Mutagenetix > Incidental Mutation

Incidental Mutation 'R0685:Sema6c'

218477

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

038870-MU

Accession Numbers

Essential gene?

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

Stock #

R0685 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

95160457-95174024 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 95172710 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Arginine at position 772 (C772R)

Ref Sequence

ENSEMBL: ENSMUSP00000129081 (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: C740R

PolyPhen 2 Score 0.335 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000088331
Gene: ENSMUSG00000038777
AA Change: C740R

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

possibly damaging
Transcript: ENSMUST00000090823
AA Change: C772R

PolyPhen 2 Score 0.462 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000088333
Gene: ENSMUSG00000038777
AA Change: C772R

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

possibly damaging
Transcript: ENSMUST00000107217
AA Change: C732R

PolyPhen 2 Score 0.462 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000102835
Gene: ENSMUSG00000038777
AA Change: C732R

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

possibly damaging
Transcript: ENSMUST00000168321
AA Change: C772R

PolyPhen 2 Score 0.462 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000129081
Gene: ENSMUSG00000038777
AA Change: C772R

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: C740R

PolyPhen 2 Score 0.335 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000144039
Gene: ENSMUSG00000038777
AA Change: C740R

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

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.6%
20x: 95.6%

Validation Efficiency

98% (89/91)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700020N01Rik	A	G	10: 21,593,438	D17G	probably damaging	Het
Abi3bp	A	G	16: 56,532,953	T82A	possibly damaging	Het
Adgre4	A	C	17: 55,792,035	E180D	probably benign	Het
Ankrd28	G	A	14: 31,743,450		probably benign	Het
Aoc3	A	G	11: 101,336,447	D382G	possibly damaging	Het
Apob	C	A	12: 8,010,742	R3075S	probably benign	Het
Aqr	A	G	2: 114,140,977	F459S	probably damaging	Het
Bcr	T	C	10: 75,131,643	W570R	probably damaging	Het
Bloc1s5	C	T	13: 38,603,919	R163K	probably benign	Het
Bod1	A	T	11: 31,669,267	N101K	possibly damaging	Het
Bysl	A	T	17: 47,602,471	S296T	probably benign	Het
Chl1	G	A	6: 103,708,542		probably null	Het
Clstn1	G	A	4: 149,646,855	A885T	probably benign	Het
Cyp3a25	G	T	5: 145,998,546	P87T	probably damaging	Het
Dync1h1	T	C	12: 110,657,192	V3633A	probably damaging	Het
Elp4	C	A	2: 105,792,277	C241F	possibly damaging	Het
Fat4	T	A	3: 39,001,178	F4182Y	probably benign	Het
Gabbr2	G	A	4: 46,787,521	H381Y	possibly damaging	Het
Gm10577	G	T	4: 101,020,318		probably benign	Het
Gm884	T	C	11: 103,616,888		probably benign	Het
Gm9955	G	T	18: 24,709,257		probably benign	Het
Gstm5	T	A	3: 107,897,319	I73N	probably damaging	Het
Gypa	T	A	8: 80,496,702		probably benign	Het
Hectd2	T	A	19: 36,569,431	V64D	probably damaging	Het
Igkv10-95	T	A	6: 68,680,559	Y20N	probably benign	Het
Il15	T	C	8: 82,337,559		probably benign	Het
Iqca	C	A	1: 90,142,731	G133V	probably null	Het
Kiz	C	A	2: 146,856,058		probably benign	Het
Lcmt2	C	A	2: 121,139,240	S234I	probably benign	Het
Lilra5	A	G	7: 4,241,957		probably benign	Het
Lin37	T	C	7: 30,555,874	E187G	probably damaging	Het
Mcmdc2	T	A	1: 9,911,814		probably null	Het
Mctp1	T	C	13: 76,825,799		probably null	Het
Mdp1	C	A	14: 55,659,269	G112*	probably null	Het
Mmp15	T	C	8: 95,372,134	Y530H	possibly damaging	Het
Mtss1l	T	C	8: 110,727,397		probably null	Het
Muc5ac	T	C	7: 141,807,709	S1586P	probably benign	Het
Nap1l5	A	T	6: 58,906,772	C66S	possibly damaging	Het
Ninl	G	T	2: 150,939,855	Q1237K	possibly damaging	Het
Olfr1160	T	C	2: 88,006,418	E111G	probably damaging	Het
Olfr495	A	T	7: 108,395,263	T48S	possibly damaging	Het
Orc6	T	G	8: 85,301,154	S37R	possibly damaging	Het
Papss1	A	C	3: 131,583,093	N119H	possibly damaging	Het
Phf13	A	T	4: 151,991,612	F278I	probably damaging	Het
Pole2	C	A	12: 69,211,413	A239S	probably damaging	Het
Ppt2	T	C	17: 34,626,572	D75G	probably damaging	Het
Psd2	A	G	18: 36,002,991	D443G	possibly damaging	Het
Psen1	C	A	12: 83,714,820	S132*	probably null	Het
Psme4	A	G	11: 30,878,415	T1812A	probably damaging	Het
Rasgrf1	T	C	9: 89,915,482		probably benign	Het
Reep3	A	G	10: 67,021,739		probably benign	Het
Rexo4	A	T	2: 26,958,574		probably benign	Het
Rnf6	A	C	5: 146,211,658	S183R	probably damaging	Het
Scai	A	T	2: 39,103,737	M297K	probably damaging	Het
Scn9a	A	T	2: 66,483,499	S1947R	probably benign	Het
Skint7	T	C	4: 111,980,345	S107P	possibly damaging	Het
Slc24a3	A	G	2: 145,606,795	N420D	probably benign	Het
Smc1b	T	C	15: 85,070,820	D1077G	possibly damaging	Het
Smg7	G	A	1: 152,866,648	P82L	probably damaging	Het
Sp3	A	C	2: 72,970,998	F268V	probably damaging	Het
Srms	T	C	2: 181,212,633	D47G	probably benign	Het
Ss18	A	C	18: 14,651,181	M150R	probably damaging	Het
Taf5	G	A	19: 47,074,854	R281Q	probably benign	Het
Tars	T	C	15: 11,385,173	K644R	probably benign	Het
Tctex1d1	T	C	4: 103,002,538	Y96H	probably damaging	Het
Tinag	C	A	9: 76,952,003	W441L	probably damaging	Het
Tmtc1	T	C	6: 148,411,240	S244G	probably benign	Het
Tpr	T	C	1: 150,433,725	V1670A	possibly damaging	Het
Trpv3	A	G	11: 73,296,814		probably benign	Het
Uhrf1	G	T	17: 56,310,742	V155L	probably damaging	Het
Ush2a	G	A	1: 188,400,278	C899Y	probably damaging	Het
Vmn2r115	G	A	17: 23,359,275	R574H	probably benign	Het
Vmn2r63	T	C	7: 42,928,010	D368G	probably benign	Het
Vps13a	A	G	19: 16,780,741	V10A	probably damaging	Het
Wbp11	A	G	6: 136,814,638		probably benign	Het
Zcwpw1	A	G	5: 137,799,592	D145G	probably benign	Het
Zfp607a	G	A	7: 27,878,476	V324I	probably damaging	Het
Zfp618	A	G	4: 63,133,774	I931V	probably benign	Het
Zfp821	T	C	8: 109,724,542	V389A	possibly damaging	Het
Zfp976	T	A	7: 42,613,717	H232L	probably 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
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
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
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
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'- CTGTGCATCACCTACCCTAAAGCTG -3'
(R):5'- AGAGGTTCGCTACCCTTCCTGG -3'

Sequencing Primer
(F):5'- CGTCGGAGCAAGGACATC -3'
(R):5'- CTTCCTGGGCGGCTGAG -3'

Posted On

2014-08-11