Mutagenetix > Incidental Mutations

Incidental Mutation 'R1056:Sema6c'

94341

Institutional Source

Beutler Lab

Gene Symbol

Sema6c

Ensembl Gene

ENSMUSG00000038777

Gene Name

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

Synonyms

Sema Y, Semay

MMRRC Submission

039146-MU

Accession Numbers

Is this an essential gene?

Possibly essential (E-score: 0.513) question?

Stock #

R1056 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

95160457-95174024 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 95171216 bp

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 543 (S543T)

Ref Sequence

ENSEMBL: ENSMUSP00000144039 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000090821] [ENSMUST00000090823] [ENSMUST00000107217] [ENSMUST00000131620] [ENSMUST00000142449] [ENSMUST00000168321] [ENSMUST00000202315] [ENSMUST00000204709]

Predicted Effect

probably benign
Transcript: ENSMUST00000090821
AA Change: S543T

PolyPhen 2 Score 0.146 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000088331
Gene: ENSMUSG00000038777
AA Change: S543T

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
transmembrane domain	604	626	N/A	INTRINSIC
low complexity region	627	638	N/A	INTRINSIC
low complexity region	646	658	N/A	INTRINSIC
low complexity region	660	669	N/A	INTRINSIC
low complexity region	693	709	N/A	INTRINSIC
low complexity region	744	761	N/A	INTRINSIC
low complexity region	907	924	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000090823
AA Change: S543T

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000088333
Gene: ENSMUSG00000038777
AA Change: S543T

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
low complexity region	591	603	N/A	INTRINSIC
transmembrane domain	636	658	N/A	INTRINSIC
low complexity region	659	670	N/A	INTRINSIC
low complexity region	678	690	N/A	INTRINSIC
low complexity region	692	701	N/A	INTRINSIC
low complexity region	725	741	N/A	INTRINSIC
low complexity region	776	793	N/A	INTRINSIC
low complexity region	939	956	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000107217
AA Change: S503T

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000102835
Gene: ENSMUSG00000038777
AA Change: S503T

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	448	1.23e-126	SMART
low complexity region	551	563	N/A	INTRINSIC
transmembrane domain	596	618	N/A	INTRINSIC
low complexity region	619	630	N/A	INTRINSIC
low complexity region	638	650	N/A	INTRINSIC
low complexity region	652	661	N/A	INTRINSIC
low complexity region	685	701	N/A	INTRINSIC
low complexity region	736	753	N/A	INTRINSIC
low complexity region	899	916	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126597

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130662

Predicted Effect

probably benign
Transcript: ENSMUST00000131620

SMART Domains

Protein: ENSMUSP00000138154
Gene: ENSMUSG00000038777

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134125

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141607

Predicted Effect

probably benign
Transcript: ENSMUST00000142449

SMART Domains

Protein: ENSMUSP00000123457
Gene: ENSMUSG00000038777

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
low complexity region	591	603	N/A	INTRINSIC
transmembrane domain	636	658	N/A	INTRINSIC
low complexity region	659	670	N/A	INTRINSIC
low complexity region	678	690	N/A	INTRINSIC
low complexity region	692	701	N/A	INTRINSIC
low complexity region	725	741	N/A	INTRINSIC
low complexity region	776	793	N/A	INTRINSIC
low complexity region	939	956	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000168321
AA Change: S543T

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000129081
Gene: ENSMUSG00000038777
AA Change: S543T

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
transmembrane domain	604	626	N/A	INTRINSIC
low complexity region	627	638	N/A	INTRINSIC
low complexity region	646	658	N/A	INTRINSIC
low complexity region	660	669	N/A	INTRINSIC
low complexity region	693	709	N/A	INTRINSIC
low complexity region	744	761	N/A	INTRINSIC
low complexity region	907	924	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000202315
AA Change: S543T

PolyPhen 2 Score 0.146 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000144039
Gene: ENSMUSG00000038777
AA Change: S543T

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	62	488	2.55e-165	SMART
transmembrane domain	604	626	N/A	INTRINSIC
low complexity region	627	638	N/A	INTRINSIC
low complexity region	646	658	N/A	INTRINSIC
low complexity region	660	669	N/A	INTRINSIC
low complexity region	693	709	N/A	INTRINSIC
low complexity region	744	761	N/A	INTRINSIC
low complexity region	907	924	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000204709

SMART Domains

Protein: ENSMUSP00000144702
Gene: ENSMUSG00000038777

Domain	Start	End	E-Value	Type
low complexity region	10	20	N/A	INTRINSIC
PDB:3OKY\|B	25	117	8e-8	PDB
Blast:Sema	62	119	9e-34	BLAST

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 96.1%
20x: 92.7%

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. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration. [provided by RefSeq, May 2010]
PHENOTYPE: Mice homozygous for a targeted mutation display a decrease in pain threshold. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932438A13Rik	C	A	3: 36,983,453	H2469N	possibly damaging	Het
4932438A13Rik	T	A	3: 37,044,680	M1152K	probably benign	Het
Abca14	A	G	7: 120,325,072	Y1649C	probably damaging	Het
Abcc10	A	C	17: 46,303,954	C1459W	possibly damaging	Het
Amfr	A	T	8: 93,985,469	F278I	probably benign	Het
Anks1b	G	T	10: 90,921,429		probably null	Het
Bak1	A	G	17: 27,021,273	S147P	possibly damaging	Het
C7	T	C	15: 5,045,778	N144S	possibly damaging	Het
Casd1	T	C	6: 4,641,967	V748A	probably benign	Het
Ccdc180	T	C	4: 45,916,375	S859P	probably benign	Het
Ccne2	T	C	4: 11,192,707	S2P	probably damaging	Het
Cdc42bpg	T	A	19: 6,314,021	I541N	probably benign	Het
Cgnl1	T	A	9: 71,725,895	N58I	probably damaging	Het
Chd7	T	C	4: 8,822,402	S832P	possibly damaging	Het
Chl1	A	T	6: 103,675,077	Y318F	possibly damaging	Het
Coq2	G	T	5: 100,657,947	N274K	probably benign	Het
Crhr2	A	T	6: 55,100,735	V214E	probably damaging	Het
Dgkg	G	C	16: 22,600,541	P70A	probably damaging	Het
Dync2h1	T	C	9: 7,147,731	I966M	probably benign	Het
Eif5b	C	G	1: 38,022,167	R380G	unknown	Het
Fat4	T	A	3: 38,891,392	I1478N	probably damaging	Het
Gm8251	C	T	1: 44,060,927	G337D	probably damaging	Het
Impact	A	T	18: 12,976,524	I92L	probably benign	Het
Ly6c2	A	G	15: 75,111,596		probably null	Het
Lypd6b	G	A	2: 49,947,456	V147I	possibly damaging	Het
Mdga2	T	C	12: 66,723,120	D192G	probably damaging	Het
Mms22l	T	C	4: 24,586,344		probably null	Het
Myo9a	C	T	9: 59,832,201	T732I	possibly damaging	Het
Myrf	C	T	19: 10,223,486	M274I	probably benign	Het
Nfx1	G	A	4: 41,003,057	R686Q	probably damaging	Het
Ofcc1	C	T	13: 40,208,829	G206R	probably benign	Het
Olfr43	C	T	11: 74,206,782	V145I	probably benign	Het
Olfr594	A	T	7: 103,220,418	E233D	probably benign	Het
Oog4	T	C	4: 143,438,011	T245A	possibly damaging	Het
Pclo	A	T	5: 14,540,055	K790*	probably null	Het
Pcm1	A	G	8: 41,321,900	E1668G	probably damaging	Het
Pkhd1l1	T	A	15: 44,591,964	N4040K	probably damaging	Het
Podnl1	T	A	8: 84,129,276	S222T	probably benign	Het
Ppil4	A	G	10: 7,799,632	T182A	possibly damaging	Het
Prdm13	T	C	4: 21,678,544	K649E	probably damaging	Het
Prob1	A	T	18: 35,653,610	H530Q	probably benign	Het
Rbbp4	A	T	4: 129,317,649	M404K	probably damaging	Het
Rilpl1	A	T	5: 124,493,837	F149I	probably damaging	Het
Sh3rf3	G	T	10: 59,007,082	W290L	probably damaging	Het
Slc2a12	T	G	10: 22,665,451	S402A	probably benign	Het
Tas2r131	T	A	6: 132,957,067	I260F	possibly damaging	Het
Tasp1	A	G	2: 140,008,764	I113T	possibly damaging	Het
Tnrc18	G	A	5: 142,773,859	R741*	probably null	Het
Ube2o	G	T	11: 116,546,464	D244E	probably damaging	Het
Vmn1r206	A	T	13: 22,620,614	M141K	probably benign	Het
Zbtb14	C	A	17: 69,388,502	F398L	probably damaging	Het
Zfp747	A	G	7: 127,374,588	S137P	probably benign	Het
Zfp951	A	T	5: 104,815,285	H138Q	possibly damaging	Het

Other mutations in Sema6c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01547:Sema6c	APN	3	95172398	missense	probably damaging	1.00
IGL01631:Sema6c	APN	3	95170403	missense	probably benign	0.10
IGL01799:Sema6c	APN	3	95170831	missense	probably damaging	1.00
IGL02237:Sema6c	APN	3	95170119	missense	probably damaging	1.00
IGL02852:Sema6c	APN	3	95169984	splice site	probably benign
IGL02874:Sema6c	APN	3	95170377	missense	probably damaging	1.00
IGL03003:Sema6c	APN	3	95169614	missense	probably damaging	1.00
PIT4418001:Sema6c	UTSW	3	95170090	missense	possibly damaging	0.57
R0558:Sema6c	UTSW	3	95168691	missense	probably damaging	1.00
R0582:Sema6c	UTSW	3	95169197	missense	probably damaging	1.00
R0590:Sema6c	UTSW	3	95172623	missense	probably damaging	1.00
R0685:Sema6c	UTSW	3	95172710	missense	possibly damaging	0.46
R1721:Sema6c	UTSW	3	95170788	missense	probably damaging	0.98
R1867:Sema6c	UTSW	3	95170788	missense	probably damaging	0.98
R1868:Sema6c	UTSW	3	95170813	missense	probably damaging	0.99
R2016:Sema6c	UTSW	3	95171234	missense	probably benign	0.00
R2343:Sema6c	UTSW	3	95167083	missense	probably damaging	1.00
R2898:Sema6c	UTSW	3	95172818	missense	probably damaging	1.00
R4095:Sema6c	UTSW	3	95173194	missense	probably benign	0.03
R4999:Sema6c	UTSW	3	95168363	missense	probably damaging	1.00
R5263:Sema6c	UTSW	3	95173152	missense	probably benign	0.02
R6914:Sema6c	UTSW	3	95173208	missense	probably benign	0.00
R6942:Sema6c	UTSW	3	95173208	missense	probably benign	0.00
R7104:Sema6c	UTSW	3	95168845	missense	possibly damaging	0.95
R7524:Sema6c	UTSW	3	95167060	missense	probably benign	0.20
R7724:Sema6c	UTSW	3	95173199	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TAGTCTGAAGTAGGCAGCCACGAG -3'
(R):5'- CTGGGATGTTGTCAGTAGCCATCAC -3'

Sequencing Primer
(F):5'- CGAGGGTCTGGAGCAGATTG -3'
(R):5'- CACAGTCATATGTAACTTTGGCTGC -3'

Posted On

2014-01-05