Mutagenetix > Incidental Mutation

Incidental Mutation 'R6942:Sema6c'

540586

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

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.273) question?

Stock #

R6942 (G1)

Quality Score

86.0076

Status

Validated

Chromosome

Chromosomal Location

95160457-95174024 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 95173208 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Leucine at position 906 (V906L)

Ref Sequence

ENSEMBL: ENSMUSP00000144039 (fasta)

Gene Model

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

AlphaFold

Q9WTM3

Predicted Effect

probably benign
Transcript: ENSMUST00000090821
AA Change: V906L

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

SMART Domains

Protein: ENSMUSP00000088331
Gene: ENSMUSG00000038777
AA Change: V906L

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: V938L

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

SMART Domains

Protein: ENSMUSP00000088333
Gene: ENSMUSG00000038777
AA Change: V938L

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: V898L

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

SMART Domains

Protein: ENSMUSP00000102835
Gene: ENSMUSG00000038777
AA Change: V898L

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

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 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: V938L

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

SMART Domains

Protein: ENSMUSP00000129081
Gene: ENSMUSG00000038777
AA Change: V938L

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: V906L

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

SMART Domains

Protein: ENSMUSP00000144039
Gene: ENSMUSG00000038777
AA Change: V906L

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: 100.0%
3x: 99.8%
10x: 98.9%
20x: 96.2%

Validation Efficiency

100% (49/49)

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: 49 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930444G20Rik	A	T	10: 22,067,261	D273E	probably benign	Het
Acacb	T	C	5: 114,191,963		probably null	Het
Adap2	A	G	11: 80,155,065	D57G	probably benign	Het
Atmin	G	T	8: 116,956,713	V371F	probably benign	Het
Cacna1h	G	T	17: 25,385,039	A1273E	probably benign	Het
Cdh23	G	A	10: 60,438,856	T483I	possibly damaging	Het
Cnot9	T	A	1: 74,518,995	V100E	probably damaging	Het
Cog2	T	A	8: 124,545,136	V463D	probably benign	Het
Crybg3	C	T	16: 59,539,820	R2500H	possibly damaging	Het
Cyp11b2	G	A	15: 74,856,245		probably benign	Het
Cyp2j12	A	T	4: 96,112,864		probably null	Het
Dlc1	T	C	8: 36,938,210	K142E	probably benign	Het
Dpp6	G	A	5: 27,469,459	V140M	possibly damaging	Het
Fam69c	A	C	18: 84,730,424	Y49S	possibly damaging	Het
Fktn	G	A	4: 53,735,128		probably null	Het
Gas7	A	T	11: 67,660,151		probably null	Het
Grin3b	T	A	10: 79,976,119		probably null	Het
Hhatl	G	A	9: 121,788,180	A329V	probably benign	Het
Homer3	C	T	8: 70,291,551	T276I	probably benign	Het
Igdcc4	G	A	9: 65,120,268	S204N	probably benign	Het
Ino80	A	G	2: 119,383,502	F1196L	probably damaging	Het
Iqsec3	C	T	6: 121,473,103	C154Y	probably damaging	Het
Kank1	A	T	19: 25,424,173	D1048V	possibly damaging	Het
Kif2c	A	G	4: 117,166,378	L379P	probably damaging	Het
Kpna6	A	T	4: 129,651,721		probably null	Het
Large2	C	T	2: 92,370,822	R28H	probably damaging	Het
Map4k2	T	A	19: 6,346,709	W552R	possibly damaging	Het
Mark3	A	G	12: 111,592,654	I43M	probably null	Het
Med13l	C	A	5: 118,745,006		probably null	Het
Mtbp	T	A	15: 55,567,200	Y218N	probably damaging	Het
Olfr669	C	T	7: 104,938,897	R124C	possibly damaging	Het
Pcdhgb5	T	C	18: 37,732,643	L497P	probably damaging	Het
Pkhd1l1	A	G	15: 44,522,629	T1221A	probably damaging	Het
Pth1r	C	T	9: 110,728,016		probably null	Het
Samd8	T	C	14: 21,775,153	I59T	possibly damaging	Het
Scgb2b18	A	G	7: 33,172,139	V85A	possibly damaging	Het
Serpinb9g	A	T	13: 33,494,905	T253S	probably benign	Het
Sipa1l3	T	C	7: 29,386,091	T694A	probably damaging	Het
Slc8a1	A	G	17: 81,408,120	L828P	probably damaging	Het
Spry1	T	A	3: 37,643,044	D145E	probably benign	Het
Stat6	A	T	10: 127,651,262	N213Y	probably damaging	Het
Tep1	A	G	14: 50,836,737	V1897A	possibly damaging	Het
Tmem45a	T	C	16: 56,825,782	N25S	probably benign	Het
Tmem70	T	A	1: 16,677,156	Y166N	probably damaging	Het
Trrap	T	A	5: 144,784,043	I230N	possibly damaging	Het
Ttn	A	G	2: 76,901,846		probably benign	Het
Unc79	T	A	12: 103,122,445		probably null	Het
Vmn1r43	T	A	6: 89,870,337	I56F	probably benign	Het
Zfyve16	A	T	13: 92,516,631	N815K	probably benign	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
BB005:Sema6c	UTSW	3	95172309	missense	probably damaging	1.00
BB015:Sema6c	UTSW	3	95172309	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
R1056:Sema6c	UTSW	3	95171216	missense	probably benign	0.15
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
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
R7928:Sema6c	UTSW	3	95172309	missense	probably damaging	1.00
R8045:Sema6c	UTSW	3	95173224	missense	probably benign	0.27
R8243:Sema6c	UTSW	3	95172605	missense	probably damaging	1.00
R8790:Sema6c	UTSW	3	95168030	missense	probably benign	0.34
R9607:Sema6c	UTSW	3	95169234	missense	probably benign	0.03
R9653:Sema6c	UTSW	3	95173214	missense	probably benign	0.40
Z1177:Sema6c	UTSW	3	95168328	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- TAGAGGTGACCACGCTGGAG -3'
(R):5'- GTTCCTCGCCAAAGGACAGG -3'

Sequencing Primer
(F):5'- AACTGCTGCGCTACCTG -3'
(R):5'- CAAGTCAATAAATAAACCGAGGCG -3'

Posted On

2018-11-06