Mutagenetix > Incidental Mutation

Incidental Mutation 'R5551:Sema4c'

435105

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

043108-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5551 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

36548639-36558349 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 36552317 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 348 (Y348H)

Ref Sequence

ENSEMBL: ENSMUSP00000141527 (fasta)

Gene Model

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

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: Y348H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000110643
Gene: ENSMUSG00000026121
AA Change: Y348H

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: Y348H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000142284
Gene: ENSMUSG00000026121
AA Change: Y348H

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: Y348H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000141263
Gene: ENSMUSG00000026121
AA Change: Y348H

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: ENSMUST00000195160

Predicted Effect

probably benign
Transcript: ENSMUST00000195339

Predicted Effect

probably damaging
Transcript: ENSMUST00000195620
AA Change: Y348H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000141527
Gene: ENSMUSG00000026121
AA Change: Y348H

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: 99.9%
3x: 99.7%
10x: 98.6%
20x: 96.1%

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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930435E12Rik	A	G	16: 38,827,974	Y258H	probably benign	Het
AB041806	G	T	4: 138,396,001	P3T	probably damaging	Het
Abl1	C	T	2: 31,801,670	A1048V	probably benign	Het
Acap2	A	G	16: 31,104,908	V659A	probably damaging	Het
Acox1	A	G	11: 116,189,491	S29P	possibly damaging	Het
Adamts1	A	G	16: 85,797,746	I405T	probably benign	Het
Afm	A	T	5: 90,531,652	E335V	probably null	Het
Akap6	C	T	12: 52,795,964	P32S	probably damaging	Het
Alk	T	C	17: 71,875,033	M1332V	possibly damaging	Het
Ankrd39	C	T	1: 36,541,981	G96R	probably damaging	Het
Atp2c1	C	A	9: 105,459,737	A16S	probably damaging	Het
Ccdc141	T	C	2: 77,014,409	E1438G	probably damaging	Het
Csmd2	T	C	4: 128,510,948	Y2376H	possibly damaging	Het
Csmd3	T	C	15: 48,314,096	T349A	probably benign	Het
Ctsr	A	T	13: 61,159,543	M313K	probably damaging	Het
D430042O09Rik	T	C	7: 125,820,077	F472S	probably damaging	Het
Dot1l	CCAGCCCCACCCTCAGCC	CCAGCC	10: 80,783,628		probably benign	Het
Dync2h1	A	G	9: 7,031,718	S3516P	possibly damaging	Het
Ehd4	A	G	2: 120,127,619	S162P	possibly damaging	Het
Ets2	T	C	16: 95,712,121	W114R	probably damaging	Het
Fignl1	A	T	11: 11,801,603	V484E	probably damaging	Het
Golph3	C	A	15: 12,321,836	S35R	probably benign	Het
Gzf1	T	C	2: 148,684,328	Y240H	probably damaging	Het
Hook3	A	G	8: 26,068,611	F75S	possibly damaging	Het
Ifi209	T	A	1: 173,641,197	S198T	probably benign	Het
Iqch	A	T	9: 63,496,253		probably null	Het
Lrrk2	C	T	15: 91,812,350	T2447I	probably benign	Het
Mesp2	T	C	7: 79,811,619	S231P	probably benign	Het
Muc5b	T	C	7: 141,868,503	C4459R	possibly damaging	Het
Myh10	A	G	11: 68,768,287	E497G	possibly damaging	Het
Nalcn	A	T	14: 123,278,286	V1701E	possibly damaging	Het
Nat8f1	T	C	6: 85,910,909	D23G	probably damaging	Het
Nfia	G	A	4: 98,014,260	E250K	probably damaging	Het
Nup155	A	G	15: 8,148,333	M1067V	probably benign	Het
Olfr1280	T	C	2: 111,315,571	F31L	possibly damaging	Het
Pde4d	T	A	13: 109,948,396		probably null	Het
Rtn4	G	A	11: 29,741,011	V1101I	probably damaging	Het
Sema6a	A	G	18: 47,248,528	V958A	possibly damaging	Het
Sez6l2	A	G	7: 126,966,830	Y677C	probably damaging	Het
Smad5	T	C	13: 56,735,841	C347R	probably damaging	Het
Smim19	A	G	8: 22,463,367	Y95H	probably benign	Het
Srrm2	C	A	17: 23,818,476		probably benign	Het
Ssb	A	G	2: 69,871,130	K390E	probably damaging	Het
Tars	G	A	15: 11,391,982	T248M	probably damaging	Het
Tcirg1	A	T	19: 3,898,858	F442L	probably damaging	Het
Tlk2	A	G	11: 105,221,307	E162G	probably benign	Het
Tmc6	A	G	11: 117,769,445	C656R	probably damaging	Het
Ttn	G	T	2: 76,889,062		probably benign	Het
Uqcrc2	C	T	7: 120,645,238	T201I	probably damaging	Het
Zfp282	G	T	6: 47,890,645	A252S	possibly damaging	Het
Zfp473	G	C	7: 44,734,151	P253A	probably benign	Het
Zfp541	A	G	7: 16,090,861	N1068D	probably damaging	Het
Zfp946	A	G	17: 22,455,384	Q373R	probably damaging	Het
Zmat2	G	A	18: 36,793,957	G6R	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
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
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'- TGTAGCCATTGTCTCGGTGC -3'
(R):5'- TACCTCATGGTCGTGACTGCTC -3'

Sequencing Primer
(F):5'- CTCGGTGCCAGTTGTTGATACAC -3'
(R):5'- ATGGTCGTGACTGCTCCATACTAAG -3'

Posted On

2016-10-24