Mutagenetix > Incidental Mutation

Incidental Mutation 'R3551:Sema4c'

268319

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

040668-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3551 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

36548639-36558349 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to C at 36553723 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 138 (T138S)

Ref Sequence

ENSEMBL: ENSMUSP00000141527 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000114991] [ENSMUST00000191642] [ENSMUST00000191677] [ENSMUST00000193382] [ENSMUST00000195339] [ENSMUST00000195620]

AlphaFold

Q64151

Predicted Effect

probably benign
Transcript: ENSMUST00000114990
AA Change: T138S

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000110641
Gene: ENSMUSG00000026121
AA Change: T138S

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: ENSMUST00000114991
AA Change: T138S

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000110643
Gene: ENSMUSG00000026121
AA Change: T138S

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: ENSMUST00000149224

Predicted Effect

probably benign
Transcript: ENSMUST00000191642
AA Change: T138S

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000142284
Gene: ENSMUSG00000026121
AA Change: T138S

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: ENSMUST00000191677
AA Change: T138S

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000141263
Gene: ENSMUSG00000026121
AA Change: T138S

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

noncoding transcript
Transcript: ENSMUST00000194426

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000195160

Predicted Effect

probably benign
Transcript: ENSMUST00000195339

Predicted Effect

probably benign
Transcript: ENSMUST00000195620
AA Change: T138S

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000141527
Gene: ENSMUSG00000026121
AA Change: T138S

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

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.1%
20x: 94.4%

Validation Efficiency

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: 45 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acaca	T	A	11: 84,261,624	Y866N	probably damaging	Het
Adam24	G	C	8: 40,679,593	W33C	probably benign	Het
Adgrl2	A	T	3: 148,858,963	V327E	probably damaging	Het
Aqp7	T	A	4: 41,045,329	N17I	probably benign	Het
Bicra	T	A	7: 15,979,733	Q848L	probably benign	Het
C4b	T	C	17: 34,741,872	E240G	possibly damaging	Het
Ccni	T	C	5: 93,187,761	S173G	probably benign	Het
Clca3a2	T	A	3: 144,803,081	N50I	probably damaging	Het
Dcaf7	A	G	11: 106,054,796	T324A	probably benign	Het
Dnah12	G	A	14: 26,770,972	R1230H	probably benign	Het
Dsg4	G	A	18: 20,451,756	V176M	probably damaging	Het
Ect2l	A	G	10: 18,163,393	I339T	probably damaging	Het
Edc4	A	T	8: 105,885,494	I138F	probably damaging	Het
Ercc6l2	T	A	13: 63,844,595	V401E	probably damaging	Het
Gm3269	T	A	14: 4,845,893	V260D	possibly damaging	Het
Gm4076	C	T	13: 85,127,150		noncoding transcript	Het
Gm4922	A	T	10: 18,784,496	N159K	probably benign	Het
Gm5134	G	T	10: 76,000,447	A421S	probably benign	Het
Gm5724	T	C	6: 141,708,596	K647E	probably benign	Het
Hrc	G	C	7: 45,336,333	E303Q	possibly damaging	Het
Ipo4	A	G	14: 55,633,103	V288A	probably benign	Het
Kng2	A	G	16: 23,011,995		probably null	Het
Lrfn1	T	C	7: 28,460,054	L466P	possibly damaging	Het
Magi1	T	A	6: 93,699,629	K916N	probably damaging	Het
Mms19	T	C	19: 41,949,798	T720A	probably benign	Het
Muc5b	A	G	7: 141,861,335	T2673A	possibly damaging	Het
Myo15	C	T	11: 60,509,663	A1767V	possibly damaging	Het
Npas2	A	T	1: 39,287,562	M43L	probably benign	Het
Nup43	A	G	10: 7,675,014	D216G	possibly damaging	Het
Olfr378	T	C	11: 73,425,852	I44V	probably benign	Het
Orc4	G	A	2: 48,937,489	P31S	probably benign	Het
Pcdhga6	G	T	18: 37,708,217	R330L	probably benign	Het
Pear1	A	G	3: 87,758,132	F145L	probably benign	Het
Pgap1	A	G	1: 54,530,143	S355P	possibly damaging	Het
Prr14l	A	T	5: 32,828,619		probably null	Het
Ptpn12	T	C	5: 20,989,049	K742E	possibly damaging	Het
Ryr1	T	A	7: 29,056,997	Q3464L	probably damaging	Het
Slc4a2	C	T	5: 24,430,101	T168M	probably benign	Het
Spice1	G	T	16: 44,357,869	S85I	probably damaging	Het
Thrb	T	A	14: 17,963,214	I59N	probably damaging	Het
Trav7-1	A	G	14: 52,655,299	D103G	probably damaging	Het
Ubap2l	G	T	3: 90,015,451	T766N	unknown	Het
Zfp692	C	T	11: 58,309,428	T170I	possibly damaging	Het
Zfp704	A	G	3: 9,474,525	V255A	probably damaging	Het
Zfp759	T	C	13: 67,138,967	V194A	probably benign	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
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
R4944:Sema4c	UTSW	1	36550311	missense	probably damaging	1.00
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'- AACGTGAGCATGTTCTAGGG -3'
(R):5'- TCAGATCTCTTGGGAGGCTC -3'

Sequencing Primer
(F):5'- CATGTTCTAGGGGCAGGAAGACATC -3'
(R):5'- TTAGAGAGCTTCCCCTGCCAG -3'

Posted On

2015-02-19