Mutagenetix > Incidental Mutation

Incidental Mutation 'R0525:Sema6b'

48880

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

038718-MU

Accession Numbers

Essential gene?

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

Stock #

R0525 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

56430085-56447343 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 56433630 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Arginine at position 426 (H426R)

Ref Sequence

ENSEMBL: ENSMUSP00000130985 (fasta)

Gene Model

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

AlphaFold

O54951

Predicted Effect

probably damaging
Transcript: ENSMUST00000001256
AA Change: H426R

PolyPhen 2 Score 0.962 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000001256
Gene: ENSMUSG00000001227
AA Change: H426R

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 damaging
Transcript: ENSMUST00000167545
AA Change: H426R

PolyPhen 2 Score 0.962 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000130985
Gene: ENSMUSG00000001227
AA Change: H426R

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

0.1433

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.8%

Validation Efficiency

100% (72/72)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933440M02Rik	T	A	7: 124,930,671 (GRCm39)		noncoding transcript	Het
A930002H24Rik	A	G	17: 64,170,642 (GRCm39)	W49R	unknown	Het
Abca13	G	A	11: 9,243,371 (GRCm39)	V1745M	probably damaging	Het
Abca16	T	G	7: 120,065,033 (GRCm39)	Y563*	probably null	Het
Acot12	C	T	13: 91,908,186 (GRCm39)		probably benign	Het
Alms1	G	A	6: 85,564,742 (GRCm39)	A39T	unknown	Het
Arid5b	T	C	10: 67,933,676 (GRCm39)	D742G	possibly damaging	Het
Atp1a4	G	A	1: 172,067,255 (GRCm39)		probably benign	Het
AU021092	T	A	16: 5,035,725 (GRCm39)	E145V	possibly damaging	Het
Calr4	A	T	4: 109,099,461 (GRCm39)		probably benign	Het
Clip4	T	A	17: 72,106,093 (GRCm39)		probably null	Het
Cnpy4	A	T	5: 138,190,878 (GRCm39)	H180L	probably benign	Het
Cyp2j9	T	C	4: 96,467,802 (GRCm39)		probably null	Het
Dgkq	A	G	5: 108,802,481 (GRCm39)	S406P	probably damaging	Het
Dhx8	G	A	11: 101,654,754 (GRCm39)	C1014Y	probably damaging	Het
Dnah3	T	C	7: 119,527,977 (GRCm39)	Y3824C	probably damaging	Het
Donson	A	T	16: 91,483,133 (GRCm39)	H69Q	probably damaging	Het
Dppa3	A	G	6: 122,606,939 (GRCm39)	E143G	probably damaging	Het
Drg1	A	G	11: 3,212,545 (GRCm39)	F96L	probably damaging	Het
Dvl1	A	C	4: 155,940,052 (GRCm39)	T395P	probably damaging	Het
Eftud2	A	T	11: 102,730,079 (GRCm39)	V897D	probably damaging	Het
Enpp6	A	G	8: 47,535,478 (GRCm39)	N341S	possibly damaging	Het
F11	A	G	8: 45,706,086 (GRCm39)	F100L	probably benign	Het
Fas	T	C	19: 34,296,727 (GRCm39)	Y189H	probably damaging	Het
Galnt14	G	T	17: 73,852,076 (GRCm39)	S114R	probably damaging	Het
Gfpt2	A	G	11: 49,720,602 (GRCm39)	I528V	probably benign	Het
Glt6d1	A	G	2: 25,684,280 (GRCm39)	V242A	possibly damaging	Het
Grm1	A	T	10: 10,594,953 (GRCm39)		probably benign	Het
Gskip	G	A	12: 105,665,224 (GRCm39)	A88T	probably damaging	Het
Gtpbp1	A	G	15: 79,597,648 (GRCm39)	I348V	probably benign	Het
Hnrnpul1	C	A	7: 25,440,308 (GRCm39)	R316L	possibly damaging	Het
Il34	T	C	8: 111,474,915 (GRCm39)	E121G	probably damaging	Het
Lrr1	T	C	12: 69,215,685 (GRCm39)	L19P	probably damaging	Het
Mat2b	A	G	11: 40,573,496 (GRCm39)		probably benign	Het
Mettl21e	T	C	1: 44,245,542 (GRCm39)	K235E	probably damaging	Het
Mir124-2hg	T	A	3: 17,839,693 (GRCm39)	E126V	possibly damaging	Het
Myh15	A	G	16: 48,952,414 (GRCm39)	K828R	probably benign	Het
Myom3	A	G	4: 135,492,237 (GRCm39)	D127G	possibly damaging	Het
Nek5	C	A	8: 22,569,093 (GRCm39)		probably benign	Het
Nudt7	A	T	8: 114,878,392 (GRCm39)		probably null	Het
Or10ag56	A	T	2: 87,139,693 (GRCm39)	T187S	probably benign	Het
Or10d4c	T	G	9: 39,558,767 (GRCm39)	C248W	probably damaging	Het
Or1j4	T	C	2: 36,740,202 (GRCm39)	L48P	probably damaging	Het
Or4a67	G	A	2: 88,597,658 (GRCm39)	Q334*	probably null	Het
Or8k23	C	T	2: 86,186,619 (GRCm39)	V36I	probably benign	Het
Phyhd1	A	G	2: 30,171,040 (GRCm39)	H241R	probably damaging	Het
Pmch	T	C	10: 87,927,262 (GRCm39)		probably benign	Het
Ror1	A	G	4: 100,298,717 (GRCm39)	S697G	probably damaging	Het
Rslcan18	A	G	13: 67,260,322 (GRCm39)	V25A	probably benign	Het
Serpina3g	T	C	12: 104,204,598 (GRCm39)	F9S	probably damaging	Het
Serpinb12	T	A	1: 106,874,432 (GRCm39)	H52Q	probably benign	Het
Sh3gl1	T	C	17: 56,324,873 (GRCm39)	K294R	probably benign	Het
Sidt1	G	T	16: 44,079,809 (GRCm39)	T615K	possibly damaging	Het
Slc16a4	A	C	3: 107,205,255 (GRCm39)		probably benign	Het
Sned1	T	A	1: 93,199,696 (GRCm39)		probably null	Het
Sp2	A	T	11: 96,846,924 (GRCm39)		probably benign	Het
Steap1	T	A	5: 5,792,903 (GRCm39)	I3F	possibly damaging	Het
Stxbp5l	A	T	16: 36,950,159 (GRCm39)		probably null	Het
Tbc1d9	G	T	8: 83,995,614 (GRCm39)	V968F	probably benign	Het
Tnfrsf21	C	T	17: 43,349,104 (GRCm39)	H239Y	probably benign	Het
Triobp	T	C	15: 78,858,098 (GRCm39)	L1233P	possibly damaging	Het
Trp53bp1	C	A	2: 121,082,349 (GRCm39)	A317S	probably null	Het
Trpc4ap	A	G	2: 155,482,398 (GRCm39)	F531L	possibly damaging	Het
Ugt1a10	C	T	1: 88,145,971 (GRCm39)	P473L	probably damaging	Het
Vmn1r86	T	C	7: 12,836,088 (GRCm39)	K213E	probably benign	Het
Vps8	G	A	16: 21,358,859 (GRCm39)		probably null	Het
Wnk1	A	T	6: 119,903,525 (GRCm39)	S2563T	probably damaging	Het
Yrdc	C	G	4: 124,745,559 (GRCm39)	R3G	probably damaging	Het
Zfp287	A	T	11: 62,606,070 (GRCm39)	V279E	probably benign	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
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
R8290:Sema6b	UTSW	17	56,431,803 (GRCm39)	missense	possibly damaging	0.93
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'- TGGGATGCACTCACTTCATGCAC -3'
(R):5'- ACGAAGATAGCTCCTGCAAAGAAGC -3'

Sequencing Primer
(F):5'- TTCATGCACCCCGAGTACAG -3'
(R):5'- CCTTGCAAAGGGCCTGAG -3'

Posted On

2013-06-12