Mutagenetix > Incidental Mutation

Incidental Mutation 'R3177:Sema4c'

476023

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

040615-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3177 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

36548639-36558349 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 36549879 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Histidine at position 722 (R722H)

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

possibly damaging
Transcript: ENSMUST00000114990
AA Change: R722H

PolyPhen 2 Score 0.646 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000110641
Gene: ENSMUSG00000026121
AA Change: R722H

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

possibly damaging
Transcript: ENSMUST00000114991
AA Change: R722H

PolyPhen 2 Score 0.646 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000110643
Gene: ENSMUSG00000026121
AA Change: R722H

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

possibly damaging
Transcript: ENSMUST00000191642
AA Change: R722H

PolyPhen 2 Score 0.646 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000142284
Gene: ENSMUSG00000026121
AA Change: R722H

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

possibly damaging
Transcript: ENSMUST00000191677
AA Change: R722H

PolyPhen 2 Score 0.646 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000141263
Gene: ENSMUSG00000026121
AA Change: R722H

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

possibly damaging
Transcript: ENSMUST00000195620
AA Change: R722H

PolyPhen 2 Score 0.646 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000141527
Gene: ENSMUSG00000026121
AA Change: R722H

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: ENSMUST00000208690

Predicted Effect

probably benign
Transcript: ENSMUST00000207843

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208269

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.1%
20x: 94.4%

Validation Efficiency

100% (21/21)

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921509C19Rik	T	C	2: 151,472,100	R553G	possibly damaging	Het
Adarb2	A	G	13: 8,752,627	N646S	probably damaging	Het
Adcy8	C	T	15: 64,699,159	G1242S	probably benign	Het
Ano9	T	A	7: 141,104,124	T543S	probably damaging	Het
Btnl10	A	G	11: 58,922,390	K282E	probably benign	Het
Btnl9	T	C	11: 49,169,676	D330G	probably damaging	Het
Ccdc178	G	T	18: 22,067,652	A416E	possibly damaging	Het
Cdx2	A	T	5: 147,303,192	S225T	probably benign	Het
Clca4b	T	C	3: 144,911,359	I843M	probably benign	Het
Cntn4	G	A	6: 106,437,964		probably null	Het
Cyb561	T	C	11: 105,935,787		probably benign	Het
Cyp4f18	T	C	8: 71,993,200	D317G	possibly damaging	Het
Dennd4a	G	T	9: 64,888,993	R767L	probably damaging	Het
Dgkb	G	A	12: 38,084,217	V41M	probably damaging	Het
Duox1	T	C	2: 122,340,116	Y1206H	probably damaging	Het
Dync1i1	T	C	6: 5,972,211		probably null	Het
Fbxw2	T	C	2: 34,822,750	T100A	probably benign	Het
Fcgbp	C	A	7: 28,091,661	H782Q	probably damaging	Het
Flg2	A	T	3: 93,214,888	Q1455L	unknown	Het
Frrs1	T	C	3: 116,899,224	F49S	probably damaging	Het
Gli3	A	T	13: 15,725,982	Q1318L	probably benign	Het
Gm5581	C	G	6: 131,166,965		noncoding transcript	Het
Gm5592	A	G	7: 41,288,380	E362G	probably benign	Het
Gm7104	A	T	12: 88,285,728		noncoding transcript	Het
Gpatch2l	A	G	12: 86,244,315	T91A	possibly damaging	Het
Hacd4	T	C	4: 88,437,510	H46R	probably damaging	Het
Hao2	T	C	3: 98,880,328		probably benign	Het
Herc2	T	C	7: 56,153,428	V2175A	probably benign	Het
Hey1	T	C	3: 8,664,891	S169G	probably benign	Het
Hivep2	C	A	10: 14,128,969	T437K	probably benign	Het
Hlf	T	C	11: 90,345,835	K199E	probably damaging	Het
Hpgd	C	A	8: 56,298,413	A92E	probably damaging	Het
Hsp90aa1	T	A	12: 110,695,680	M1L	possibly damaging	Het
Hsp90aa1	C	A	12: 110,695,681		probably null	Het
Itgad	C	A	7: 128,190,981	H651N	possibly damaging	Het
Itgav	A	G	2: 83,776,542	D409G	probably damaging	Het
Kif2a	A	G	13: 106,976,756	I455T	probably damaging	Het
Klk14	G	A	7: 43,692,077	C51Y	probably damaging	Het
Lamc3	G	T	2: 31,908,625	G448C	probably damaging	Het
Ltbp1	G	A	17: 75,276,480	G425D	possibly damaging	Het
Ltbp1	T	A	17: 75,359,278		probably null	Het
Mag	C	T	7: 30,901,648		probably null	Het
Mdh1b	G	A	1: 63,711,531	T426M	possibly damaging	Het
Nr1h4	G	A	10: 89,478,788	T282I	possibly damaging	Het
Nsf	C	T	11: 103,930,752	E26K	possibly damaging	Het
Olfr1231	C	T	2: 89,303,218	V125M	possibly damaging	Het
Olfr1412	A	G	1: 92,588,813	N161S	probably benign	Het
Olfr552	T	C	7: 102,604,576	V74A	possibly damaging	Het
Padi6	A	G	4: 140,735,389	L307P	probably damaging	Het
Parp9	T	C	16: 35,948,208	S20P	probably damaging	Het
Pdcd11	T	C	19: 47,113,264	F963L	probably damaging	Het
Pwp1	C	T	10: 85,882,079	L294F	probably benign	Het
Radil	A	G	5: 142,506,856	L339P	probably damaging	Het
Raver1	G	A	9: 21,079,277	P316S	possibly damaging	Het
Rell1	A	G	5: 63,926,987		probably null	Het
Rxrg	A	G	1: 167,635,700	D257G	possibly damaging	Het
Sgk1	C	T	10: 21,996,601	R171W	probably damaging	Het
Spata7	A	G	12: 98,637,598	N75D	possibly damaging	Het
Ttc23l	A	G	15: 10,547,232	F99L	possibly damaging	Het
Unc13a	A	C	8: 71,629,695	C1642G	probably benign	Het
Usp36	C	T	11: 118,276,759		probably null	Het
Wrn	A	G	8: 33,317,554	M292T	probably damaging	Het
Zfp423	A	G	8: 87,782,331	Y462H	probably damaging	Het
Zscan5b	T	A	7: 6,231,346	Y124N	possibly damaging	Het
Zswim9	T	C	7: 13,277,270	T51A	possibly damaging	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
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

Posted On

2017-05-11