Mutagenetix > Incidental Mutation

Incidental Mutation 'R0558:Sema6c'

45702

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

038750-MU

Accession Numbers

Essential gene?

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

Stock #

R0558 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

95067768-95081335 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 95076002 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 219 (S219P)

Ref Sequence

ENSEMBL: ENSMUSP00000144039 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000090821] [ENSMUST00000090823] [ENSMUST00000107217] [ENSMUST00000131620] [ENSMUST00000202315] [ENSMUST00000168321] [ENSMUST00000204709] [ENSMUST00000142449] [ENSMUST00000131742]

AlphaFold

Q9WTM3

Predicted Effect

probably damaging
Transcript: ENSMUST00000090821
AA Change: S219P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000088331
Gene: ENSMUSG00000038777
AA Change: S219P

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 damaging
Transcript: ENSMUST00000090823
AA Change: S219P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000088333
Gene: ENSMUSG00000038777
AA Change: S219P

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

SMART Domains

Protein: ENSMUSP00000102835
Gene: ENSMUSG00000038777

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

noncoding transcript
Transcript: ENSMUST00000130814

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

probably damaging
Transcript: ENSMUST00000202315
AA Change: S219P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000144039
Gene: ENSMUSG00000038777
AA Change: S219P

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 damaging
Transcript: ENSMUST00000168321
AA Change: S219P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000129081
Gene: ENSMUSG00000038777
AA Change: S219P

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

noncoding transcript
Transcript: ENSMUST00000141607

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142306

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134125

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

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: ENSMUST00000131742

Meta Mutation Damage Score

0.7096

Coding Region Coverage

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

Validation Efficiency

100% (80/80)

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc2	G	A	19: 43,789,163 (GRCm39)	G273R	probably benign	Het
Adamts10	T	C	17: 33,769,583 (GRCm39)	V935A	probably benign	Het
Anapc15-ps	T	C	10: 95,508,983 (GRCm39)	D90G	probably damaging	Het
Atic	T	A	1: 71,602,947 (GRCm39)	V107E	probably benign	Het
Atp4b	T	C	8: 13,443,523 (GRCm39)	T52A	possibly damaging	Het
Cacna1h	C	T	17: 25,600,524 (GRCm39)	A1606T	probably damaging	Het
Cacng6	T	A	7: 3,483,324 (GRCm39)	Y217*	probably null	Het
Cc2d2a	T	G	5: 43,881,729 (GRCm39)		probably benign	Het
Cd226	T	A	18: 89,225,338 (GRCm39)	H78Q	probably benign	Het
Cers3	A	G	7: 66,433,166 (GRCm39)	D161G	probably damaging	Het
Ces1f	T	C	8: 94,002,017 (GRCm39)	H37R	probably benign	Het
Cfhr4	A	G	1: 139,667,230 (GRCm39)	V376A	probably damaging	Het
Chek1	T	A	9: 36,623,411 (GRCm39)	N421I	possibly damaging	Het
Cibar1	T	C	4: 12,164,095 (GRCm39)	D248G	probably damaging	Het
Cma2	T	C	14: 56,210,249 (GRCm39)	Y45H	probably damaging	Het
Cmas	C	A	6: 142,720,970 (GRCm39)	Y401*	probably null	Het
Cyp2j8	A	T	4: 96,332,871 (GRCm39)	S492T	probably benign	Het
Dnah12	T	C	14: 26,430,465 (GRCm39)	S358P	probably benign	Het
Dnajc13	T	C	9: 104,079,151 (GRCm39)		probably null	Het
Ep400	A	C	5: 110,832,933 (GRCm39)		probably benign	Het
Fam209	T	A	2: 172,314,758 (GRCm39)	N82K	probably benign	Het
G3bp2	A	T	5: 92,221,056 (GRCm39)	Y20N	probably damaging	Het
Gli2	T	C	1: 118,765,379 (GRCm39)	D924G	probably benign	Het
Gm10787	T	C	10: 76,857,850 (GRCm39)		noncoding transcript	Het
Gm11568	A	G	11: 99,748,872 (GRCm39)	R26G	unknown	Het
Hivep3	T	G	4: 119,953,763 (GRCm39)	L693R	probably damaging	Het
Hook1	A	G	4: 95,881,449 (GRCm39)		probably benign	Het
Ibtk	A	C	9: 85,619,591 (GRCm39)	D116E	probably damaging	Het
Insrr	C	T	3: 87,718,288 (GRCm39)	T927I	possibly damaging	Het
Irx1	T	G	13: 72,107,747 (GRCm39)	S312R	probably benign	Het
Itga11	T	C	9: 62,659,570 (GRCm39)	Y441H	probably benign	Het
Itsn1	A	G	16: 91,696,511 (GRCm39)	D38G	possibly damaging	Het
Kat6b	G	T	14: 21,719,489 (GRCm39)	E1280D	probably benign	Het
Kcnk10	T	A	12: 98,402,560 (GRCm39)	Y293F	possibly damaging	Het
Krt74	T	A	15: 101,669,398 (GRCm39)		noncoding transcript	Het
Lars1	T	G	18: 42,347,902 (GRCm39)	I974L	probably benign	Het
Limch1	A	G	5: 67,126,498 (GRCm39)	D42G	probably damaging	Het
Mau2	G	C	8: 70,495,082 (GRCm39)	T85R	probably damaging	Het
Mkrn3	A	G	7: 62,068,612 (GRCm39)	I393T	probably benign	Het
Mpl	A	C	4: 118,301,217 (GRCm39)	S541R	probably damaging	Het
Nfrkb	T	C	9: 31,321,564 (GRCm39)	S754P	possibly damaging	Het
Or4c125	A	G	2: 89,170,580 (GRCm39)	L22P	probably benign	Het
Or5bw2	T	C	7: 6,573,652 (GRCm39)	Y221H	possibly damaging	Het
Or5d41	A	G	2: 88,054,818 (GRCm39)	V186A	possibly damaging	Het
Or8g18	T	A	9: 39,149,496 (GRCm39)	T75S	probably damaging	Het
P2rx7	A	T	5: 122,811,861 (GRCm39)	I391F	possibly damaging	Het
Pbrm1	T	A	14: 30,807,016 (GRCm39)		probably null	Het
Pcdh8	T	C	14: 80,007,516 (GRCm39)	D349G	probably damaging	Het
Pias1	A	G	9: 62,789,291 (GRCm39)	S639P	possibly damaging	Het
Pkhd1l1	A	T	15: 44,347,820 (GRCm39)	I232F	probably damaging	Het
Plxnc1	C	T	10: 94,673,797 (GRCm39)	R995Q	probably damaging	Het
Pnliprp2	T	A	19: 58,762,519 (GRCm39)	S375T	probably benign	Het
Prkar1b	C	T	5: 139,005,847 (GRCm39)	V313M	probably benign	Het
Prr35	T	C	17: 26,166,523 (GRCm39)	N338S	probably benign	Het
Ptpn13	T	C	5: 103,677,583 (GRCm39)	S734P	probably damaging	Het
Rdh1	T	C	10: 127,595,810 (GRCm39)	W2R	possibly damaging	Het
Rsph10b	A	T	5: 143,886,156 (GRCm39)	I285L	probably benign	Het
Rubcnl	T	C	14: 75,284,987 (GRCm39)	F502S	probably damaging	Het
Ryr2	T	A	13: 11,653,329 (GRCm39)	I3693F	probably damaging	Het
Ryr2	T	C	13: 11,814,747 (GRCm39)	Y675C	probably damaging	Het
Scaper	T	C	9: 55,593,207 (GRCm39)	T477A	probably benign	Het
Scn2a	G	T	2: 65,542,269 (GRCm39)	V791L	probably benign	Het
Sdk1	A	T	5: 142,117,820 (GRCm39)	T1573S	probably damaging	Het
Sema3c	A	T	5: 17,919,413 (GRCm39)	H483L	probably benign	Het
Slc10a5	T	G	3: 10,400,177 (GRCm39)	E161A	probably damaging	Het
Slc22a23	C	T	13: 34,528,366 (GRCm39)	G139S	possibly damaging	Het
Slc34a3	C	T	2: 25,123,077 (GRCm39)		probably benign	Het
Slc38a9	A	T	13: 112,865,730 (GRCm39)		probably null	Het
Taok1	A	C	11: 77,450,670 (GRCm39)	S367R	possibly damaging	Het
Tlr6	G	A	5: 65,112,203 (GRCm39)	Q235*	probably null	Het
Top2a	A	G	11: 98,887,665 (GRCm39)	V1281A	probably benign	Het
Tpgs1	T	C	10: 79,511,616 (GRCm39)	Y253H	probably damaging	Het
Tubgcp3	T	C	8: 12,703,462 (GRCm39)	T288A	probably benign	Het
Ubr4	A	G	4: 139,154,213 (GRCm39)	E2140G	probably benign	Het
Uso1	A	G	5: 92,321,878 (GRCm39)	Q257R	probably benign	Het
Zfp106	A	G	2: 120,362,677 (GRCm39)	V48A	probably damaging	Het
Zfp174	T	A	16: 3,666,118 (GRCm39)	S128T	possibly damaging	Het
Zscan26	T	A	13: 21,629,225 (GRCm39)	D426V	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
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
R2016:Sema6c	UTSW	3	95,078,545 (GRCm39)	missense	probably benign	0.00
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'- GCAGATTCTGAGCTTTCTGTGACCC -3'
(R):5'- CAGGAGAACTGTCCAGCATCCATC -3'

Sequencing Primer
(F):5'- GAGCTTTCTGTGACCCCACTC -3'
(R):5'- CCTCCACAGAGACTTCTCGG -3'

Posted On

2013-06-11