Mutagenetix > Incidental Mutation

Incidental Mutation 'R1669:Sema3d'

187442

Institutional Source

Beutler Lab

Gene Symbol

Sema3d

Ensembl Gene

ENSMUSG00000040254

Gene Name

sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D

Synonyms

4631426B19Rik

MMRRC Submission

039705-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.207) question?

Stock #

R1669 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

12433352-12638915 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

T to A at 12558051 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000142453 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030868] [ENSMUST00000197927]

AlphaFold

Q8BH34

Predicted Effect

probably benign
Transcript: ENSMUST00000030868

SMART Domains

Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254

Domain	Start	End	E-Value	Type
transmembrane domain	16	35	N/A	INTRINSIC
Sema	70	515	2.97e-207	SMART
PSI	533	585	2.03e-13	SMART
IG	598	682	1.39e-2	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196093

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196618

Predicted Effect

probably benign
Transcript: ENSMUST00000197927

SMART Domains

Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254

Domain	Start	End	E-Value	Type
signal peptide	1	37	N/A	INTRINSIC
Sema	70	515	1e-209	SMART
PSI	533	585	8.5e-16	SMART
Blast:Sema	590	622	1e-9	BLAST

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.5%
20x: 93.3%

Validation Efficiency

99% (85/86)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit pulmonary vein connection to the right atrium and atrial septal defect. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ano10	A	C	9: 122,086,249 (GRCm39)	L258R	possibly damaging	Het
Ap3d1	A	G	10: 80,546,670 (GRCm39)		probably benign	Het
Aplp2	G	T	9: 31,079,029 (GRCm39)		probably benign	Het
Arhgap11a	T	C	2: 113,672,257 (GRCm39)	D237G	possibly damaging	Het
Arhgef4	A	T	1: 34,771,239 (GRCm39)	H1182L	possibly damaging	Het
Ash1l	G	A	3: 88,974,549 (GRCm39)		probably null	Het
Bicdl1	C	A	5: 115,794,075 (GRCm39)	V224L	possibly damaging	Het
Cacna1h	C	A	17: 25,602,445 (GRCm39)	V1422L	probably damaging	Het
Card10	T	C	15: 78,678,153 (GRCm39)	E365G	probably benign	Het
Cd180	C	T	13: 102,841,998 (GRCm39)	T348I	probably damaging	Het
Cds2	T	A	2: 132,137,439 (GRCm39)		probably null	Het
Chaf1a	C	A	17: 56,370,339 (GRCm39)	D601E	probably benign	Het
Coprs	C	T	8: 13,935,704 (GRCm39)	W12*	probably null	Het
Cpsf3	T	A	12: 21,355,332 (GRCm39)	M424K	probably damaging	Het
Cxcl13	T	A	5: 96,106,600 (GRCm39)	N57K	probably damaging	Het
Dact1	C	T	12: 71,365,547 (GRCm39)	T776M	probably damaging	Het
Depdc1a	A	G	3: 159,228,561 (GRCm39)	K438E	probably benign	Het
Dop1b	T	A	16: 93,566,548 (GRCm39)	S992T	probably damaging	Het
Dusp11	A	T	6: 85,927,008 (GRCm39)	H202Q	probably benign	Het
Ezr	T	C	17: 7,006,712 (GRCm39)	E584G	probably damaging	Het
F830104G03Rik	A	G	3: 56,797,998 (GRCm39)	V6A	unknown	Het
Fam227a	G	A	15: 79,504,878 (GRCm39)		probably null	Het
Gapvd1	T	G	2: 34,620,694 (GRCm39)		probably null	Het
Gm10267	T	C	18: 44,290,367 (GRCm39)	R47G	probably damaging	Het
Hectd3	T	A	4: 116,856,840 (GRCm39)	D462E	probably damaging	Het
Hfe	A	T	13: 23,890,110 (GRCm39)	L133*	probably null	Het
Hpcal4	T	C	4: 123,082,869 (GRCm39)	F72L	probably damaging	Het
Itgb4	G	A	11: 115,882,156 (GRCm39)	R825H	probably benign	Het
Kcnh8	T	A	17: 53,200,996 (GRCm39)	Y477N	probably damaging	Het
Kctd1	T	C	18: 15,195,517 (GRCm39)	N369D	possibly damaging	Het
Kdm1b	C	T	13: 47,222,024 (GRCm39)	R488C	probably damaging	Het
Kif1c	C	T	11: 70,619,223 (GRCm39)	L953F	probably damaging	Het
Klra8	A	T	6: 130,092,592 (GRCm39)	C236*	probably null	Het
Lca5l	T	C	16: 95,961,008 (GRCm39)	R485G	possibly damaging	Het
Lrrc2	A	G	9: 110,810,718 (GRCm39)	T363A	probably damaging	Het
Lsmem1	GTACATACATACATACATACATACATACA	GTACATACATACATACATACATACATACATACA	12: 40,235,260 (GRCm39)		probably null	Het
Lyst	G	A	13: 13,818,672 (GRCm39)	G1314D	possibly damaging	Het
Mmp10	A	T	9: 7,505,526 (GRCm39)		probably null	Het
Mmp13	A	G	9: 7,277,926 (GRCm39)	D273G	probably benign	Het
Morc2a	G	A	11: 3,625,885 (GRCm39)	V162M	probably benign	Het
Msh4	C	T	3: 153,582,357 (GRCm39)	R417Q	possibly damaging	Het
Nedd9	A	T	13: 41,465,270 (GRCm39)	V790E	probably damaging	Het
Nlgn1	C	A	3: 25,490,298 (GRCm39)	L476F	probably damaging	Het
Nox4	C	A	7: 86,945,097 (GRCm39)	Q118K	probably benign	Het
Nxf1	A	G	19: 8,749,495 (GRCm39)	T131A	possibly damaging	Het
Oog3	C	A	4: 143,885,008 (GRCm39)	R309S	probably benign	Het
Oosp3	C	T	19: 11,678,378 (GRCm39)		probably benign	Het
Or10a3	T	A	7: 108,479,920 (GRCm39)	T298S	probably benign	Het
Or2a7	T	A	6: 43,151,755 (GRCm39)	S278R	probably damaging	Het
Or2w6	A	T	13: 21,843,456 (GRCm39)	S12R	possibly damaging	Het
Or4c126	T	A	2: 89,824,144 (GRCm39)		probably null	Het
Or51a42	A	T	7: 103,708,516 (GRCm39)	S98T	probably benign	Het
Or5b97	A	T	19: 12,878,652 (GRCm39)	I164K	possibly damaging	Het
P2ry6	A	G	7: 100,587,630 (GRCm39)	V243A	probably damaging	Het
Pgc	C	A	17: 48,044,715 (GRCm39)	P321T	probably damaging	Het
Pramel22	T	G	4: 143,380,916 (GRCm39)	E369A	possibly damaging	Het
Prkd1	G	A	12: 50,441,709 (GRCm39)	H277Y	probably damaging	Het
Prkdc	T	A	16: 15,551,922 (GRCm39)	S2043T	probably damaging	Het
Rasal3	T	C	17: 32,622,072 (GRCm39)	N96D	possibly damaging	Het
Rnf4	T	C	5: 34,508,624 (GRCm39)	F162S	probably damaging	Het
Ros1	A	T	10: 52,037,907 (GRCm39)	N421K	probably damaging	Het
Rtn4rl1	A	G	11: 75,156,753 (GRCm39)	D395G	probably benign	Het
Scn8a	T	G	15: 100,909,001 (GRCm39)	V823G	probably damaging	Het
Slc12a2	T	C	18: 58,037,307 (GRCm39)	I501T	probably damaging	Het
Slc12a7	C	T	13: 73,943,232 (GRCm39)	T382I	probably benign	Het
Slc16a12	T	A	19: 34,657,781 (GRCm39)	I41L	probably benign	Het
Slc1a1	C	A	19: 28,889,194 (GRCm39)	T489K	probably benign	Het
Slc24a3	C	T	2: 145,455,512 (GRCm39)	P467L	probably damaging	Het
Slco1a8	T	A	6: 141,933,415 (GRCm39)	I457F	probably benign	Het
Snai2	A	T	16: 14,524,908 (GRCm39)	Y138F	possibly damaging	Het
Sorcs1	A	C	19: 50,463,860 (GRCm39)	Y197D	probably damaging	Het
Sppl2a	T	A	2: 126,759,714 (GRCm39)		probably benign	Het
Srgap3	G	A	6: 112,699,865 (GRCm39)	P1038S	probably benign	Het
Ttn	T	C	2: 76,554,807 (GRCm39)	E30699G	probably damaging	Het
Vmn2r124	T	A	17: 18,283,206 (GRCm39)	M300K	possibly damaging	Het
Vwf	T	C	6: 125,624,869 (GRCm39)	S1873P	possibly damaging	Het
Wrap73	A	G	4: 154,240,588 (GRCm39)	D360G	probably damaging	Het
Zfp366	T	C	13: 99,366,069 (GRCm39)	M410T	probably damaging	Het
Zfp608	C	T	18: 55,120,811 (GRCm39)	V259I	probably benign	Het
Zfp69	C	T	4: 120,804,695 (GRCm39)		probably benign	Het
Zfp995	T	C	17: 22,098,945 (GRCm39)	T430A	probably benign	Het

Other mutations in Sema3d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00559:Sema3d	APN	5	12,613,189 (GRCm39)	missense	probably benign	0.01
IGL00582:Sema3d	APN	5	12,635,162 (GRCm39)	missense	probably damaging	1.00
IGL00661:Sema3d	APN	5	12,555,806 (GRCm39)	missense	probably damaging	1.00
IGL00780:Sema3d	APN	5	12,574,293 (GRCm39)	missense	probably damaging	1.00
IGL01531:Sema3d	APN	5	12,591,047 (GRCm39)	missense	probably benign
IGL01957:Sema3d	APN	5	12,613,282 (GRCm39)	missense	probably damaging	1.00
IGL02100:Sema3d	APN	5	12,634,958 (GRCm39)	missense	probably benign	0.29
IGL02676:Sema3d	APN	5	12,620,945 (GRCm39)	missense	probably benign	0.38
IGL02749:Sema3d	APN	5	12,613,112 (GRCm39)	splice site	probably benign
IGL02827:Sema3d	APN	5	12,635,085 (GRCm39)	missense	probably benign	0.04
IGL03325:Sema3d	APN	5	12,513,189 (GRCm39)	missense	probably damaging	0.99
R0050:Sema3d	UTSW	5	12,634,920 (GRCm39)	missense	probably benign	0.00
R0085:Sema3d	UTSW	5	12,620,953 (GRCm39)	missense	probably benign	0.00
R0095:Sema3d	UTSW	5	12,613,314 (GRCm39)	missense	probably damaging	1.00
R0157:Sema3d	UTSW	5	12,558,104 (GRCm39)	missense	possibly damaging	0.95
R0328:Sema3d	UTSW	5	12,498,042 (GRCm39)	missense	possibly damaging	0.48
R0924:Sema3d	UTSW	5	12,513,183 (GRCm39)	missense	possibly damaging	0.69
R0930:Sema3d	UTSW	5	12,513,183 (GRCm39)	missense	possibly damaging	0.69
R1609:Sema3d	UTSW	5	12,591,023 (GRCm39)	missense	probably damaging	1.00
R1657:Sema3d	UTSW	5	12,634,941 (GRCm39)	missense	possibly damaging	0.82
R1795:Sema3d	UTSW	5	12,634,854 (GRCm39)	missense	probably benign	0.02
R1861:Sema3d	UTSW	5	12,547,570 (GRCm39)	missense	probably benign	0.00
R1889:Sema3d	UTSW	5	12,534,988 (GRCm39)	splice site	probably null
R1895:Sema3d	UTSW	5	12,623,810 (GRCm39)	missense	probably damaging	1.00
R1946:Sema3d	UTSW	5	12,623,810 (GRCm39)	missense	probably damaging	1.00
R1975:Sema3d	UTSW	5	12,634,965 (GRCm39)	missense	probably benign
R1975:Sema3d	UTSW	5	12,613,285 (GRCm39)	missense	probably damaging	1.00
R2117:Sema3d	UTSW	5	12,613,240 (GRCm39)	missense	probably benign
R2148:Sema3d	UTSW	5	12,534,926 (GRCm39)	missense	probably damaging	0.99
R2276:Sema3d	UTSW	5	12,592,549 (GRCm39)	missense	possibly damaging	0.63
R3761:Sema3d	UTSW	5	12,621,004 (GRCm39)	missense	probably damaging	1.00
R4063:Sema3d	UTSW	5	12,635,091 (GRCm39)	missense	probably benign	0.25
R4428:Sema3d	UTSW	5	12,498,087 (GRCm39)	missense	probably benign	0.32
R4903:Sema3d	UTSW	5	12,613,125 (GRCm39)	missense	probably benign	0.00
R4999:Sema3d	UTSW	5	12,558,054 (GRCm39)	splice site	probably null
R5000:Sema3d	UTSW	5	12,498,005 (GRCm39)	missense	probably benign	0.01
R5022:Sema3d	UTSW	5	12,634,923 (GRCm39)	missense	probably damaging	1.00
R5186:Sema3d	UTSW	5	12,634,875 (GRCm39)	missense	probably benign
R5584:Sema3d	UTSW	5	12,620,954 (GRCm39)	missense	possibly damaging	0.73
R5584:Sema3d	UTSW	5	12,615,975 (GRCm39)	missense	possibly damaging	0.49
R6270:Sema3d	UTSW	5	12,498,074 (GRCm39)	missense	probably benign
R6368:Sema3d	UTSW	5	12,620,980 (GRCm39)	missense	probably damaging	1.00
R6426:Sema3d	UTSW	5	12,613,231 (GRCm39)	missense	probably damaging	1.00
R6750:Sema3d	UTSW	5	12,635,067 (GRCm39)	nonsense	probably null
R7403:Sema3d	UTSW	5	12,547,551 (GRCm39)	missense	probably damaging	0.97
R7450:Sema3d	UTSW	5	12,634,901 (GRCm39)	nonsense	probably null
R7470:Sema3d	UTSW	5	12,558,152 (GRCm39)	missense	probably damaging	1.00
R7548:Sema3d	UTSW	5	12,627,783 (GRCm39)	missense	unknown
R7593:Sema3d	UTSW	5	12,558,112 (GRCm39)	missense	probably benign	0.02
R7683:Sema3d	UTSW	5	12,623,823 (GRCm39)	nonsense	probably null
R8155:Sema3d	UTSW	5	12,498,148 (GRCm39)	critical splice donor site	probably null
R8442:Sema3d	UTSW	5	12,592,608 (GRCm39)	missense	probably damaging	0.99
R8725:Sema3d	UTSW	5	12,555,822 (GRCm39)	missense	probably damaging	1.00
R8754:Sema3d	UTSW	5	12,603,191 (GRCm39)	critical splice donor site	probably null
R9293:Sema3d	UTSW	5	12,603,181 (GRCm39)	missense	probably damaging	1.00
R9771:Sema3d	UTSW	5	12,613,207 (GRCm39)	missense	probably damaging	0.99
Z1176:Sema3d	UTSW	5	12,635,026 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- ACACGGTCATCTCCAGGAATGCAG -3'
(R):5'- AGAGACATCTCTAACCATTGAGCCAGT -3'

Sequencing Primer
(F):5'- gcgttgacagctctctttcc -3'
(R):5'- CCAGTGGTGCTCTGAAATGTC -3'

Posted On

2014-05-09