Mutagenetix > Incidental Mutations

Incidental Mutation 'R4999:Sema3d'

389712

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

042593-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.168) question?

Stock #

R4999 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

12383385-12588948 bp(+) (GRCm38)

Type of Mutation

splice site

DNA Base Change (assembly)

T to A at 12508087 bp

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000142453 (fasta)

Gene Model

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

Predicted Effect

probably null
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 null
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

Predicted Effect

probably null
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: 98.3%
10x: 96.4%
20x: 92.7%

Validation Efficiency

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930444P10Rik	A	G	1: 16,068,798		probably null	Het
Abca4	T	A	3: 122,105,370	V667D	probably damaging	Het
Aco1	A	G	4: 40,176,507	I224V	probably damaging	Het
Arel1	C	T	12: 84,931,767	V364M	probably damaging	Het
Arhgap42	A	G	9: 9,009,434	V484A	probably damaging	Het
Asap2	T	C	12: 21,252,765	F681L	probably benign	Het
Atrn	C	A	2: 130,975,954	D809E	probably damaging	Het
BC037034	T	A	5: 138,261,622	T391S	probably damaging	Het
Ccdc70	G	A	8: 21,973,250	V19M	possibly damaging	Het
Ccp110	G	T	7: 118,730,012	E73*	probably null	Het
Cfap57	A	C	4: 118,595,848	S553A	probably benign	Het
Cftr	A	G	6: 18,221,614	K212E	probably benign	Het
Chkb	A	T	15: 89,428,165	Y216N	probably damaging	Het
Cntnap2	G	T	6: 45,920,834	D149Y	probably damaging	Het
Cpd	A	G	11: 76,846,222		probably null	Het
Creb3l1	C	T	2: 91,983,226	D489N	probably benign	Het
Crhbp	A	G	13: 95,442,245	F123L	probably damaging	Het
Cryab	T	C	9: 50,754,609	V100A	possibly damaging	Het
Csmd2	T	C	4: 128,521,930	I2684T	probably benign	Het
Ctbp2	G	T	7: 133,014,649	P186T	possibly damaging	Het
Ctnna2	T	C	6: 76,915,762	N814S	possibly damaging	Het
Dntt	T	C	19: 41,039,856	V197A	probably damaging	Het
Fam135a	G	A	1: 24,020,677	A1187V	possibly damaging	Het
Filip1l	A	T	16: 57,570,415	Q455H	probably benign	Het
Grm2	T	C	9: 106,653,990	E100G	probably damaging	Het
Gtf2ird2	G	A	5: 134,217,464	V855M	probably damaging	Het
Heatr9	A	T	11: 83,518,792	I118N	possibly damaging	Het
Htra3	T	C	5: 35,671,125	H137R	probably benign	Het
Iars	A	G	13: 49,709,661	S530G	probably damaging	Het
Klhdc4	T	A	8: 121,796,603	M510L	probably benign	Het
Lipc	T	C	9: 70,816,731	T204A	probably benign	Het
Lrp1	A	G	10: 127,553,779	V3129A	probably damaging	Het
Macf1	G	A	4: 123,494,909	T1120I	probably benign	Het
Map4	T	C	9: 110,038,377		probably benign	Het
Mbtps1	A	T	8: 119,533,348	V420D	probably damaging	Het
Mta2	G	T	19: 8,950,383	D523Y	probably benign	Het
Muc4	A	G	16: 32,756,296		probably benign	Het
Mug1	C	T	6: 121,878,943	Q965*	probably null	Het
Myo1e	T	A	9: 70,353,312	I584N	probably damaging	Het
Nolc1	T	C	19: 46,078,920	V80A	probably damaging	Het
Nop56	G	T	2: 130,275,725	V91L	probably benign	Het
Olfr1451	A	T	19: 12,999,219	M78L	probably benign	Het
Olfr191	A	T	16: 59,086,402	L27Q	probably damaging	Het
Olfr523	T	C	7: 140,177,020	V300A	probably damaging	Het
Osbpl3	T	C	6: 50,336,297	E107G	probably damaging	Het
Pde3a	T	A	6: 141,250,025	C146S	probably benign	Het
Pfkm	A	G	15: 98,128,242	M573V	probably damaging	Het
Pkd1l2	C	T	8: 117,047,374		probably null	Het
Plekhg3	T	C	12: 76,565,247	I374T	possibly damaging	Het
Ppig	T	A	2: 69,741,486	V183D	unknown	Het
Prom1	T	G	5: 44,037,534	I290L	probably benign	Het
Rufy3	T	A	5: 88,637,226	M387K	probably damaging	Het
Selenoo	G	A	15: 89,094,184	R270H	probably damaging	Het
Sema6c	C	T	3: 95,168,363	T175I	probably damaging	Het
Serpina3k	T	C	12: 104,341,046	I179T	probably damaging	Het
Sf3b3	T	C	8: 110,841,203	T207A	probably benign	Het
Slc22a26	C	A	19: 7,802,181	R90L	probably damaging	Het
Slitrk5	T	C	14: 111,680,216	V424A	probably damaging	Het
Smarca2	G	T	19: 26,720,855	E89*	probably null	Het
Soga1	C	T	2: 157,022,856	G1144D	probably benign	Het
Stab2	T	A	10: 86,937,909	S853C	probably damaging	Het
Stk17b	A	T	1: 53,761,147		probably null	Het
Taar5	T	A	10: 23,971,547	I281N	possibly damaging	Het
Tarsl2	A	T	7: 65,658,935	E284D	probably damaging	Het
Tbx15	C	A	3: 99,316,333	T279K	probably damaging	Het
Tfr2	G	A	5: 137,586,925	V740I	probably benign	Het
Tlr12	T	C	4: 128,617,680	E259G	probably benign	Het
Tmem145	A	G	7: 25,309,034	T302A	probably benign	Het
Tmem57	A	G	4: 134,828,133	I343T	probably benign	Het
Trpa1	G	T	1: 14,875,861	H1015Q	probably benign	Het
Tspan8	A	G	10: 115,817,629	Y10C	possibly damaging	Het
Ttll7	A	G	3: 146,894,469	N44S	probably damaging	Het
Uba7	T	C	9: 107,979,839		probably null	Het
Ube2j2	G	A	4: 155,946,384	M1I	probably null	Het
Ubr5	C	A	15: 38,009,668	A1022S	probably benign	Het
Usf1	T	G	1: 171,415,763	I36S	probably damaging	Het
Vmn1r181	A	T	7: 23,984,365	D85V	probably damaging	Het
Vmn1r3	A	T	4: 3,185,009	Y99*	probably null	Het
Vmn1r72	T	C	7: 11,670,373	I49M	possibly damaging	Het
Vmn2r99	A	G	17: 19,362,135	M1V	probably null	Het
Vsig10	T	A	5: 117,343,975	V410E	probably damaging	Het
Zc3h7b	A	G	15: 81,779,133	Y442C	probably damaging	Het
Zfyve26	G	T	12: 79,280,385	Y730*	probably null	Het

Other mutations in Sema3d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00559:Sema3d	APN	5	12563222	missense	probably benign	0.01
IGL00582:Sema3d	APN	5	12585195	missense	probably damaging	1.00
IGL00661:Sema3d	APN	5	12505839	missense	probably damaging	1.00
IGL00780:Sema3d	APN	5	12524326	missense	probably damaging	1.00
IGL01531:Sema3d	APN	5	12541080	missense	probably benign
IGL01957:Sema3d	APN	5	12563315	missense	probably damaging	1.00
IGL02100:Sema3d	APN	5	12584991	missense	probably benign	0.29
IGL02676:Sema3d	APN	5	12570978	missense	probably benign	0.38
IGL02749:Sema3d	APN	5	12563145	splice site	probably benign
IGL02827:Sema3d	APN	5	12585118	missense	probably benign	0.04
IGL03325:Sema3d	APN	5	12463222	missense	probably damaging	0.99
R0050:Sema3d	UTSW	5	12584953	missense	probably benign	0.00
R0085:Sema3d	UTSW	5	12570986	missense	probably benign	0.00
R0095:Sema3d	UTSW	5	12563347	missense	probably damaging	1.00
R0157:Sema3d	UTSW	5	12508137	missense	possibly damaging	0.95
R0328:Sema3d	UTSW	5	12448075	missense	possibly damaging	0.48
R0924:Sema3d	UTSW	5	12463216	missense	possibly damaging	0.69
R0930:Sema3d	UTSW	5	12463216	missense	possibly damaging	0.69
R1609:Sema3d	UTSW	5	12541056	missense	probably damaging	1.00
R1657:Sema3d	UTSW	5	12584974	missense	possibly damaging	0.82
R1669:Sema3d	UTSW	5	12508084	splice site	probably benign
R1795:Sema3d	UTSW	5	12584887	missense	probably benign	0.02
R1861:Sema3d	UTSW	5	12497603	missense	probably benign	0.00
R1889:Sema3d	UTSW	5	12485021	splice site	probably null
R1895:Sema3d	UTSW	5	12573843	missense	probably damaging	1.00
R1946:Sema3d	UTSW	5	12573843	missense	probably damaging	1.00
R1975:Sema3d	UTSW	5	12563318	missense	probably damaging	1.00
R1975:Sema3d	UTSW	5	12584998	missense	probably benign
R2117:Sema3d	UTSW	5	12563273	missense	probably benign
R2148:Sema3d	UTSW	5	12484959	missense	probably damaging	0.99
R2276:Sema3d	UTSW	5	12542582	missense	possibly damaging	0.63
R3761:Sema3d	UTSW	5	12571037	missense	probably damaging	1.00
R4063:Sema3d	UTSW	5	12585124	missense	probably benign	0.25
R4428:Sema3d	UTSW	5	12448120	missense	probably benign	0.32
R4903:Sema3d	UTSW	5	12563158	missense	probably benign	0.00
R5000:Sema3d	UTSW	5	12448038	missense	probably benign	0.01
R5022:Sema3d	UTSW	5	12584956	missense	probably damaging	1.00
R5186:Sema3d	UTSW	5	12584908	missense	probably benign
R5584:Sema3d	UTSW	5	12566008	missense	possibly damaging	0.49
R5584:Sema3d	UTSW	5	12570987	missense	possibly damaging	0.73
R6270:Sema3d	UTSW	5	12448107	missense	probably benign
R6368:Sema3d	UTSW	5	12571013	missense	probably damaging	1.00
R6426:Sema3d	UTSW	5	12563264	missense	probably damaging	1.00
R6750:Sema3d	UTSW	5	12585100	nonsense	probably null
R7403:Sema3d	UTSW	5	12497584	missense	probably damaging	0.97
R7450:Sema3d	UTSW	5	12584934	nonsense	probably null
R7470:Sema3d	UTSW	5	12508185	missense	probably damaging	1.00
R7548:Sema3d	UTSW	5	12577816	missense	unknown
R7593:Sema3d	UTSW	5	12508145	missense	probably benign	0.02
R7683:Sema3d	UTSW	5	12573856	nonsense	probably null
R8155:Sema3d	UTSW	5	12448181	critical splice donor site	probably null
R8442:Sema3d	UTSW	5	12542641	missense	probably damaging	0.99
Z1176:Sema3d	UTSW	5	12585059	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- AGCAAATACGGATTTCACTATCCAG -3'
(R):5'- TGGTGCACTAAAACAACTCTCATC -3'

Sequencing Primer
(F):5'- GGATTTCACTATCCAGCTTTTTAGG -3'
(R):5'- CAACACATTTGGATGCATAGTAATG -3'

Posted On

2016-06-06