Mutagenetix > Incidental Mutation

Incidental Mutation 'R4883:Sema4c'

375365

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

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

MMRRC Submission

042491-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4883 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

36587720-36597430 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 36591097 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 414 (V414A)

Ref Sequence

ENSEMBL: ENSMUSP00000141527 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001172] [ENSMUST00000114991] [ENSMUST00000191642] [ENSMUST00000191677] [ENSMUST00000193382] [ENSMUST00000194894] [ENSMUST00000195620] [ENSMUST00000207843] [ENSMUST00000195339]

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: V414A

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000110643
Gene: ENSMUSG00000026121
AA Change: V414A

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: V414A

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000142284
Gene: ENSMUSG00000026121
AA Change: V414A

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: V414A

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000141263
Gene: ENSMUSG00000026121
AA Change: V414A

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

probably damaging
Transcript: ENSMUST00000195620
AA Change: V414A

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000141527
Gene: ENSMUSG00000026121
AA Change: V414A

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: ENSMUST00000195160

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208690

Predicted Effect

probably benign
Transcript: ENSMUST00000207843

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208269

Predicted Effect

probably benign
Transcript: ENSMUST00000195339

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.9%
20x: 94.2%

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: 96 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca5	T	C	11: 110,217,457 (GRCm39)	D133G	probably damaging	Het
Abcg4	G	T	9: 44,190,616 (GRCm39)	H55Q	probably damaging	Het
Acaca	T	A	11: 84,142,116 (GRCm39)	V641E	probably benign	Het
Adam28	T	C	14: 68,875,552 (GRCm39)	I229V	probably damaging	Het
Adgrl3	T	A	5: 81,837,493 (GRCm39)	I793N	probably damaging	Het
Akr1d1	A	T	6: 37,535,336 (GRCm39)	D240V	possibly damaging	Het
Arhgef25	T	C	10: 127,018,802 (GRCm39)	D548G	probably benign	Het
Asl	A	G	5: 130,042,802 (GRCm39)		probably null	Het
Atg14	C	T	14: 47,788,771 (GRCm39)	R194Q	probably damaging	Het
BC004004	T	A	17: 29,501,166 (GRCm39)	F38L	probably damaging	Het
Btg1	T	C	10: 96,453,259 (GRCm39)	F25L	probably benign	Het
Btrc	C	T	19: 45,445,026 (GRCm39)	P35S	probably benign	Het
Calcr	T	A	6: 3,714,705 (GRCm39)	N142Y	probably damaging	Het
Ccdc138	A	G	10: 58,397,818 (GRCm39)	I553V	probably benign	Het
Ccdc198	T	A	14: 49,482,560 (GRCm39)	N52I	probably damaging	Het
Cdc42	T	A	4: 137,056,115 (GRCm39)	N132I	probably benign	Het
Ces1e	A	G	8: 93,950,716 (GRCm39)	S22P	probably benign	Het
Clmn	G	T	12: 104,748,307 (GRCm39)	D413E	probably benign	Het
Cramp1	T	C	17: 25,201,293 (GRCm39)	T730A	probably benign	Het
Dnah5	A	T	15: 28,343,784 (GRCm39)	M2395L	probably benign	Het
Ephx1	G	T	1: 180,829,488 (GRCm39)	S20Y	possibly damaging	Het
Exoc5	T	G	14: 49,289,821 (GRCm39)	E19A	probably damaging	Het
Fam120b	T	C	17: 15,623,294 (GRCm39)	L424P	probably benign	Het
Fam89a	G	A	8: 125,467,823 (GRCm39)	T163I	possibly damaging	Het
Fcrl2	G	A	3: 87,166,922 (GRCm39)	L24F	possibly damaging	Het
Fgd6	G	T	10: 93,975,715 (GRCm39)	V1377L	probably benign	Het
Glud1	T	A	14: 34,057,347 (GRCm39)	I337K	possibly damaging	Het
Gm6370	T	A	5: 146,430,736 (GRCm39)	I303N	probably benign	Het
Gm7995	T	C	14: 42,133,383 (GRCm39)	Y88H	probably damaging	Het
Gsdma3	T	C	11: 98,520,393 (GRCm39)		probably null	Het
Gsdmc2	T	C	15: 63,707,614 (GRCm39)	D60G	probably damaging	Het
Hcn1	T	A	13: 118,039,431 (GRCm39)		probably null	Het
Hectd1	A	T	12: 51,831,030 (GRCm39)	C936*	probably null	Het
Herc4	T	A	10: 63,121,433 (GRCm39)	S358T	probably benign	Het
Hk3	A	G	13: 55,158,735 (GRCm39)	C515R	probably benign	Het
Ighg1	A	G	12: 113,291,138 (GRCm39)		probably benign	Het
Iqgap3	T	A	3: 88,014,842 (GRCm39)	C853S	probably benign	Het
Irx4	G	A	13: 73,415,750 (GRCm39)	A180T	probably damaging	Het
Kif20b	A	G	19: 34,943,522 (GRCm39)	T1441A	probably benign	Het
Lifr	A	G	15: 7,215,106 (GRCm39)	K738E	possibly damaging	Het
Lmntd2	A	T	7: 140,792,531 (GRCm39)	S218T	probably damaging	Het
Lnx1	A	T	5: 74,768,530 (GRCm39)	W353R	probably benign	Het
Lrfn3	G	T	7: 30,055,238 (GRCm39)	P569Q	possibly damaging	Het
Mamstr	A	G	7: 45,293,838 (GRCm39)	I11V	probably benign	Het
Med31	T	C	11: 72,104,975 (GRCm39)	N32S	possibly damaging	Het
Mob3c	A	T	4: 115,690,928 (GRCm39)	I173F	probably benign	Het
Morc3	A	G	16: 93,667,250 (GRCm39)		probably null	Het
Mphosph9	T	C	5: 124,437,108 (GRCm39)	K412R	probably damaging	Het
Mtcl3	A	T	10: 29,072,537 (GRCm39)	N610Y	probably damaging	Het
Mthfd1l	C	T	10: 3,957,775 (GRCm39)	P271S	probably benign	Het
Ncam1	C	T	9: 49,453,183 (GRCm39)		probably null	Het
Ncbp3	T	A	11: 72,960,578 (GRCm39)	Y279N	probably damaging	Het
Ncoa6	G	A	2: 155,248,687 (GRCm39)	T1539I	probably benign	Het
Nedd4	G	A	9: 72,647,515 (GRCm39)		probably null	Het
Neil1	A	G	9: 57,054,206 (GRCm39)	V38A	probably damaging	Het
Ngf	T	A	3: 102,427,961 (GRCm39)	F237I	probably damaging	Het
Nol3	A	G	8: 106,005,888 (GRCm39)	Q94R	possibly damaging	Het
Obox1	A	G	7: 15,290,263 (GRCm39)	N202S	probably damaging	Het
Odc1	T	A	12: 17,597,386 (GRCm39)	N29K	possibly damaging	Het
Or2b7	C	T	13: 21,739,658 (GRCm39)	R178H	probably benign	Het
Or2h15	T	C	17: 38,441,508 (GRCm39)	T192A	probably damaging	Het
Or4a69	C	T	2: 89,312,652 (GRCm39)	V276I	probably benign	Het
Or52a20	A	C	7: 103,365,914 (GRCm39)	I38L	probably benign	Het
P2rx7	T	A	5: 122,819,129 (GRCm39)	V517E	probably damaging	Het
Parm1	A	G	5: 91,741,775 (GRCm39)	T48A	possibly damaging	Het
Pcdh9	T	A	14: 94,126,164 (GRCm39)	D2V	possibly damaging	Het
Pgm3	G	T	9: 86,451,378 (GRCm39)	T92N	probably damaging	Het
Plcg2	G	T	8: 118,333,872 (GRCm39)	G882*	probably null	Het
Ptpn14	C	T	1: 189,582,997 (GRCm39)	P615S	probably damaging	Het
Ptprk	A	T	10: 28,464,928 (GRCm39)	Y1244F	probably damaging	Het
Rere	G	A	4: 150,700,510 (GRCm39)	A1162T	probably damaging	Het
Rfx2	T	C	17: 57,090,747 (GRCm39)	E391G	probably damaging	Het
Serpinb10	A	T	1: 107,468,681 (GRCm39)	N185I	probably damaging	Het
Shroom3	T	G	5: 93,098,993 (GRCm39)	M1410R	probably benign	Het
Slc13a1	A	T	6: 24,134,356 (GRCm39)	S176T	probably benign	Het
Sntb1	A	T	15: 55,506,198 (GRCm39)	Y458*	probably null	Het
Sorcs1	C	T	19: 50,220,741 (GRCm39)	V570I	probably benign	Het
Sp8	T	A	12: 118,812,805 (GRCm39)	V220E	probably damaging	Het
Spry1	C	T	3: 37,696,868 (GRCm39)	T37M	possibly damaging	Het
Sspo	A	T	6: 48,437,756 (GRCm39)	H1305L	probably benign	Het
Tbc1d22a	A	G	15: 86,381,117 (GRCm39)	D509G	possibly damaging	Het
Tmem108	A	T	9: 103,376,276 (GRCm39)	V391D	possibly damaging	Het
Tmem132d	T	A	5: 128,346,366 (GRCm39)	H52L	possibly damaging	Het
Tmem132d	T	A	5: 128,346,364 (GRCm39)	I53F	probably damaging	Het
Tnnt2	A	T	1: 135,775,496 (GRCm39)	R87*	probably null	Het
Ube3a	A	T	7: 58,893,198 (GRCm39)	M1L	probably benign	Het
Unc79	A	G	12: 103,060,592 (GRCm39)	T1119A	probably damaging	Het
Usf3	A	T	16: 44,039,942 (GRCm39)	H1474L	probably damaging	Het
Vcpip1	G	A	1: 9,817,423 (GRCm39)	T320I	probably damaging	Het
Vmn1r56	A	G	7: 5,199,443 (GRCm39)	L58P	probably damaging	Het
Wdr53	A	T	16: 32,075,796 (GRCm39)	K334*	probably null	Het
Zbtb40	T	A	4: 136,728,241 (GRCm39)	R459W	probably benign	Het
Zfc3h1	T	A	10: 115,246,547 (GRCm39)	L878Q	probably damaging	Het
Zfp286	T	C	11: 62,671,455 (GRCm39)	D206G	probably benign	Het
Zfp46	T	A	4: 136,017,792 (GRCm39)	C209S	probably damaging	Het
Zup1	G	T	10: 33,825,038 (GRCm39)	T148K	probably damaging	Het

Other mutations in Sema4c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00420:Sema4c	APN	1	36,593,001 (GRCm39)	critical splice donor site	probably benign	0.00
IGL01824:Sema4c	APN	1	36,592,110 (GRCm39)	missense	possibly damaging	0.76
IGL02236:Sema4c	APN	1	36,592,166 (GRCm39)	missense	probably damaging	1.00
IGL02262:Sema4c	APN	1	36,589,422 (GRCm39)	missense	probably damaging	1.00
IGL02282:Sema4c	APN	1	36,589,284 (GRCm39)	splice site	probably null
IGL02476:Sema4c	APN	1	36,595,031 (GRCm39)	missense	probably damaging	0.98
IGL02900:Sema4c	APN	1	36,589,826 (GRCm39)	nonsense	probably null
swirl	UTSW	1	36,589,392 (GRCm39)	missense	probably damaging	1.00
IGL02837:Sema4c	UTSW	1	36,591,965 (GRCm39)	missense	probably damaging	1.00
R0427:Sema4c	UTSW	1	36,592,892 (GRCm39)	nonsense	probably null
R0497:Sema4c	UTSW	1	36,588,689 (GRCm39)	missense	probably benign	0.04
R1066:Sema4c	UTSW	1	36,589,281 (GRCm39)	missense	possibly damaging	0.95
R1099:Sema4c	UTSW	1	36,591,191 (GRCm39)	missense	probably damaging	1.00
R1146:Sema4c	UTSW	1	36,589,646 (GRCm39)	missense	probably benign	0.04
R1146:Sema4c	UTSW	1	36,589,646 (GRCm39)	missense	probably benign	0.04
R1639:Sema4c	UTSW	1	36,592,615 (GRCm39)	missense	probably benign	0.00
R1644:Sema4c	UTSW	1	36,589,885 (GRCm39)	missense	probably damaging	1.00
R3176:Sema4c	UTSW	1	36,588,960 (GRCm39)	missense	possibly damaging	0.65
R3177:Sema4c	UTSW	1	36,588,960 (GRCm39)	missense	possibly damaging	0.65
R3276:Sema4c	UTSW	1	36,588,960 (GRCm39)	missense	possibly damaging	0.65
R3277:Sema4c	UTSW	1	36,588,960 (GRCm39)	missense	possibly damaging	0.65
R3551:Sema4c	UTSW	1	36,592,804 (GRCm39)	missense	probably benign	0.02
R4452:Sema4c	UTSW	1	36,592,837 (GRCm39)	missense	probably benign	0.31
R4895:Sema4c	UTSW	1	36,592,651 (GRCm39)	splice site	probably null
R4913:Sema4c	UTSW	1	36,589,266 (GRCm39)	missense	probably benign	0.11
R4944:Sema4c	UTSW	1	36,589,392 (GRCm39)	missense	probably damaging	1.00
R5062:Sema4c	UTSW	1	36,592,059 (GRCm39)	critical splice donor site	probably null
R5077:Sema4c	UTSW	1	36,590,812 (GRCm39)	missense	probably benign	0.20
R5109:Sema4c	UTSW	1	36,591,381 (GRCm39)	frame shift	probably null
R5208:Sema4c	UTSW	1	36,589,407 (GRCm39)	missense	probably damaging	1.00
R5551:Sema4c	UTSW	1	36,591,398 (GRCm39)	missense	probably damaging	1.00
R5912:Sema4c	UTSW	1	36,593,469 (GRCm39)	missense	possibly damaging	0.83
R6578:Sema4c	UTSW	1	36,589,834 (GRCm39)	missense	probably benign	0.02
R7111:Sema4c	UTSW	1	36,592,160 (GRCm39)	missense	possibly damaging	0.48
R7141:Sema4c	UTSW	1	36,592,101 (GRCm39)	missense	probably damaging	0.99
R7252:Sema4c	UTSW	1	36,589,096 (GRCm39)	missense	probably damaging	1.00
R7495:Sema4c	UTSW	1	36,589,774 (GRCm39)	missense	probably benign	0.00
R7891:Sema4c	UTSW	1	36,588,995 (GRCm39)	missense	probably damaging	0.98
R7895:Sema4c	UTSW	1	36,592,199 (GRCm39)	missense	probably damaging	1.00
R8264:Sema4c	UTSW	1	36,591,966 (GRCm39)	missense	probably damaging	1.00
R8478:Sema4c	UTSW	1	36,590,871 (GRCm39)	missense	probably benign	0.04
R8680:Sema4c	UTSW	1	36,589,867 (GRCm39)	missense	probably benign	0.00
R8733:Sema4c	UTSW	1	36,591,954 (GRCm39)	missense	probably damaging	1.00
R9017:Sema4c	UTSW	1	36,592,079 (GRCm39)	missense	probably damaging	1.00
R9344:Sema4c	UTSW	1	36,592,395 (GRCm39)	missense	probably damaging	1.00
R9488:Sema4c	UTSW	1	36,591,067 (GRCm39)	missense	probably benign
X0019:Sema4c	UTSW	1	36,592,077 (GRCm39)	missense	probably damaging	1.00
X0028:Sema4c	UTSW	1	36,589,047 (GRCm39)	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- TCAAACACCTGCAGTTCCTC -3'
(R):5'- CACTTATTCGCCAGCTGACTG -3'

Sequencing Primer
(F):5'- ACCATGTGGATCCAGGGC -3'
(R):5'- TGACTGACAGCCGCCCTC -3'

Posted On

2016-03-17