Mutagenetix > Incidental Mutation

Incidental Mutation 'R1895:Sema3d'

209725

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

039915-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.188) question?

Stock #

R1895 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

12433352-12638915 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 12623810 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Arginine at position 573 (Q573R)

Ref Sequence

ENSEMBL: ENSMUSP00000142453 (fasta)

Gene Model

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

AlphaFold

Q8BH34

Predicted Effect

probably damaging
Transcript: ENSMUST00000030868
AA Change: Q573R

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: Q573R

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000197927
AA Change: Q573R

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: Q573R

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

Meta Mutation Damage Score

0.4223

Coding Region Coverage

1x: 97.1%
3x: 96.2%
10x: 93.2%
20x: 86.6%

Validation Efficiency

96% (100/104)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aasdh	A	G	5: 77,039,551 (GRCm39)	S253P	probably damaging	Het
Adgrb1	A	G	15: 74,412,314 (GRCm39)	D431G	probably damaging	Het
Adgrv1	C	T	13: 81,522,368 (GRCm39)	C5923Y	probably damaging	Het
Akr1b10	T	A	6: 34,365,805 (GRCm39)	I110N	probably damaging	Het
Apba2	T	C	7: 64,394,378 (GRCm39)		probably null	Het
Arhgef12	G	T	9: 42,917,152 (GRCm39)	Q396K	probably damaging	Het
Arpc1b	A	G	5: 145,059,443 (GRCm39)	T56A	probably null	Het
Atoh1	T	C	6: 64,706,443 (GRCm39)	V46A	probably benign	Het
AU015836	T	C	X: 93,012,985 (GRCm39)		probably benign	Het
Cacna1c	C	T	6: 118,589,586 (GRCm39)	R1446H	probably damaging	Het
Capn13	T	C	17: 73,657,520 (GRCm39)	E240G	possibly damaging	Het
Cdh8	T	C	8: 100,006,189 (GRCm39)	T133A	possibly damaging	Het
Cep295	T	C	9: 15,243,399 (GRCm39)	T1686A	possibly damaging	Het
Col4a3	A	T	1: 82,656,829 (GRCm39)	K749N	unknown	Het
Col6a3	T	A	1: 90,731,433 (GRCm39)	M1000L	probably benign	Het
Coq8b	G	A	7: 26,939,299 (GRCm39)	V150I	possibly damaging	Het
Dmxl1	G	T	18: 50,088,981 (GRCm39)		probably null	Het
Dnah10	A	G	5: 124,835,494 (GRCm39)	D990G	probably benign	Het
Dpp7	G	T	2: 25,243,691 (GRCm39)		probably null	Het
Eif3l	A	G	15: 78,973,677 (GRCm39)	N364S	possibly damaging	Het
Epb41l5	T	C	1: 119,476,902 (GRCm39)	D718G	possibly damaging	Het
F930017D23Rik	G	A	10: 43,469,440 (GRCm39)		noncoding transcript	Het
Fam20a	T	C	11: 109,564,380 (GRCm39)	K458E	probably benign	Het
Fbxo44	C	G	4: 148,240,726 (GRCm39)	R220S	probably damaging	Het
Fut2	A	G	7: 45,300,748 (GRCm39)	F8S	probably damaging	Het
Gad2	A	T	2: 22,575,440 (GRCm39)	T515S	probably benign	Het
Glmn	T	C	5: 107,718,110 (GRCm39)	D269G	probably benign	Het
Gpatch4	A	G	3: 87,959,409 (GRCm39)	Y106C	probably damaging	Het
Grm3	A	G	5: 9,562,123 (GRCm39)	W576R	probably damaging	Het
Hdac7	T	C	15: 97,694,767 (GRCm39)	D701G	probably damaging	Het
Hectd2	T	A	19: 36,591,860 (GRCm39)	I687K	probably damaging	Het
Hmcn2	T	C	2: 31,295,647 (GRCm39)	S2619P	probably damaging	Het
Ilf3	T	A	9: 21,316,063 (GRCm39)		probably benign	Het
Kdm4b	T	A	17: 56,704,340 (GRCm39)	V272E	probably damaging	Het
Kera	A	G	10: 97,445,009 (GRCm39)	K123E	probably benign	Het
Kif11	G	A	19: 37,375,847 (GRCm39)	R220K	probably damaging	Het
Kmt2c	A	T	5: 25,520,152 (GRCm39)	V1986E	probably benign	Het
Lrp11	T	C	10: 7,499,540 (GRCm39)	Y244H	probably damaging	Het
Lrp1b	T	A	2: 40,555,159 (GRCm39)	D320V	unknown	Het
Map4k5	A	T	12: 69,892,529 (GRCm39)	D133E	probably damaging	Het
Megf11	A	T	9: 64,586,558 (GRCm39)	D461V	probably damaging	Het
Muc5b	A	C	7: 141,411,382 (GRCm39)	T1443P	unknown	Het
Mxi1	G	A	19: 53,358,775 (GRCm39)	R236H	probably benign	Het
Nav1	A	T	1: 135,386,396 (GRCm39)	W1211R	probably damaging	Het
Ncoa3	T	A	2: 165,901,097 (GRCm39)	N896K	possibly damaging	Het
Nmt2	T	A	2: 3,323,672 (GRCm39)	I355N	probably benign	Het
Nxpe5	T	C	5: 138,249,785 (GRCm39)	V525A	probably damaging	Het
Oas1f	A	T	5: 120,993,648 (GRCm39)	T287S	probably benign	Het
Or1n1b	A	T	2: 36,780,458 (GRCm39)	M134K	possibly damaging	Het
Or5ae1	T	C	7: 84,565,487 (GRCm39)	S167P	probably benign	Het
Or6ae1	T	A	7: 139,742,726 (GRCm39)	I46F	possibly damaging	Het
Or7a38	T	A	10: 78,752,758 (GRCm39)	I28N	probably damaging	Het
Or8b3	T	A	9: 38,314,182 (GRCm39)	M1K	probably null	Het
Pakap	T	C	4: 57,638,068 (GRCm39)	V35A	probably benign	Het
Panx1	A	G	9: 14,918,822 (GRCm39)	C346R	probably benign	Het
Plekha7	T	C	7: 115,744,209 (GRCm39)	E764G	probably damaging	Het
Plet1	A	G	9: 50,415,652 (GRCm39)		probably null	Het
Plod2	A	G	9: 92,489,188 (GRCm39)	S707G	probably damaging	Het
Plscr4	G	A	9: 92,365,889 (GRCm39)	V120I	probably damaging	Het
Pramel31	T	A	4: 144,088,435 (GRCm39)	V77E	probably benign	Het
Prob1	T	A	18: 35,785,942 (GRCm39)	T771S	possibly damaging	Het
Rasa3	A	G	8: 13,681,768 (GRCm39)		probably benign	Het
Ror2	T	C	13: 53,285,885 (GRCm39)	I110V	probably damaging	Het
Sec24d	A	T	3: 123,147,043 (GRCm39)	H667L	probably benign	Het
Serpinb2	T	A	1: 107,452,337 (GRCm39)	V305D	probably damaging	Het
Slc11a2	G	A	15: 100,301,775 (GRCm39)	R249C	probably benign	Het
Slc14a1	T	C	18: 78,152,912 (GRCm39)	I276V	possibly damaging	Het
Snx19	T	A	9: 30,343,620 (GRCm39)	N593K	probably damaging	Het
Ssh2	C	G	11: 77,340,571 (GRCm39)	D574E	probably damaging	Het
Stil	T	C	4: 114,881,072 (GRCm39)	S539P	probably benign	Het
Syt4	T	C	18: 31,577,141 (GRCm39)	K71R	probably damaging	Het
Tenm4	A	T	7: 96,385,015 (GRCm39)	H524L	probably damaging	Het
Tex30	C	T	1: 44,130,564 (GRCm39)	G68D	probably damaging	Het
Tm4sf19	A	G	16: 32,226,500 (GRCm39)	Y138C	probably damaging	Het
Tmem43	A	T	6: 91,463,891 (GRCm39)	I389F	probably benign	Het
Trpm1	A	T	7: 63,873,556 (GRCm39)	N488Y	probably damaging	Het
Tshz1	A	T	18: 84,031,558 (GRCm39)	L950Q	probably damaging	Het
Vmn1r16	T	C	6: 57,299,885 (GRCm39)	I246V	probably benign	Het
Vmn1r188	T	G	13: 22,272,815 (GRCm39)	S256R	possibly damaging	Het
Zfp12	G	A	5: 143,231,133 (GRCm39)	E487K	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
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'- TCTGATCATCTTAATGCAAGACAGG -3'
(R):5'- CCTGTTACTTTTCTAGAACATACGC -3'

Sequencing Primer
(F):5'- TCATCTTAATGCAAGACAGGATTTG -3'
(R):5'- AGAACATACGCATTATACAGAATGAG -3'

Posted On

2014-06-30