Mutagenetix > Incidental Mutation

Incidental Mutation 'R1861:Sema3d'

203896

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

039884-MU

Accession Numbers

Essential gene?

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

Stock #

R1861 (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 12547570 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Arginine at position 164 (K164R)

Ref Sequence

ENSEMBL: ENSMUSP00000142453 (fasta)

Gene Model

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

AlphaFold

Q8BH34

Predicted Effect

probably benign
Transcript: ENSMUST00000030868
AA Change: K164R

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: K164R

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
AA Change: K164R

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: K164R

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

0.0610

Coding Region Coverage

1x: 97.4%
3x: 96.9%
10x: 95.2%
20x: 92.0%

Validation Efficiency

97% (117/121)

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: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930579C12Rik	C	A	9: 89,034,884 (GRCm39)		noncoding transcript	Het
Abra	C	A	15: 41,732,430 (GRCm39)	R212L	probably damaging	Het
Actr1a	T	C	19: 46,372,714 (GRCm39)	E87G	probably damaging	Het
Adam26a	A	G	8: 44,022,578 (GRCm39)	V304A	possibly damaging	Het
Alg2	T	A	4: 47,471,670 (GRCm39)	K379N	probably benign	Het
Alk	G	T	17: 72,181,933 (GRCm39)		probably benign	Het
Aopep	A	G	13: 63,163,597 (GRCm39)	Y206C	probably damaging	Het
Arhgef17	A	G	7: 100,531,475 (GRCm39)	Y331H	probably damaging	Het
Art3	A	G	5: 92,560,094 (GRCm39)		probably benign	Het
Asap1	G	A	15: 64,007,647 (GRCm39)		probably benign	Het
Atad2	A	T	15: 57,960,114 (GRCm39)		probably null	Het
Atp8b5	G	A	4: 43,372,906 (GRCm39)	R1150H	probably damaging	Het
Bltp2	C	T	11: 78,178,755 (GRCm39)		probably benign	Het
Brdt	T	C	5: 107,507,324 (GRCm39)	S575P	probably benign	Het
Capn3	T	A	2: 120,316,963 (GRCm39)		probably benign	Het
Casd1	T	A	6: 4,640,951 (GRCm39)	Y691N	probably damaging	Het
Ccdc127	T	G	13: 74,505,098 (GRCm39)	H215Q	possibly damaging	Het
Cenpe	T	C	3: 134,974,740 (GRCm39)	L2300P	probably damaging	Het
Clasp1	T	C	1: 118,498,661 (GRCm39)	F898L	possibly damaging	Het
Clcn1	C	A	6: 42,290,925 (GRCm39)	P933Q	possibly damaging	Het
Cntn3	T	A	6: 102,222,032 (GRCm39)	N489I	probably benign	Het
Col16a1	T	C	4: 129,955,517 (GRCm39)		probably benign	Het
Col24a1	G	A	3: 145,243,022 (GRCm39)		probably null	Het
Col8a2	C	T	4: 126,205,417 (GRCm39)		probably benign	Het
Cpd	T	C	11: 76,675,208 (GRCm39)		probably benign	Het
Csmd3	A	T	15: 47,522,588 (GRCm39)	C2694S	probably damaging	Het
Cyp2c40	T	C	19: 39,775,319 (GRCm39)	Y311C	probably benign	Het
Dennd5b	T	A	6: 148,969,760 (GRCm39)	N231I	probably damaging	Het
Dgkh	T	A	14: 78,816,232 (GRCm39)	H936L	probably benign	Het
Dmtf1	T	C	5: 9,170,347 (GRCm39)		probably null	Het
Dnai2	T	C	11: 114,643,777 (GRCm39)	V481A	possibly damaging	Het
Dnai3	T	C	3: 145,788,801 (GRCm39)	Y260C	probably damaging	Het
Dpyd	T	G	3: 118,710,780 (GRCm39)	V396G	probably damaging	Het
Elmo3	A	G	8: 106,035,213 (GRCm39)	D448G	probably damaging	Het
Emsy	A	T	7: 98,290,822 (GRCm39)	V100E	probably damaging	Het
Erbb2	T	C	11: 98,303,563 (GRCm39)		probably null	Het
Faah	T	C	4: 115,865,432 (GRCm39)	K85R	probably benign	Het
Fam149a	A	T	8: 45,792,399 (GRCm39)	Y686*	probably null	Het
Fat4	T	C	3: 39,064,633 (GRCm39)	V4863A	probably benign	Het
Fbxl8	A	G	8: 105,995,561 (GRCm39)	T358A	probably damaging	Het
Fcgbpl1	A	G	7: 27,854,157 (GRCm39)	Y1707C	probably damaging	Het
Fgfr3	A	G	5: 33,887,090 (GRCm39)	T165A	probably damaging	Het
Fnbp1l	A	T	3: 122,354,581 (GRCm39)	H180Q	probably damaging	Het
Gm8180	T	A	14: 44,021,196 (GRCm39)	H4L	probably benign	Het
Gon4l	T	C	3: 88,802,794 (GRCm39)	V1135A	probably damaging	Het
Gstcd	G	T	3: 132,688,868 (GRCm39)	N627K	probably damaging	Het
Gtf2a1l	G	A	17: 89,022,382 (GRCm39)	V458I	probably damaging	Het
Gtf3c3	T	C	1: 54,477,997 (GRCm39)	E26G	possibly damaging	Het
Hrct1	A	T	4: 43,727,404 (GRCm39)	T15S	probably benign	Het
Ift122	C	A	6: 115,868,889 (GRCm39)	R459S	probably damaging	Het
Irf1	T	A	11: 53,665,183 (GRCm39)	C187S	possibly damaging	Het
Kcnh7	A	G	2: 62,607,736 (GRCm39)	V615A	probably damaging	Het
Kif1c	T	C	11: 70,594,168 (GRCm39)	S61P	probably damaging	Het
Mamdc2	T	C	19: 23,336,517 (GRCm39)	T331A	probably damaging	Het
Mark2	T	C	19: 7,268,128 (GRCm39)	D25G	possibly damaging	Het
Me2	T	C	18: 73,918,785 (GRCm39)	D432G	probably benign	Het
Mfap3	T	C	11: 57,419,032 (GRCm39)	V64A	probably benign	Het
Nadk2	T	A	15: 9,108,399 (GRCm39)	M416K	probably benign	Het
Ndufs1	C	T	1: 63,186,576 (GRCm39)	G631D	probably benign	Het
Nomo1	G	A	7: 45,727,525 (GRCm39)	V1055I	probably benign	Het
Nuggc	T	A	14: 65,879,450 (GRCm39)		probably benign	Het
Nwd2	T	C	5: 63,962,197 (GRCm39)	S594P	probably damaging	Het
Or13c3	T	A	4: 52,856,373 (GRCm39)	I47L	probably benign	Het
Or4a27	T	G	2: 88,559,674 (GRCm39)	I90L	probably damaging	Het
Or4b1b	C	A	2: 90,112,502 (GRCm39)	C139F	probably damaging	Het
Or5b113	T	A	19: 13,342,705 (GRCm39)	S238T	possibly damaging	Het
Or6p1	T	C	1: 174,258,657 (GRCm39)	I221T	probably damaging	Het
Or8c10	C	T	9: 38,278,902 (GRCm39)	S10L	probably benign	Het
Pakap	A	G	4: 57,709,468 (GRCm39)	I138V	probably damaging	Het
Pcyt2	G	A	11: 120,501,968 (GRCm39)	P332S	probably benign	Het
Phaf1	A	G	8: 105,966,703 (GRCm39)	E150G	probably null	Het
Phf14	A	T	6: 11,987,610 (GRCm39)	M630L	probably benign	Het
Piezo1	T	C	8: 123,222,489 (GRCm39)	N919S	possibly damaging	Het
Pif1	A	T	9: 65,496,735 (GRCm39)	I283F	probably damaging	Het
Pknox2	G	A	9: 36,834,957 (GRCm39)	H171Y	probably damaging	Het
Pramel17	A	T	4: 101,694,135 (GRCm39)	D249E	probably benign	Het
Prkg2	T	A	5: 99,095,275 (GRCm39)	D632V	probably damaging	Het
Prr29	G	A	11: 106,266,264 (GRCm39)	A6T	probably damaging	Het
Rims1	T	A	1: 22,635,639 (GRCm39)	Y114F	probably damaging	Het
Ryr1	A	T	7: 28,708,977 (GRCm39)	D4796E	unknown	Het
Scnn1b	G	A	7: 121,513,484 (GRCm39)	C399Y	probably damaging	Het
Scp2	T	C	4: 107,948,518 (GRCm39)	Y153C	probably damaging	Het
Siglecf	A	G	7: 43,001,648 (GRCm39)	T153A	probably benign	Het
Siglecf	A	G	7: 43,004,967 (GRCm39)	N399S	probably benign	Het
Skint2	T	C	4: 112,504,315 (GRCm39)		probably benign	Het
Slc22a8	G	A	19: 8,583,503 (GRCm39)	R236H	probably damaging	Het
Slc25a40	T	A	5: 8,492,431 (GRCm39)		probably null	Het
Slc26a5	T	C	5: 22,021,956 (GRCm39)	D490G	possibly damaging	Het
Slc26a7	G	T	4: 14,522,873 (GRCm39)	D482E	probably benign	Het
Smarca2	A	T	19: 26,601,284 (GRCm39)	M77L	probably benign	Het
Sos2	A	G	12: 69,664,137 (GRCm39)	L449P	probably damaging	Het
Spaca1	A	G	4: 34,044,206 (GRCm39)	V96A	probably damaging	Het
Spata31d1b	T	A	13: 59,865,150 (GRCm39)	I766N	possibly damaging	Het
Specc1l	T	C	10: 75,145,693 (GRCm39)	Y1113H	probably damaging	Het
Speg	A	G	1: 75,365,649 (GRCm39)	R677G	probably damaging	Het
Taf5l	A	T	8: 124,724,729 (GRCm39)	D363E	probably damaging	Het
Tex56	A	T	13: 35,116,490 (GRCm39)	I80F	possibly damaging	Het
Tmem208	A	G	8: 106,061,438 (GRCm39)	K155E	possibly damaging	Het
Tppp2	A	C	14: 52,158,062 (GRCm39)	N169T	probably benign	Het
Trrap	T	A	5: 144,752,727 (GRCm39)		probably null	Het
Ttll6	T	A	11: 96,029,700 (GRCm39)	Y204*	probably null	Het
Ttn	A	T	2: 76,602,992 (GRCm39)	I18410K	probably benign	Het
V1rd19	T	A	7: 23,703,149 (GRCm39)	V205D	probably damaging	Het
Vdac3	A	T	8: 23,070,515 (GRCm39)	I132K	possibly damaging	Het
Vmn2r95	T	G	17: 18,672,530 (GRCm39)	C756G	probably damaging	Het
Zc3h15	A	G	2: 83,494,334 (GRCm39)	T421A	unknown	Het
Zc3hc1	T	C	6: 30,374,837 (GRCm39)	T235A	probably benign	Het
Zcchc14	A	G	8: 122,335,990 (GRCm39)		probably benign	Het
Zfp318	T	A	17: 46,722,366 (GRCm39)	N1456K	possibly damaging	Het
Zfp606	A	G	7: 12,214,858 (GRCm39)		probably benign	Het
Zfp811	T	A	17: 33,016,399 (GRCm39)	H546L	probably damaging	Het
Zfp94	A	T	7: 24,008,541 (GRCm39)	Y33N	probably damaging	Het
Zfyve9	G	T	4: 108,539,492 (GRCm39)		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
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
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'- AATCACCCCTTTAACCACTGTG -3'
(R):5'- ATGAGTGAGTGTCTACATAGAGTC -3'

Sequencing Primer
(F):5'- CGTGCTTTTTAAGTCAAGTGTTC -3'
(R):5'- TGAGTGTCTACATAGAGTCAAGAAAC -3'

Posted On

2014-06-23