Mutagenetix > Incidental Mutation

Incidental Mutation 'R2016:Sema6c'

222982

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

040025-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.303) question?

Stock #

R2016 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

95067768-95081335 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 95078545 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 549 (I549V)

Ref Sequence

ENSEMBL: ENSMUSP00000144039 (fasta)

Gene Model

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

AlphaFold

Q9WTM3

Predicted Effect

probably benign
Transcript: ENSMUST00000090821
AA Change: I549V

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000088331
Gene: ENSMUSG00000038777
AA Change: I549V

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: I549V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000088333
Gene: ENSMUSG00000038777
AA Change: I549V

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: I509V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000102835
Gene: ENSMUSG00000038777
AA Change: I509V

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

probably benign
Transcript: ENSMUST00000168321
AA Change: I549V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000129081
Gene: ENSMUSG00000038777
AA Change: I549V

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: I549V

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000144039
Gene: ENSMUSG00000038777
AA Change: I549V

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

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

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.0%
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. 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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700025C18Rik	T	C	2: 164,920,946 (GRCm39)	D29G	unknown	Het
Abca13	A	T	11: 9,240,619 (GRCm39)	L827F	probably damaging	Het
Abca8a	A	G	11: 109,961,213 (GRCm39)	F570L	probably damaging	Het
Adck1	T	A	12: 88,427,862 (GRCm39)	I493N	probably damaging	Het
Adra2c	T	C	5: 35,437,656 (GRCm39)	C143R	probably damaging	Het
Afg2a	T	C	3: 37,632,911 (GRCm39)	V839A	possibly damaging	Het
Akap13	C	T	7: 75,354,279 (GRCm39)	T1800M	probably damaging	Het
Angpt2	T	C	8: 18,755,747 (GRCm39)	N240S	probably damaging	Het
Apob	G	A	12: 8,057,751 (GRCm39)	D2078N	possibly damaging	Het
Atp8b1	T	C	18: 64,673,405 (GRCm39)	N989S	probably damaging	Het
B3gnt2	T	C	11: 22,786,621 (GRCm39)	D189G	probably damaging	Het
Bcam	G	A	7: 19,494,274 (GRCm39)	T374M	probably benign	Het
Blm	T	C	7: 80,155,674 (GRCm39)	D335G	probably benign	Het
Cbfa2t2	T	C	2: 154,359,727 (GRCm39)	L264P	probably damaging	Het
Col4a2	T	C	8: 11,495,086 (GRCm39)	F1515L	probably benign	Het
Csf2ra	T	G	19: 61,215,331 (GRCm39)	M95L	probably benign	Het
Cyp2c70	T	A	19: 40,152,856 (GRCm39)	T300S	possibly damaging	Het
Cyp4f15	A	T	17: 32,921,133 (GRCm39)	H440L	probably damaging	Het
Dcaf1	T	A	9: 106,716,287 (GRCm39)	D360E	probably benign	Het
Ddr2	T	C	1: 169,812,537 (GRCm39)	M652V	probably damaging	Het
Dnah2	T	A	11: 69,327,896 (GRCm39)	I3370F	probably damaging	Het
Dpysl5	G	A	5: 30,948,941 (GRCm39)	D399N	probably damaging	Het
Efemp1	G	T	11: 28,871,613 (GRCm39)	R376L	probably damaging	Het
Efl1	A	C	7: 82,402,917 (GRCm39)	D673A	probably damaging	Het
Eid1	A	G	2: 125,515,121 (GRCm39)	M4V	probably benign	Het
Emc10	G	A	7: 44,142,616 (GRCm39)	R109W	probably damaging	Het
Emilin3	G	A	2: 160,751,530 (GRCm39)	R170C	possibly damaging	Het
Erap1	T	C	13: 74,812,270 (GRCm39)	W362R	probably damaging	Het
Fam234a	A	G	17: 26,437,290 (GRCm39)	F91L	probably benign	Het
Flnc	G	A	6: 29,443,796 (GRCm39)		probably null	Het
Fsip2	A	G	2: 82,813,076 (GRCm39)	K3132E	possibly damaging	Het
Garin5b	A	T	7: 4,762,397 (GRCm39)	I244N	probably damaging	Het
Gm10608	CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA	CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA	9: 118,989,784 (GRCm39)		probably benign	Het
Gnl3	A	G	14: 30,738,326 (GRCm39)		probably null	Het
Has1	A	T	17: 18,068,532 (GRCm39)	I274N	probably damaging	Het
Ift70a1	A	G	2: 75,811,801 (GRCm39)	L94P	probably benign	Het
Itsn1	T	C	16: 91,702,389 (GRCm39)		probably null	Het
Kcnh8	GAGACCAACGAGCAGCTGATGCTTCAGA	GAGA	17: 53,032,934 (GRCm39)	74	probably benign	Het
Kif13a	T	C	13: 46,964,275 (GRCm39)	D475G	probably benign	Het
Klhl20	A	T	1: 160,930,608 (GRCm39)	M298K	probably damaging	Het
Kynu	G	T	2: 43,494,289 (GRCm39)	G241*	probably null	Het
Lrif1	G	T	3: 106,639,522 (GRCm39)	L202F	possibly damaging	Het
Lrp5	T	C	19: 3,660,056 (GRCm39)	K1003E	probably benign	Het
Mamdc2	T	C	19: 23,311,393 (GRCm39)	D487G	probably damaging	Het
Mapk8ip1	A	G	2: 92,221,379 (GRCm39)		probably null	Het
Mettl25	T	A	10: 105,633,167 (GRCm39)	E425D	probably benign	Het
Midn	G	T	10: 79,985,949 (GRCm39)	R13L	possibly damaging	Het
Mtmr9	T	C	14: 63,777,713 (GRCm39)	Y136C	possibly damaging	Het
Mylk	G	A	16: 34,817,187 (GRCm39)	V61M	probably damaging	Het
Nalcn	T	C	14: 123,831,993 (GRCm39)		probably null	Het
Nle1	G	T	11: 82,796,373 (GRCm39)	P166Q	probably damaging	Het
Nr4a3	G	A	4: 48,083,252 (GRCm39)	C595Y	probably damaging	Het
Or10d4	A	G	9: 39,580,851 (GRCm39)	Y166C	probably damaging	Het
Or4g7	G	T	2: 111,309,532 (GRCm39)	M134I	probably benign	Het
Or4l15	A	G	14: 50,197,959 (GRCm39)	I190T	probably benign	Het
Or5w1b	C	T	2: 87,476,396 (GRCm39)	V24M	probably benign	Het
Or8b1	A	T	9: 38,399,309 (GRCm39)		probably null	Het
Pds5a	T	A	5: 65,805,350 (GRCm39)		probably null	Het
Pitpnm1	T	C	19: 4,161,873 (GRCm39)	V955A	probably benign	Het
Plcb1	T	A	2: 135,204,340 (GRCm39)	I898N	possibly damaging	Het
Plcl2	G	A	17: 50,913,722 (GRCm39)	V244M	probably damaging	Het
Plk1	A	G	7: 121,761,663 (GRCm39)	K257R	probably damaging	Het
Prkcg	A	T	7: 3,372,066 (GRCm39)	T460S	probably damaging	Het
Prl7d1	G	A	13: 27,894,156 (GRCm39)	H138Y	probably damaging	Het
Prss35	A	G	9: 86,637,565 (GRCm39)	S112G	probably benign	Het
Ptprj	C	T	2: 90,294,958 (GRCm39)	V417M	probably damaging	Het
Pwwp2b	A	T	7: 138,836,067 (GRCm39)	I503F	possibly damaging	Het
Rasgrp2	T	C	19: 6,463,195 (GRCm39)	V498A	probably benign	Het
Sall1	A	G	8: 89,755,037 (GRCm39)	V1314A	probably benign	Het
Slc17a1	A	G	13: 24,062,522 (GRCm39)	S230G	probably benign	Het
Slc5a4a	T	G	10: 75,989,414 (GRCm39)	F106V	probably benign	Het
Stat6	T	C	10: 127,486,665 (GRCm39)	L147P	probably damaging	Het
Taar7d	T	A	10: 23,903,642 (GRCm39)	S175T	probably benign	Het
Tasor2	A	T	13: 3,626,770 (GRCm39)	I1060K	probably benign	Het
Tmem132b	A	G	5: 125,700,080 (GRCm39)	Q206R	probably benign	Het
Tmem229a	T	C	6: 24,955,061 (GRCm39)	D231G	probably benign	Het
Trim66	A	G	7: 109,071,439 (GRCm39)		probably null	Het
Ttll9	A	T	2: 152,844,214 (GRCm39)	E374V	probably damaging	Het
Vmn2r69	A	T	7: 85,056,493 (GRCm39)	D548E	probably damaging	Het
Zcchc2	T	A	1: 105,931,851 (GRCm39)		probably null	Het
Zfp282	T	A	6: 47,874,721 (GRCm39)		probably null	Het
Zfp352	A	G	4: 90,113,408 (GRCm39)	E516G	probably benign	Het

Other mutations in Sema6c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01547:Sema6c	APN	3	95,079,709 (GRCm39)	missense	probably damaging	1.00
IGL01631:Sema6c	APN	3	95,077,714 (GRCm39)	missense	probably benign	0.10
IGL01799:Sema6c	APN	3	95,078,142 (GRCm39)	missense	probably damaging	1.00
IGL02237:Sema6c	APN	3	95,077,430 (GRCm39)	missense	probably damaging	1.00
IGL02852:Sema6c	APN	3	95,077,295 (GRCm39)	splice site	probably benign
IGL02874:Sema6c	APN	3	95,077,688 (GRCm39)	missense	probably damaging	1.00
IGL03003:Sema6c	APN	3	95,076,925 (GRCm39)	missense	probably damaging	1.00
BB005:Sema6c	UTSW	3	95,079,620 (GRCm39)	missense	probably damaging	1.00
BB015:Sema6c	UTSW	3	95,079,620 (GRCm39)	missense	probably damaging	1.00
PIT4418001:Sema6c	UTSW	3	95,077,401 (GRCm39)	missense	possibly damaging	0.57
R0558:Sema6c	UTSW	3	95,076,002 (GRCm39)	missense	probably damaging	1.00
R0582:Sema6c	UTSW	3	95,076,508 (GRCm39)	missense	probably damaging	1.00
R0590:Sema6c	UTSW	3	95,079,934 (GRCm39)	missense	probably damaging	1.00
R0685:Sema6c	UTSW	3	95,080,021 (GRCm39)	missense	possibly damaging	0.46
R1056:Sema6c	UTSW	3	95,078,527 (GRCm39)	missense	probably benign	0.15
R1721:Sema6c	UTSW	3	95,078,099 (GRCm39)	missense	probably damaging	0.98
R1867:Sema6c	UTSW	3	95,078,099 (GRCm39)	missense	probably damaging	0.98
R1868:Sema6c	UTSW	3	95,078,124 (GRCm39)	missense	probably damaging	0.99
R2343:Sema6c	UTSW	3	95,074,394 (GRCm39)	missense	probably damaging	1.00
R2898:Sema6c	UTSW	3	95,080,129 (GRCm39)	missense	probably damaging	1.00
R4095:Sema6c	UTSW	3	95,080,505 (GRCm39)	missense	probably benign	0.03
R4999:Sema6c	UTSW	3	95,075,674 (GRCm39)	missense	probably damaging	1.00
R5263:Sema6c	UTSW	3	95,080,463 (GRCm39)	missense	probably benign	0.02
R6914:Sema6c	UTSW	3	95,080,519 (GRCm39)	missense	probably benign	0.00
R6942:Sema6c	UTSW	3	95,080,519 (GRCm39)	missense	probably benign	0.00
R7104:Sema6c	UTSW	3	95,076,156 (GRCm39)	missense	possibly damaging	0.95
R7524:Sema6c	UTSW	3	95,074,371 (GRCm39)	missense	probably benign	0.20
R7724:Sema6c	UTSW	3	95,080,510 (GRCm39)	missense	probably damaging	1.00
R7928:Sema6c	UTSW	3	95,079,620 (GRCm39)	missense	probably damaging	1.00
R8045:Sema6c	UTSW	3	95,080,535 (GRCm39)	missense	probably benign	0.27
R8243:Sema6c	UTSW	3	95,079,916 (GRCm39)	missense	probably damaging	1.00
R8790:Sema6c	UTSW	3	95,075,341 (GRCm39)	missense	probably benign	0.34
R9607:Sema6c	UTSW	3	95,076,545 (GRCm39)	missense	probably benign	0.03
R9653:Sema6c	UTSW	3	95,080,525 (GRCm39)	missense	probably benign	0.40
Z1177:Sema6c	UTSW	3	95,075,639 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- AGTCTGAAGTAGGCAGCCAC -3'
(R):5'- TAACTTTGGCTGCAGCTGC -3'

Sequencing Primer
(F):5'- CACGAGGGTCTGGAGCAGATTG -3'
(R):5'- TGCCGCCGTCCCTTGTG -3'

Posted On

2014-08-25