Mutagenetix > Incidental Mutation

Incidental Mutation 'R2211:Sema6b'

239415

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

040213-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.225) question?

Stock #

R2211 (G1)

Quality Score

185

Status

Not validated

Chromosome

Chromosomal Location

56123085-56140343 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 56124741 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Phenylalanine at position 641 (I641F)

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: I641F

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000001256
Gene: ENSMUSG00000001227
AA Change: I641F

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: I641F

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000130985
Gene: ENSMUSG00000001227
AA Change: I641F

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: 99.1%
3x: 98.5%
10x: 97.1%
20x: 94.5%

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A430078G23Rik	T	C	8: 3,387,680	S268P	possibly damaging	Het
Adam18	A	G	8: 24,628,155	S34P	probably damaging	Het
Adam23	T	A	1: 63,573,129		probably benign	Het
Adcy10	A	T	1: 165,518,212	I277F	probably damaging	Het
Arfgef3	A	T	10: 18,592,245	S1736T	possibly damaging	Het
Arhgap21	A	T	2: 20,881,640	M242K	possibly damaging	Het
Astn1	A	G	1: 158,657,306	R4G	probably benign	Het
AU041133	G	A	10: 82,150,921	C135Y	probably damaging	Het
Cdc42bpb	A	G	12: 111,301,854	V53A	probably benign	Het
Cdh23	T	C	10: 60,466,004	D428G	possibly damaging	Het
Cebpa	T	C	7: 35,120,466	S350P	probably damaging	Het
Cftr	A	G	6: 18,214,280	M152V	probably null	Het
Cpa4	A	G	6: 30,583,650	N255S	possibly damaging	Het
Ddx51	T	A	5: 110,655,768	D343E	probably damaging	Het
Dnah7a	T	C	1: 53,479,773	I2942V	probably benign	Het
Dnajc1	G	T	2: 18,392,475	A9E	probably damaging	Het
Dpysl5	G	A	5: 30,791,597	D399N	probably damaging	Het
Edem3	A	G	1: 151,804,702	D526G	possibly damaging	Het
Emc10	G	A	7: 44,493,192	R109W	probably damaging	Het
Etaa1	G	A	11: 17,952,686	Q84*	probably null	Het
Fabp3	C	T	4: 130,312,387	T57I	probably benign	Het
Fam149a	G	A	8: 45,341,009	T674I	probably damaging	Het
Fam98a	A	G	17: 75,538,945		probably null	Het
Fat4	A	G	3: 38,891,527	N1523S	possibly damaging	Het
Fbxw10	A	G	11: 62,867,535	T529A	probably damaging	Het
Gzf1	C	T	2: 148,684,950	A447V	probably damaging	Het
Hap1	G	A	11: 100,354,724	T138M	probably benign	Het
Hic1	T	A	11: 75,169,384	R46W	possibly damaging	Het
Id4	T	A	13: 48,261,802	L102Q	probably damaging	Het
Il3ra	T	C	14: 14,355,029	C271R	probably benign	Het
Ints4	T	C	7: 97,509,750	I443T	possibly damaging	Het
Lmln	A	G	16: 33,109,778	E535G	probably benign	Het
Lrrtm4	A	G	6: 80,022,640	H345R	probably benign	Het
Ltbp3	T	C	19: 5,753,962	I834T	possibly damaging	Het
Mnd1	C	A	3: 84,134,109	C62F	probably benign	Het
Mpp5	A	T	12: 78,797,248	K75N	possibly damaging	Het
Ms4a18	C	A	19: 10,997,305	V341L	probably benign	Het
Nbr1	T	C	11: 101,567,264		probably null	Het
Nf1	T	C	11: 79,444,064	M914T	probably benign	Het
Notch3	T	A	17: 32,147,978	H861L	probably benign	Het
Nupl1	A	G	14: 60,232,640	F341L	probably damaging	Het
Ogfod2	C	A	5: 124,112,780		probably null	Het
Oit3	T	C	10: 59,428,070	D414G	probably damaging	Het
Olfr1079	T	C	2: 86,538,513	Y132C	probably damaging	Het
Olfr1497	T	A	19: 13,795,369	M81L	probably benign	Het
Olfr787	A	T	10: 129,462,940	K88M	probably damaging	Het
Olfr804	A	G	10: 129,705,451	H191R	probably benign	Het
Pcbp4	C	A	9: 106,460,734	H74Q	probably benign	Het
Pip5k1b	A	T	19: 24,378,850	D241E	probably damaging	Het
Plcb2	T	C	2: 118,723,534	D102G	probably benign	Het
Plekha5	G	A	6: 140,525,861	E4K	possibly damaging	Het
Ppargc1a	A	C	5: 51,474,259	S343A	possibly damaging	Het
Ppwd1	G	A	13: 104,207,142	S585L	probably benign	Het
Rarg	T	C	15: 102,239,524	N284S	probably benign	Het
Rnpepl1	C	T	1: 92,916,380	L278F	probably damaging	Het
Rp1	A	C	1: 4,348,139	S917A	probably damaging	Het
Rsf1	ATGGCG	ATGGCGAGGGTGGCG	7: 97,579,904		probably benign	Het
Rsph3b	T	C	17: 6,941,740	S189G	probably benign	Het
Sec31b	A	T	19: 44,523,150	L604Q	probably damaging	Het
Slc35f5	A	T	1: 125,579,264	I309F	possibly damaging	Het
Smarca4	A	G	9: 21,686,029	E1360G	probably damaging	Het
Spata31d1c	T	C	13: 65,035,939	S432P	probably benign	Het
Spsb3	T	C	17: 24,890,937		probably null	Het
Sptbn4	T	C	7: 27,367,609	D1960G	probably damaging	Het
Srgap1	A	G	10: 121,853,740	V345A	possibly damaging	Het
Tiam2	C	A	17: 3,414,918	C307*	probably null	Het
Trim43b	T	A	9: 89,085,249	T444S	possibly damaging	Het
Trmt13	A	G	3: 116,594,754	I11T	probably benign	Het
Ylpm1	A	T	12: 85,044,378	R1073*	probably null	Het
Zfp524	T	C	7: 5,017,919	S149P	probably damaging	Het
Zfp777	T	C	6: 48,043,885	I312V	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
R0010:Sema6b	UTSW	17	56124105	missense	probably benign	0.06
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
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'- TGTCCAGGTCGTGAGGGC -3'
(R):5'- AAATCGCACTGCCACTTTCTC -3'

Sequencing Primer
(F):5'- TGAGGGCCACCATGCAG -3'
(R):5'- TCCCCAGGACTCTTGCG -3'

Posted On

2014-10-15