Mutagenetix > Incidental Mutation

Incidental Mutation 'R5022:Sema3d'

389236

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

042613-MU

Accession Numbers

Essential gene?

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

Stock #

R5022 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

12433352-12638915 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 12634923 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Serine at position 663 (Y663S)

Ref Sequence

ENSEMBL: ENSMUSP00000030868 (fasta)

Gene Model

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

AlphaFold

Q8BH34

Predicted Effect

probably damaging
Transcript: ENSMUST00000030868
AA Change: Y663S

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: Y663S

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: ENSMUST00000195923

Meta Mutation Damage Score

0.9554

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.4%
20x: 92.6%

Validation Efficiency

99% (110/111)

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: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca1	TCGACTGC	T	4: 53,041,570 (GRCm39)		probably null	Het
Abca15	T	C	7: 119,945,319 (GRCm39)	I465T	probably damaging	Het
Abca3	C	T	17: 24,593,274 (GRCm39)	R224C	probably damaging	Het
Abcb4	T	A	5: 8,959,054 (GRCm39)		probably null	Het
Acan	T	C	7: 78,742,556 (GRCm39)		probably null	Het
Aebp2	G	A	6: 140,583,456 (GRCm39)	R109Q	possibly damaging	Het
Agfg2	A	T	5: 137,658,422 (GRCm39)		probably null	Het
Ankib1	T	A	5: 3,784,011 (GRCm39)	I322F	possibly damaging	Het
AW551984	A	T	9: 39,509,261 (GRCm39)	N293K	probably benign	Het
BC028528	T	A	3: 95,796,135 (GRCm39)		probably benign	Het
Bicc1	A	G	10: 70,783,713 (GRCm39)	S393P	possibly damaging	Het
Birc6	A	G	17: 74,999,327 (GRCm39)	Y4656C	probably damaging	Het
Bmp3	A	G	5: 99,020,683 (GRCm39)	R369G	probably damaging	Het
C1d	T	A	11: 17,216,674 (GRCm39)	N135K	probably benign	Het
Ccdc148	G	A	2: 58,717,644 (GRCm39)	A453V	probably damaging	Het
Cd163	C	T	6: 124,302,247 (GRCm39)	T937I	probably damaging	Het
Celf2	C	T	2: 6,612,658 (GRCm39)		probably benign	Het
Chga	T	C	12: 102,529,096 (GRCm39)	W358R	probably damaging	Het
Clec4b2	A	T	6: 123,177,915 (GRCm39)	S77C	probably null	Het
Crim1	T	C	17: 78,587,558 (GRCm39)	V221A	possibly damaging	Het
D630003M21Rik	A	T	2: 158,059,553 (GRCm39)	S116T	probably damaging	Het
Dlg5	T	C	14: 24,186,690 (GRCm39)	E1847G	probably damaging	Het
Dmxl1	T	A	18: 50,028,194 (GRCm39)	I2206K	probably damaging	Het
Dusp7	T	A	9: 106,250,940 (GRCm39)	L355Q	probably damaging	Het
Eif1ad15	T	C	12: 88,288,071 (GRCm39)	I61V	probably benign	Het
Eif1ad16	A	T	12: 87,985,481 (GRCm39)	S21T	unknown	Het
Exd2	T	A	12: 80,543,564 (GRCm39)	N582K	probably damaging	Het
Fbln1	G	A	15: 85,121,827 (GRCm39)	S316N	probably damaging	Het
Fchsd1	A	G	18: 38,097,863 (GRCm39)	I340T	possibly damaging	Het
Fn1	T	C	1: 71,663,338 (GRCm39)	Y1050C	probably damaging	Het
Fsip2	A	G	2: 82,809,773 (GRCm39)	I2031V	probably benign	Het
Gm10803	A	C	2: 93,394,517 (GRCm39)	L96F	probably damaging	Het
Gm14569	T	C	X: 35,694,470 (GRCm39)	D1413G	probably benign	Het
Gm15455	T	C	1: 33,876,432 (GRCm39)		noncoding transcript	Het
Gm1818	G	C	12: 48,602,318 (GRCm39)		noncoding transcript	Het
Gm5420	A	T	10: 21,567,626 (GRCm39)		noncoding transcript	Het
Gm7104	A	T	12: 88,252,529 (GRCm39)		noncoding transcript	Het
Gp2	A	G	7: 119,048,337 (GRCm39)	I427T	probably damaging	Het
Gpc4	G	A	X: 51,163,440 (GRCm39)	R148C	probably damaging	Het
Gpr142	A	C	11: 114,695,214 (GRCm39)	S60R	probably benign	Het
Helz2	T	C	2: 180,882,362 (GRCm39)	R144G	probably benign	Het
Herc1	A	T	9: 66,377,608 (GRCm39)	K3458M	possibly damaging	Het
Hnf4g	G	T	3: 3,709,647 (GRCm39)	A144S	probably damaging	Het
Irs2	A	C	8: 11,037,012 (GRCm39)	*1322G	probably null	Het
Keg1	A	G	19: 12,696,521 (GRCm39)	N288S	probably damaging	Het
Kif19a	G	A	11: 114,658,053 (GRCm39)	M37I	probably benign	Het
Klhl1	G	A	14: 96,374,142 (GRCm39)	P635S	probably benign	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Lsm11	T	C	11: 45,835,666 (GRCm39)	D25G	probably damaging	Het
Manea	A	T	4: 26,336,630 (GRCm39)	Y215*	probably null	Het
Mdga2	C	T	12: 66,517,534 (GRCm39)	C100Y	possibly damaging	Het
Mthfd1	T	A	12: 76,348,102 (GRCm39)	M582K	probably damaging	Het
Mthfd1	T	G	12: 76,341,148 (GRCm39)	V480G	probably damaging	Het
Myh7b	G	C	2: 155,474,293 (GRCm39)	R1669S	possibly damaging	Het
Nanos1	T	C	19: 60,745,418 (GRCm39)	Y239H	probably damaging	Het
Nat8	G	A	6: 85,807,839 (GRCm39)	T98I	possibly damaging	Het
Ndufs3	C	A	2: 90,729,004 (GRCm39)	A161S	probably benign	Het
Nexmif	A	T	X: 103,130,956 (GRCm39)	N320K	probably damaging	Het
Or10h1	T	C	17: 33,418,751 (GRCm39)	F239S	probably damaging	Het
Or2m12	A	T	16: 19,104,809 (GRCm39)	V228D	probably damaging	Het
Or2r3	A	T	6: 42,448,221 (GRCm39)	V297E	possibly damaging	Het
Or4c111	A	G	2: 88,844,387 (GRCm39)	V7A	probably damaging	Het
Or4c122	C	T	2: 89,079,761 (GRCm39)	M92I	probably benign	Het
Or4k15	T	C	14: 50,364,469 (GRCm39)	V145A	possibly damaging	Het
Or52e2	G	A	7: 102,804,942 (GRCm39)	P4L	probably benign	Het
Or6c69c	T	C	10: 129,910,462 (GRCm39)	L61P	probably damaging	Het
Pcdhb14	T	A	18: 37,583,223 (GRCm39)	N776K	probably benign	Het
Pip5k1c	G	A	10: 81,146,723 (GRCm39)		probably null	Het
Plk4	G	A	3: 40,756,512 (GRCm39)		probably null	Het
Prmt8	A	G	6: 127,688,126 (GRCm39)	Y231H	possibly damaging	Het
Prpf4b	T	C	13: 35,067,582 (GRCm39)		probably benign	Het
Ptpn21	G	A	12: 98,645,666 (GRCm39)	R1091C	probably damaging	Het
Pwwp2b	C	T	7: 138,835,494 (GRCm39)	P312S	possibly damaging	Het
Rad21	A	T	15: 51,830,102 (GRCm39)	I503K	probably benign	Het
Rai14	A	G	15: 10,574,592 (GRCm39)	S789P	probably damaging	Het
Rbm26	C	T	14: 105,381,688 (GRCm39)	D486N	probably damaging	Het
Rnf20	A	G	4: 49,642,016 (GRCm39)		probably benign	Het
Ros1	A	G	10: 52,000,171 (GRCm39)	V1118A	possibly damaging	Het
Serpina6	A	G	12: 103,617,971 (GRCm39)	W281R	probably damaging	Het
Slc8a3	A	G	12: 81,246,332 (GRCm39)	V900A	probably damaging	Het
Spats2l	G	T	1: 57,918,715 (GRCm39)	V30L	probably damaging	Het
Spg21	A	G	9: 65,383,231 (GRCm39)	D139G	probably damaging	Het
Sun3	T	C	11: 8,988,314 (GRCm39)	T3A	probably damaging	Het
Tep1	A	G	14: 51,066,456 (GRCm39)	Y2335H	probably benign	Het
Tesl1	G	A	X: 23,773,480 (GRCm39)	G327E	probably damaging	Het
Timd5	T	A	11: 46,419,359 (GRCm39)	D58E	probably damaging	Het
Timm21	C	A	18: 84,967,539 (GRCm39)	V112L	possibly damaging	Het
Tlk1	A	T	2: 70,572,409 (GRCm39)	N386K	probably benign	Het
Trappc10	G	T	10: 78,052,994 (GRCm39)	F260L	possibly damaging	Het
Trgv1	T	A	13: 19,524,401 (GRCm39)	S42T	probably benign	Het
Trmt112	T	C	19: 6,888,121 (GRCm39)	V91A	probably benign	Het
Ucp2	A	T	7: 100,147,579 (GRCm39)	N186I	possibly damaging	Het
Vmn1r119	A	G	7: 20,746,245 (GRCm39)	S46P	probably benign	Het
Vmn2r101	A	T	17: 19,831,649 (GRCm39)		probably null	Het
Vmn2r105	T	A	17: 20,428,676 (GRCm39)	H800L	probably damaging	Het
Vmn2r69	T	C	7: 85,060,367 (GRCm39)	M406V	possibly damaging	Het
Vmn2r84	A	G	10: 130,222,417 (GRCm39)	L601P	probably damaging	Het
Vps16	A	G	2: 130,281,372 (GRCm39)	S235G	probably benign	Het
Wap	T	C	11: 6,587,339 (GRCm39)		probably benign	Het
Wdr11	A	G	7: 129,226,435 (GRCm39)	I744M	probably benign	Het
Xiap	T	C	X: 41,183,342 (GRCm39)	F23L	probably benign	Het
Xkr7	A	G	2: 152,896,300 (GRCm39)	T385A	probably benign	Het
Zfp524	A	T	7: 5,021,416 (GRCm39)	I315F	probably benign	Het
Zfp62	T	A	11: 49,106,556 (GRCm39)	S216T	probably damaging	Het
Znfx1	T	C	2: 166,881,746 (GRCm39)	Y217C	probably damaging	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
R1669:Sema3d	UTSW	5	12,558,051 (GRCm39)	splice site	probably benign
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
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'- AACCATCTTCAACTATGGCTGACAATG -3'
(R):5'- CTGAAGTTCGGGCTGCTAAG -3'

Sequencing Primer
(F):5'- GGCTGACAATGTTATAGTTGATGAC -3'
(R):5'- AAGTTCGGGCTGCTAAGGATTTG -3'

Posted On

2016-06-06