
Inpp5d	G	A	1: 87,697,546		probably null	Het
Itpr3	T	G	17: 27,120,977	V2610G	probably damaging	Het
Kmt5c	T	A	7: 4,746,208	M88K	probably benign	Het
Lrp12	C	T	15: 39,878,276	A367T	probably damaging	Het
Ltbp1	A	G	17: 75,363,391	T1476A	probably damaging	Het
Mcoln2	C	T	3: 146,183,561	T374M	probably damaging	Het
Milr1	T	G	11: 106,767,003	*209G	probably null	Het
Mitf	A	G	6: 97,807,281	K33R	probably benign	Het
Mon2	A	C	10: 123,032,694	S485A	probably damaging	Het
Mpdu1	C	T	11: 69,658,841	G47R	probably damaging	Het
Ms4a4d	A	G	19: 11,554,826	N112S	probably damaging	Het
Mybpc3	G	A	2: 91,134,833	W1082*	probably null	Het
Myl3	A	C	9: 110,767,929	D119A	probably damaging	Het
Naa15	A	T	3: 51,436,213		probably null	Het
Nav3	A	G	10: 109,823,226		probably benign	Het
Nek7	T	A	1: 138,544,204	Q66L	possibly damaging	Het
Nktr	G	A	9: 121,741,166		probably benign	Het
Nlgn1	G	T	3: 25,435,842		probably benign	Het
Npr1	T	C	3: 90,454,832	E1002G	probably damaging	Het
Nup133	A	T	8: 123,904,579	I1072N	probably damaging	Het
Oc90	C	T	15: 65,876,548	C371Y	probably damaging	Het
Olfr835	A	T	9: 19,035,322	L66F	probably damaging	Het
Olfr901	A	T	9: 38,430,920	I213F	possibly damaging	Het
Olfr994	A	T	2: 85,429,895	D311E	probably benign	Het
Pradc1	A	T	6: 85,447,231	N44K	probably damaging	Het
Pradc1	T	C	6: 85,447,620	D116G	probably damaging	Het
Ptprk	G	A	10: 28,585,969	C91Y	probably damaging	Het
Pus7	T	C	5: 23,747,845	I491V	probably benign	Het
Rock1	T	A	18: 10,084,380	D951V	probably damaging	Het
Scgb2b26	T	A	7: 33,944,349	E55D	probably damaging	Het
Scn8a	T	C	15: 101,013,573	V958A	probably damaging	Het
Sec14l1	T	C	11: 117,143,770		probably benign	Het
Sec24c	A	G	14: 20,689,261		probably benign	Het
Sgk1	G	A	10: 21,997,438		probably null	Het
Shprh	C	T	10: 11,151,931	T94I	probably benign	Het
Slc16a3	T	C	11: 120,956,705	S240P	probably benign	Het
Slc5a8	T	C	10: 88,886,590	V95A	probably benign	Het
Smg1	A	T	7: 118,171,859		probably benign	Het
Spta1	G	A	1: 174,217,943	V1556I	probably benign	Het
Svs1	A	T	6: 48,988,906	H616L	probably damaging	Het
Trappc4	G	A	9: 44,405,231		probably benign	Het
Tubgcp6	A	G	15: 89,103,183	S1188P	probably benign	Het
Txlna	T	G	4: 129,629,086	D487A	probably benign	Het
Ube2d2b	T	C	5: 107,830,636	F51S	possibly damaging	Het
Vmn2r6	G	A	3: 64,559,545	Q178*	probably null	Het
Wdfy3	T	C	5: 101,848,349	T3234A	probably damaging	Het
Ylpm1	C	A	12: 85,029,026	Q384K	probably damaging	Het
Zbtb41	T	G	1: 139,423,530	V127G	probably damaging	Het
Zfp605	T	A	5: 110,127,534	C173S	probably benign	Het
Zfp608	A	T	18: 54,895,214		probably benign	Het
Zhx2	T	C	15: 57,821,274	V13A	possibly damaging	Het

Other mutations in Sema6b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00324:Sema6b	APN	17	56130048	missense	probably damaging	1.00
IGL01102:Sema6b	APN	17	56132761	missense	possibly damaging	0.91
IGL01533:Sema6b	APN	17	56129499	splice site	probably benign
IGL01611:Sema6b	APN	17	56129969	splice site	probably null
IGL01996:Sema6b	APN	17	56131157	missense	probably damaging	1.00
IGL02118:Sema6b	APN	17	56132821	missense	probably benign
R0066:Sema6b	UTSW	17	56128271	missense	possibly damaging	0.83
R0066:Sema6b	UTSW	17	56128271	missense	possibly damaging	0.83
R0525:Sema6b	UTSW	17	56126630	missense	probably damaging	0.96
R0635:Sema6b	UTSW	17	56129971	critical splice donor site	probably null
R1129:Sema6b	UTSW	17	56124347	missense	probably benign
R1927:Sema6b	UTSW	17	56132797	missense	probably benign	0.00
R2211:Sema6b	UTSW	17	56124741	missense	probably benign	0.00
R4081:Sema6b	UTSW	17	56128307	missense	probably damaging	0.99
R5013:Sema6b	UTSW	17	56132497	critical splice donor site	probably null
R5296:Sema6b	UTSW	17	56127091	critical splice acceptor site	probably null
R5314:Sema6b	UTSW	17	56128413	nonsense	probably null
R6317:Sema6b	UTSW	17	56124047	missense	probably benign	0.26
R6419:Sema6b	UTSW	17	56132784	nonsense	probably null
R7255:Sema6b	UTSW	17	56125336	missense	probably benign	0.01
R7289:Sema6b	UTSW	17	56125573	missense	possibly damaging	0.77
R7805:Sema6b	UTSW	17	56131555	missense	probably damaging	1.00
R8157:Sema6b	UTSW	17	56128448	missense	probably damaging	1.00
R8290:Sema6b	UTSW	17	56124803	missense	possibly damaging	0.93
R8305:Sema6b	UTSW	17	56127084	missense	probably damaging	1.00
R9502:Sema6b	UTSW	17	56132500	missense	probably benign	0.13

Predicted Primers

PCR Primer
(F):5'- CTTGTGCTTCCCTGTGGCGA -3'
(R):5'- CCGCTTATGCAGAATGGCTGGAC -3'

Sequencing Primer
(F):5'- TGAGGAACAAACGCGCC -3'
(R):5'- CTCACGACCTGGACACG -3'

Posted On

2013-06-20