Mutagenetix > Incidental Mutation

Incidental Mutation 'R9017:Sema4c'

686043

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

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9017 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

36548639-36558349 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 36552998 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Histidine at position 256 (R256H)

Ref Sequence

ENSEMBL: ENSMUSP00000110643 (fasta)

Gene Model

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

AlphaFold

Q64151

Predicted Effect

probably damaging
Transcript: ENSMUST00000114991
AA Change: R256H

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

SMART Domains

Protein: ENSMUSP00000110643
Gene: ENSMUSG00000026121
AA Change: R256H

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: R256H

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

SMART Domains

Protein: ENSMUSP00000142284
Gene: ENSMUSG00000026121
AA Change: R256H

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: R256H

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

SMART Domains

Protein: ENSMUSP00000141263
Gene: ENSMUSG00000026121
AA Change: R256H

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: ENSMUST00000193382

Predicted Effect

probably benign
Transcript: ENSMUST00000195339

Predicted Effect

probably damaging
Transcript: ENSMUST00000195620
AA Change: R256H

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

SMART Domains

Protein: ENSMUSP00000141527
Gene: ENSMUSG00000026121
AA Change: R256H

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: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.3%

Validation Efficiency

100% (65/65)

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
Adgrg7	T	C	16: 56,732,848	T629A	probably benign	Het
Afg3l2	A	G	18: 67,409,480	V632A	possibly damaging	Het
Ahnak	G	A	19: 9,010,123	E2924K	probably damaging	Het
Ampd1	A	G	3: 103,088,470	Y232C	probably benign	Het
Ank1	G	A	8: 23,116,248	G1219S	probably null	Het
Atp8b4	A	T	2: 126,433,921	N130K	probably benign	Het
Cdh15	T	C	8: 122,857,517		probably null	Het
Cep70	T	C	9: 99,299,776	I613T	possibly damaging	Het
Cfap54	C	T	10: 92,816,021	V3056I	probably benign	Het
Chrna2	T	C	14: 66,148,833	F143L	probably benign	Het
Cmya5	C	T	13: 93,092,064	R2172H	probably benign	Het
Col17a1	T	C	19: 47,669,459	E424G	probably benign	Het
Crybg1	T	C	10: 44,004,481	E237G	probably benign	Het
Ctnnd2	G	A	15: 30,881,170	C732Y	probably damaging	Het
Dcaf12	T	C	4: 41,299,411	N264S	probably benign	Het
Dennd4c	A	G	4: 86,825,112	S1064G	probably benign	Het
Dsc2	A	T	18: 20,043,911	Y360N	probably damaging	Het
E2f3	T	G	13: 29,913,495	D295A	probably damaging	Het
Eef2	T	C	10: 81,179,653	L336P	possibly damaging	Het
Fanca	A	G	8: 123,308,568	S213P	possibly damaging	Het
Fpgt	A	T	3: 155,087,266	S375T	probably benign	Het
Gad1	G	A	2: 70,585,862	V222I	probably benign	Het
Gm5930	A	T	14: 44,331,401	Y255N	possibly damaging	Het
Gpr55	T	C	1: 85,940,902	N319S	probably benign	Het
Grik2	T	A	10: 49,113,459	I825F	possibly damaging	Het
Hcn4	T	C	9: 58,824,199	S230P	unknown	Het
Kansl3	T	C	1: 36,354,780	I222V	probably benign	Het
Kif20b	T	C	19: 34,949,803	S822P	probably benign	Het
Kremen2	T	A	17: 23,745,763		probably benign	Het
Krt71	G	T	15: 101,742,665	R128S	possibly damaging	Het
Lrp4	A	T	2: 91,494,052	N1244I	possibly damaging	Het
Lrrc66	T	C	5: 73,607,901	S600G	possibly damaging	Het
Mrc2	T	A	11: 105,325,885	C167S	probably damaging	Het
Mrps17	T	C	5: 129,716,793	V17A	probably damaging	Het
Muc20	A	T	16: 32,794,470	L179Q	unknown	Het
Olfr1209	G	T	2: 88,909,607	T262K	probably damaging	Het
Olfr1340	T	A	4: 118,726,368	F40L	probably benign	Het
Olfr309	A	T	7: 86,306,749	Y121*	probably null	Het
Otop2	T	C	11: 115,323,605	F63L	probably benign	Het
Pde3b	C	T	7: 114,416,460	Q304*	probably null	Het
Pex19	GTCTCTTGTCTCCGAAGGTGCTCTTGATGATTTCTCTTGTCTCCGAAGGTGCTCTTGATGATTTC	GTCTCTTGTCTCCGAAGGTGCTCTTGATGATTTC	1: 172,128,583		probably null	Het
Plekhg4	A	G	8: 105,378,700	E599G	possibly damaging	Het
Ppargc1a	C	A	5: 51,472,909	R622L	unknown	Het
Ppip5k2	A	G	1: 97,727,414	L879P	probably damaging	Het
Prepl	C	T	17: 85,068,938	V563M	possibly damaging	Het
Prom1	G	T	5: 44,047,528	D201E	probably damaging	Het
Psmd1	T	A	1: 86,126,509	D723E	probably damaging	Het
Sall2	A	T	14: 52,313,262	N825K	possibly damaging	Het
Sds	A	T	5: 120,480,590	M70L	probably benign	Het
Sik1	T	C	17: 31,851,571	Y100C	probably damaging	Het
Slc13a5	T	A	11: 72,247,762	I452F	probably damaging	Het
Slc25a24	A	G	3: 109,155,079	I162V	possibly damaging	Het
Sorbs2	T	G	8: 45,795,737	V675G	probably benign	Het
Tenm3	T	A	8: 48,254,633	N1710I	probably damaging	Het
Tmem115	T	A	9: 107,534,681	M68K	probably benign	Het
Tmem132d	T	C	5: 127,789,872	I655V	probably benign	Het
Tmem132d	T	C	5: 128,269,252	I69V	probably benign	Het
Tnfrsf11a	G	A	1: 105,827,129	A309T	possibly damaging	Het
Trim9	A	G	12: 70,267,239	M544T	probably benign	Het
Ttll3	G	A	6: 113,412,889	R745H	probably benign	Het
Ttn	G	T	2: 76,907,587	L4249I	unknown	Het
Unc79	G	A	12: 103,108,615		probably null	Het
Vmn1r196	T	C	13: 22,294,084	C298R	probably benign	Het
Vmn1r216	A	G	13: 23,099,911	I255V	probably benign	Het
Zfp853	A	G	5: 143,288,488	L474P	unknown	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
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
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'- AAGTAGACCTTCCAGTCAGGGG -3'
(R):5'- ACAGAGCCGGTTATCCTTCG -3'

Sequencing Primer
(F):5'- TTCCAGTCAGGGGCTGAG -3'
(R):5'- AGAGCCGGTTATCCTTCGATACATG -3'

Posted On

2021-10-11