Mutagenetix > Incidental Mutation

Incidental Mutation 'R4944:Sema4c'

383314

Institutional Source

Beutler Lab

Gene Symbol

Sema4c

Ensembl Gene

ENSMUSG00000026121

Gene Name

sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C

Synonyms

Semaf, Semacl1, M-Sema F, Semacl1, Semai

MMRRC Submission

042541-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4944 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

36548639-36558349 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 36550311 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Phenylalanine at position 578 (C578F)

Ref Sequence

ENSEMBL: ENSMUSP00000141527 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001172] [ENSMUST00000114991] [ENSMUST00000191642] [ENSMUST00000191677] [ENSMUST00000193382] [ENSMUST00000194894] [ENSMUST00000195620] [ENSMUST00000207843]

AlphaFold

Q64151

Predicted Effect

probably benign
Transcript: ENSMUST00000001172

SMART Domains

Protein: ENSMUSP00000001172
Gene: ENSMUSG00000079610

Domain	Start	End	E-Value	Type
ANK	30	59	8.77e2	SMART
ANK	63	92	1.08e-5	SMART
ANK	96	127	1.27e-2	SMART
ANK	129	158	5.62e-4	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000114991
AA Change: C578F

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

SMART Domains

Protein: ENSMUSP00000110643
Gene: ENSMUSG00000026121
AA Change: C578F

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Sema	53	481	2.54e-183	SMART
PSI	499	552	4.52e-11	SMART
IG	563	647	1.77e-4	SMART
transmembrane domain	665	687	N/A	INTRINSIC
low complexity region	754	774	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000191642
AA Change: C578F

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

SMART Domains

Protein: ENSMUSP00000142284
Gene: ENSMUSG00000026121
AA Change: C578F

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Sema	53	481	2.54e-183	SMART
PSI	499	552	4.52e-11	SMART
IG	563	647	1.77e-4	SMART
transmembrane domain	665	687	N/A	INTRINSIC
low complexity region	754	774	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000191677
AA Change: C578F

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

SMART Domains

Protein: ENSMUSP00000141263
Gene: ENSMUSG00000026121
AA Change: C578F

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Sema	53	481	2.54e-183	SMART
PSI	499	552	4.52e-11	SMART
IG	563	647	1.77e-4	SMART
transmembrane domain	665	687	N/A	INTRINSIC
low complexity region	754	774	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000191785

Predicted Effect

probably benign
Transcript: ENSMUST00000193382

Predicted Effect

probably benign
Transcript: ENSMUST00000194894

SMART Domains

Protein: ENSMUSP00000141712
Gene: ENSMUSG00000079610

Domain	Start	End	E-Value	Type
ANK	30	59	5.6e0	SMART
ANK	63	92	7.1e-8	SMART
ANK	96	127	8.2e-5	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000195160

Predicted Effect

probably damaging
Transcript: ENSMUST00000195620
AA Change: C578F

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

SMART Domains

Protein: ENSMUSP00000141527
Gene: ENSMUSG00000026121
AA Change: C578F

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Sema	53	481	2.54e-183	SMART
PSI	499	552	4.52e-11	SMART
IG	563	647	1.77e-4	SMART
transmembrane domain	665	687	N/A	INTRINSIC
low complexity region	754	774	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000207843

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208269

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208690

Meta Mutation Damage Score

0.9401

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.9%

Validation Efficiency

100% (67/67)

MGI Phenotype

FUNCTION: This gene encodes a member of the semaphorin family of proteins that have diverse functions in neuronal development, heart morphogenesis, vascular growth, tumor progression and immune cell regulation. Lack of the encoded protein in some mice causes exencephaly resulting in neonatal lethality. Mice that bypass exencephaly show no obvious behavioral defects but display distinct pigmentation defects. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2015]
PHENOTYPE: Mice homozygous for a targeted mutation exhibit exencephaly, neonatal lethality, and abnormal cerebellum morphology. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb4	G	A	5: 8,934,327		probably null	Het
Angptl7	C	G	4: 148,500,077	Q71H	probably damaging	Het
Arhgap30	A	T	1: 171,402,254	N176Y	probably damaging	Het
Armc9	T	A	1: 86,274,534	S805T	probably damaging	Het
Atxn1	T	G	13: 45,566,931	H496P	probably damaging	Het
Cabin1	C	T	10: 75,721,363	G1147D	probably damaging	Het
Cabin1	A	G	10: 75,739,421	S597P	probably damaging	Het
Catsperd	T	C	17: 56,662,744	S613P	probably damaging	Het
Cdh2	A	G	18: 16,650,409	Y88H	probably damaging	Het
Cntn1	C	A	15: 92,228,668	P47Q	probably damaging	Het
Col11a2	T	C	17: 34,042,190	L38P	possibly damaging	Het
Col5a2	T	G	1: 45,376,695	I1431L	possibly damaging	Het
Csmd1	C	T	8: 15,998,772	G2310D	probably damaging	Het
Dhcr7	T	A	7: 143,837,791	I39N	probably damaging	Het
Diexf	A	T	1: 193,114,954	M530K	probably damaging	Het
Dnajc13	C	T	9: 104,167,387		probably benign	Het
Folr2	T	C	7: 101,840,290		probably null	Het
Galnt11	T	C	5: 25,265,338	I595T	probably damaging	Het
Gm884	T	C	11: 103,613,460	T2561A	possibly damaging	Het
Gp5	G	A	16: 30,309,508	A116V	possibly damaging	Het
Gpn3	T	C	5: 122,382,240		probably benign	Het
Gprin3	T	C	6: 59,354,659	N221S	probably benign	Het
Hfm1	T	C	5: 106,874,213	E989G	possibly damaging	Het
Ints1	T	C	5: 139,758,092		probably null	Het
Josd2	T	C	7: 44,471,168	S110P	probably damaging	Het
Kat14	C	A	2: 144,375,953	T123K	probably damaging	Het
Lamtor1	C	T	7: 101,909,764	T48I	probably damaging	Het
Lrrc24	A	G	15: 76,718,346	L113P	probably damaging	Het
Mog	T	C	17: 37,020,541	E89G	probably damaging	Het
Mon2	A	G	10: 123,038,459		probably null	Het
Mtx1	T	C	3: 89,213,898	Y143C	probably benign	Het
Nacad	T	C	11: 6,598,507	E1409G	possibly damaging	Het
Ndst3	T	C	3: 123,607,027	H410R	probably damaging	Het
Nkx6-2	T	C	7: 139,581,570	E233G	possibly damaging	Het
Oas1h	A	G	5: 120,862,783	E152G	probably damaging	Het
Olfr936	A	G	9: 39,046,862	S186P	probably damaging	Het
Ovgp1	T	C	3: 105,979,953	F222L	possibly damaging	Het
Pkhd1	T	C	1: 20,288,205	S2716G	probably null	Het
Pla2g4e	T	C	2: 120,171,237	T644A	probably benign	Het
Plxnd1	A	G	6: 115,955,765	I1918T	probably damaging	Het
Prrxl1	G	T	14: 32,608,249	Q136H	probably damaging	Het
Psmg1	A	T	16: 95,989,612		probably benign	Het
Ptprd	G	A	4: 76,128,899	R364C	probably damaging	Het
Rgs22	T	C	15: 36,025,942	I945V	possibly damaging	Het
Rgs7bp	T	C	13: 104,951,564	N234S	probably benign	Het
Rrp7a	T	C	15: 83,119,809		probably benign	Het
Scg2	T	A	1: 79,436,476	R177*	probably null	Het
Slc1a5	T	A	7: 16,797,743		probably benign	Het
Slc5a3	A	G	16: 92,078,683	T543A	possibly damaging	Het
Slx4ip	T	A	2: 137,046,767	F123I	probably benign	Het
Smtn	C	T	11: 3,522,916	R737H	probably damaging	Het
Stox2	A	G	8: 47,413,265	I14T	possibly damaging	Het
Stradb	T	C	1: 58,980,440	F43L	probably benign	Het
Szt2	T	C	4: 118,388,669	D1029G	probably benign	Het
Taar6	T	C	10: 23,984,715	Y311C	probably damaging	Het
Tcea3	A	T	4: 136,268,093	N249I	probably damaging	Het
Tecta	A	G	9: 42,330,277	M2134T	probably benign	Het
Tg	G	A	15: 66,764,337	G591D	probably damaging	Het
Tm4sf20	T	A	1: 82,768,363	I19F	probably benign	Het
Top2a	T	C	11: 98,997,850	K1262E	probably benign	Het
Ube2r2	A	G	4: 41,190,742		probably benign	Het
Usp29	T	C	7: 6,961,928	S257P	possibly damaging	Het
Usp40	T	C	1: 87,952,355	N1038S	probably benign	Het
Vmn1r121	C	T	7: 21,097,613	E301K	probably benign	Het
Vmn2r49	T	A	7: 9,989,032	H105L	probably benign	Het
Zgrf1	C	T	3: 127,561,868	Q248*	probably null	Het

Other mutations in Sema4c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00420:Sema4c	APN	1	36553920	critical splice donor site	probably benign	0.00
IGL01824:Sema4c	APN	1	36553029	missense	possibly damaging	0.76
IGL02236:Sema4c	APN	1	36553085	missense	probably damaging	1.00
IGL02262:Sema4c	APN	1	36550341	missense	probably damaging	1.00
IGL02282:Sema4c	APN	1	36550203	splice site	probably null
IGL02476:Sema4c	APN	1	36555950	missense	probably damaging	0.98
IGL02900:Sema4c	APN	1	36550745	nonsense	probably null
swirl	UTSW	1	36550311	missense	probably damaging	1.00
IGL02837:Sema4c	UTSW	1	36552884	missense	probably damaging	1.00
R0427:Sema4c	UTSW	1	36553811	nonsense	probably null
R0497:Sema4c	UTSW	1	36549608	missense	probably benign	0.04
R1066:Sema4c	UTSW	1	36550200	missense	possibly damaging	0.95
R1099:Sema4c	UTSW	1	36552110	missense	probably damaging	1.00
R1146:Sema4c	UTSW	1	36550565	missense	probably benign	0.04
R1146:Sema4c	UTSW	1	36550565	missense	probably benign	0.04
R1639:Sema4c	UTSW	1	36553534	missense	probably benign	0.00
R1644:Sema4c	UTSW	1	36550804	missense	probably damaging	1.00
R3176:Sema4c	UTSW	1	36549879	missense	possibly damaging	0.65
R3177:Sema4c	UTSW	1	36549879	missense	possibly damaging	0.65
R3276:Sema4c	UTSW	1	36549879	missense	possibly damaging	0.65
R3277:Sema4c	UTSW	1	36549879	missense	possibly damaging	0.65
R3551:Sema4c	UTSW	1	36553723	missense	probably benign	0.02
R4452:Sema4c	UTSW	1	36553756	missense	probably benign	0.31
R4883:Sema4c	UTSW	1	36552016	missense	probably damaging	0.98
R4895:Sema4c	UTSW	1	36553570	splice site	probably null
R4913:Sema4c	UTSW	1	36550185	missense	probably benign	0.11
R5062:Sema4c	UTSW	1	36552978	critical splice donor site	probably null
R5077:Sema4c	UTSW	1	36551731	missense	probably benign	0.20
R5109:Sema4c	UTSW	1	36552300	frame shift	probably null
R5208:Sema4c	UTSW	1	36550326	missense	probably damaging	1.00
R5551:Sema4c	UTSW	1	36552317	missense	probably damaging	1.00
R5912:Sema4c	UTSW	1	36554388	missense	possibly damaging	0.83
R6578:Sema4c	UTSW	1	36550753	missense	probably benign	0.02
R7111:Sema4c	UTSW	1	36553079	missense	possibly damaging	0.48
R7141:Sema4c	UTSW	1	36553020	missense	probably damaging	0.99
R7252:Sema4c	UTSW	1	36550015	missense	probably damaging	1.00
R7495:Sema4c	UTSW	1	36550693	missense	probably benign	0.00
R7891:Sema4c	UTSW	1	36549914	missense	probably damaging	0.98
R7895:Sema4c	UTSW	1	36553118	missense	probably damaging	1.00
R8264:Sema4c	UTSW	1	36552885	missense	probably damaging	1.00
R8478:Sema4c	UTSW	1	36551790	missense	probably benign	0.04
R8680:Sema4c	UTSW	1	36550786	missense	probably benign	0.00
R8733:Sema4c	UTSW	1	36552873	missense	probably damaging	1.00
R9017:Sema4c	UTSW	1	36552998	missense	probably damaging	1.00
R9344:Sema4c	UTSW	1	36553314	missense	probably damaging	1.00
R9488:Sema4c	UTSW	1	36551986	missense	probably benign
X0019:Sema4c	UTSW	1	36552996	missense	probably damaging	1.00
X0028:Sema4c	UTSW	1	36549966	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- CCTGCTCCTCTGAATAGCAAC -3'
(R):5'- ATGTGGCGAACTTGGACAC -3'

Sequencing Primer
(F):5'- TCCTCTGAATAGCAACGATAGGGTC -3'
(R):5'- CGAACTTGGACACTTCAAAGATGTG -3'

Posted On

2016-04-27