Mutagenetix > Incidental Mutation

Incidental Mutation 'R1644:Sema4c'

173729

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

039680-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1644 (G1)

Quality Score

200

Status

Validated

Chromosome

Chromosomal Location

36548639-36558349 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 36550804 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 490 (S490P)

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: ENSMUST00000114990
AA Change: S490P

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

SMART Domains

Protein: ENSMUSP00000110641
Gene: ENSMUSG00000026121
AA Change: S490P

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: ENSMUST00000114991
AA Change: S490P

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

SMART Domains

Protein: ENSMUSP00000110643
Gene: ENSMUSG00000026121
AA Change: S490P

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: S490P

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

SMART Domains

Protein: ENSMUSP00000142284
Gene: ENSMUSG00000026121
AA Change: S490P

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: S490P

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

SMART Domains

Protein: ENSMUSP00000141263
Gene: ENSMUSG00000026121
AA Change: S490P

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: S490P

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

SMART Domains

Protein: ENSMUSP00000141527
Gene: ENSMUSG00000026121
AA Change: S490P

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

0.4341

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 96.0%
20x: 91.6%

Validation Efficiency

98% (62/63)

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: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A830018L16Rik	C	T	1: 11,414,590	R8*	probably null	Het
Acacb	A	T	5: 114,195,285	H490L	probably damaging	Het
Ace	C	A	11: 105,985,106	H417N	probably damaging	Het
Adamtsl3	A	G	7: 82,450,090	N151D	possibly damaging	Het
Agap1	A	G	1: 89,663,730	N114S	probably damaging	Het
Arap3	A	T	18: 37,984,245	V926D	probably damaging	Het
Arhgap12	A	T	18: 6,112,340	I8N	probably benign	Het
Arhgef17	A	T	7: 100,929,504	F746I	probably damaging	Het
Atp6v0a1	T	C	11: 101,038,786	S471P	possibly damaging	Het
Bdp1	A	G	13: 100,060,940	V979A	probably benign	Het
Ccdc88c	C	A	12: 100,913,474	R1789L	probably damaging	Het
Cckar	A	T	5: 53,699,873	N327K	probably benign	Het
Cfap65	T	C	1: 74,917,175	T1082A	probably damaging	Het
Clcn7	T	A	17: 25,159,698	I719N	probably damaging	Het
Col27a1	C	G	4: 63,328,631		probably benign	Het
Cspp1	C	T	1: 10,126,438	T179I	probably damaging	Het
Dnah1	C	T	14: 31,302,292		probably benign	Het
Dnah6	A	G	6: 73,155,296	V1141A	probably benign	Het
Dusp4	A	G	8: 34,818,479	Y298C	probably damaging	Het
Efhc1	C	A	1: 20,967,401	Y267*	probably null	Het
Eif2s1	T	A	12: 78,866,521		probably null	Het
Epo	A	G	5: 137,483,155	V169A	possibly damaging	Het
Esr1	A	T	10: 5,001,380	Y586F	probably benign	Het
Fat2	T	C	11: 55,287,783	T1484A	possibly damaging	Het
Fat2	T	C	11: 55,296,181	T1280A	possibly damaging	Het
Gm5828	T	C	1: 16,769,261		noncoding transcript	Het
Idh3b	T	C	2: 130,281,510	I187V	possibly damaging	Het
Kif13a	A	C	13: 46,793,922	V862G	probably benign	Het
Kndc1	A	G	7: 139,930,756	D1327G	probably damaging	Het
Mfsd9	T	A	1: 40,773,798	R452S	probably benign	Het
Myh15	C	T	16: 49,132,203	R879C	probably benign	Het
Naip2	T	C	13: 100,182,929	R260G	possibly damaging	Het
Npat	T	G	9: 53,570,172	L1060R	probably damaging	Het
Olfr1211	A	T	2: 88,929,387	D309E	probably benign	Het
Olfr1261	A	T	2: 89,993,953	T187S	possibly damaging	Het
Olfr169	T	A	16: 19,566,406	H159L	probably benign	Het
Olfr523	T	C	7: 140,176,648	V176A	probably benign	Het
Olfr667	A	C	7: 104,916,808	F163V	probably benign	Het
Pld5	T	C	1: 175,975,626	T296A	possibly damaging	Het
Polq	C	T	16: 37,060,264	A651V	probably damaging	Het
Polr3a	G	A	14: 24,470,624	P607S	probably damaging	Het
Ranbp9	G	A	13: 43,412,539	R424C	probably damaging	Het
Rsl1	G	A	13: 67,177,165		probably benign	Het
Setd3	A	T	12: 108,113,344	L300Q	possibly damaging	Het
Slc15a3	T	C	19: 10,857,231	I492T	possibly damaging	Het
Stag1	T	C	9: 100,880,900		probably benign	Het
Tgm4	A	G	9: 123,051,416	Y294C	probably damaging	Het
Tm9sf1	A	G	14: 55,641,300	S212P	probably benign	Het
Tmcc1	A	G	6: 116,133,865	S156P	probably damaging	Het
Vmn1r184	A	C	7: 26,267,245	M139L	probably benign	Het
Vmn1r209	A	C	13: 22,806,482	F13V	possibly damaging	Het
Xkr5	T	C	8: 18,934,125	E467G	probably benign	Het
Zdbf2	C	T	1: 63,308,972	S2170L	possibly damaging	Het
Zfp277	G	T	12: 40,329,610		probably null	Het
Zfp62	T	C	11: 49,215,769	I229T	probably damaging	Het
Zfp810	A	G	9: 22,279,028	S195P	possibly damaging	Het
Zfp94	G	A	7: 24,311,502		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
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
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'- GAAGTGGCATCAGAGATCCAACTCC -3'
(R):5'- AAACTGAGTTTCCTGGCCCGAGTG -3'

Sequencing Primer
(F):5'- GAGATCCAACTCCAATCACCTTAG -3'
(R):5'- GTCCCTGTCTAAGAAGGTCATGTC -3'

Posted On

2014-04-24