Mutagenetix > Incidental Mutation

Incidental Mutation 'R1795:Sema3d'

202117

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

039825-MU

Accession Numbers

Essential gene?

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

Stock #

R1795 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

12433352-12638915 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 12634854 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 640 (D640G)

Ref Sequence

ENSEMBL: ENSMUSP00000030868 (fasta)

Gene Model

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

AlphaFold

Q8BH34

Predicted Effect

probably benign
Transcript: ENSMUST00000030868
AA Change: D640G

PolyPhen 2 Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: D640G

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

Coding Region Coverage

1x: 97.5%
3x: 96.9%
10x: 95.4%
20x: 92.6%

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: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8a	A	G	11: 109,941,792 (GRCm39)	I1159T	probably benign	Het
Abcc1	T	C	16: 14,283,001 (GRCm39)	V1159A	possibly damaging	Het
Abcg5	A	G	17: 84,981,007 (GRCm39)	I194T	probably damaging	Het
Abtb2	A	G	2: 103,397,369 (GRCm39)	T100A	probably benign	Het
Adam4	C	T	12: 81,468,068 (GRCm39)	M184I	probably benign	Het
Afap1l2	T	C	19: 56,916,841 (GRCm39)	D155G	probably damaging	Het
Ahnak	T	C	19: 8,979,802 (GRCm39)	V362A	possibly damaging	Het
Ak7	C	T	12: 105,692,482 (GRCm39)	R179*	probably null	Het
Akap8	C	A	17: 32,534,451 (GRCm39)	G332C	probably damaging	Het
Akr1e1	T	A	13: 4,645,071 (GRCm39)	Q204L	probably damaging	Het
Ankrd12	T	C	17: 66,293,222 (GRCm39)	E737G	possibly damaging	Het
Atrn	A	G	2: 130,814,208 (GRCm39)	D718G	probably benign	Het
Bco2	A	G	9: 50,452,469 (GRCm39)	S200P	possibly damaging	Het
C030005K15Rik	A	T	10: 97,561,648 (GRCm39)	S28T	unknown	Het
Cdc14a	T	A	3: 116,092,122 (GRCm39)	Q356L	possibly damaging	Het
Cdk5rap3	A	G	11: 96,799,654 (GRCm39)	L387P	probably damaging	Het
Celsr1	A	T	15: 85,914,524 (GRCm39)	S1150T	probably damaging	Het
Cntfr	A	G	4: 41,670,841 (GRCm39)		probably null	Het
Cramp1	T	C	17: 25,183,884 (GRCm39)	N1244D	probably damaging	Het
Csmd3	G	T	15: 47,721,316 (GRCm39)	D1542E	possibly damaging	Het
Cyp4f17	A	T	17: 32,736,943 (GRCm39)	I92F	probably benign	Het
Dhx30	A	T	9: 109,937,051 (GRCm39)		probably null	Het
Dlg1	T	A	16: 31,561,965 (GRCm39)	H120Q	probably benign	Het
Dmgdh	A	T	13: 93,843,207 (GRCm39)	M348L	probably benign	Het
Dnmt3b	G	A	2: 153,525,559 (GRCm39)	E741K	possibly damaging	Het
Dock3	T	G	9: 106,902,534 (GRCm39)	H292P	probably damaging	Het
Ercc6	T	A	14: 32,238,985 (GRCm39)	N24K	probably benign	Het
Esco2	T	C	14: 66,064,726 (GRCm39)	Q338R	probably benign	Het
Etl4	T	C	2: 20,812,837 (GRCm39)		probably null	Het
Exoc7	A	T	11: 116,183,347 (GRCm39)	I498N	probably damaging	Het
Fap	G	A	2: 62,378,933 (GRCm39)	S123L	probably damaging	Het
Foxn1	T	C	11: 78,262,051 (GRCm39)	E106G	probably benign	Het
Fscb	T	A	12: 64,521,175 (GRCm39)	D97V	probably damaging	Het
Gabrg1	T	C	5: 70,939,596 (GRCm39)	T174A	possibly damaging	Het
Gan	C	T	8: 117,923,199 (GRCm39)	A461V	possibly damaging	Het
Gbp2	T	A	3: 142,336,284 (GRCm39)	D211E	possibly damaging	Het
Gm10271	A	T	10: 116,792,746 (GRCm39)	Y47N	unknown	Het
Gm17333	G	T	16: 77,649,711 (GRCm39)		noncoding transcript	Het
Gm1758	T	A	16: 14,320,142 (GRCm39)		noncoding transcript	Het
Golga3	A	G	5: 110,355,493 (GRCm39)	K989R	possibly damaging	Het
Gucy2g	C	A	19: 55,187,973 (GRCm39)	V1041F	probably damaging	Het
Guk1	A	T	11: 59,077,639 (GRCm39)	F25I	probably benign	Het
H2al1o	C	T	X: 9,438,329 (GRCm39)	E87K	possibly damaging	Het
Hemgn	C	A	4: 46,395,958 (GRCm39)	C426F	probably damaging	Het
Hps3	A	G	3: 20,066,859 (GRCm39)		probably null	Het
Il2rb	A	T	15: 78,368,187 (GRCm39)	D287E	probably damaging	Het
Ino80	A	T	2: 119,237,340 (GRCm39)	V1123D	probably damaging	Het
Kdm2b	A	G	5: 123,122,523 (GRCm39)		probably null	Het
Kif21a	A	T	15: 90,856,930 (GRCm39)		probably null	Het
Klhl33	A	T	14: 51,129,583 (GRCm39)	N347K	probably damaging	Het
Krt1c	A	G	15: 101,724,861 (GRCm39)	F250L	possibly damaging	Het
Krt82	T	A	15: 101,451,819 (GRCm39)	N332I	possibly damaging	Het
Lgi1	A	G	19: 38,294,631 (GRCm39)	I444V	probably benign	Het
Lmod1	G	A	1: 135,252,862 (GRCm39)	V39M	probably damaging	Het
Lonrf2	G	A	1: 38,852,357 (GRCm39)	P165S	probably benign	Het
Mex3d	T	C	10: 80,217,376 (GRCm39)	T149A	probably benign	Het
Mideas	A	G	12: 84,205,748 (GRCm39)		probably null	Het
Mlxipl	A	C	5: 135,136,024 (GRCm39)	D83A	probably damaging	Het
Mroh8	T	A	2: 157,111,471 (GRCm39)	E161V	probably benign	Het
Mroh9	G	A	1: 162,884,347 (GRCm39)	T397I	probably damaging	Het
Mtss1	T	C	15: 58,930,249 (GRCm39)	D32G	possibly damaging	Het
Mus81	T	C	19: 5,533,504 (GRCm39)	D495G	probably benign	Het
Neurod1	A	C	2: 79,284,673 (GRCm39)	S237A	probably benign	Het
Npas1	G	A	7: 16,208,725 (GRCm39)	R51C	probably damaging	Het
Or11g27	T	C	14: 50,771,159 (GRCm39)	S97P	possibly damaging	Het
P2ry14	T	C	3: 59,023,274 (GRCm39)	N62S	probably damaging	Het
Pcdh15	A	G	10: 74,460,087 (GRCm39)	Y1308C	probably damaging	Het
Pcdhb14	A	T	18: 37,582,588 (GRCm39)	M565L	probably benign	Het
Pde6a	A	G	18: 61,390,283 (GRCm39)	E502G	probably damaging	Het
Pde8b	A	G	13: 95,178,527 (GRCm39)	V566A	probably benign	Het
Phf11b	G	T	14: 59,565,554 (GRCm39)	Q108K	probably benign	Het
Pikfyve	T	C	1: 65,291,716 (GRCm39)	Y1312H	probably damaging	Het
Plcb3	T	C	19: 6,933,381 (GRCm39)		probably benign	Het
Plxna2	G	A	1: 194,488,611 (GRCm39)	G1629D	probably damaging	Het
Plxnb1	T	C	9: 108,929,813 (GRCm39)	V223A	probably benign	Het
Prkca	A	T	11: 107,903,518 (GRCm39)	Y285N	possibly damaging	Het
Prl2a1	A	T	13: 27,992,554 (GRCm39)	N226I	probably damaging	Het
Pus7	A	C	5: 23,946,914 (GRCm39)	M636R	probably damaging	Het
Samd9l	G	A	6: 3,375,264 (GRCm39)	Q666*	probably null	Het
Slc6a15	A	G	10: 103,236,121 (GRCm39)	I279V	probably benign	Het
Slk	T	C	19: 47,608,973 (GRCm39)	V642A	possibly damaging	Het
Spata31e2	C	A	1: 26,722,070 (GRCm39)	G1037*	probably null	Het
Spta1	T	A	1: 174,073,296 (GRCm39)	M2305K	probably damaging	Het
Srrt	T	C	5: 137,301,274 (GRCm39)		probably benign	Het
Stfa2l1	A	T	16: 35,977,228 (GRCm39)	I8L	probably benign	Het
Tap1	T	C	17: 34,413,899 (GRCm39)	L638P	probably benign	Het
Tbccd1	A	T	16: 22,640,995 (GRCm39)	L461M	probably benign	Het
Tecta	T	C	9: 42,289,345 (GRCm39)	T407A	probably benign	Het
Tmbim7	T	C	5: 3,707,493 (GRCm39)		probably null	Het
Tnrc18	C	A	5: 142,800,869 (GRCm39)	V30L	probably benign	Het
Tomm7	A	G	5: 24,049,025 (GRCm39)	F16S	probably damaging	Het
Ugt2a2	A	G	5: 87,622,315 (GRCm39)	S428P	probably benign	Het
Vmn1r189	T	C	13: 22,286,324 (GRCm39)	E171G	probably benign	Het
Vmn1r61	T	C	7: 5,614,324 (GRCm39)		probably benign	Het
Vmn2r120	A	T	17: 57,832,038 (GRCm39)	S250R	probably benign	Het
Vmn2r8	T	C	5: 108,950,972 (GRCm39)	R158G	probably benign	Het
Vmn2r98	A	T	17: 19,286,702 (GRCm39)	Y400F	probably damaging	Het
Vps13c	C	A	9: 67,801,267 (GRCm39)	Y582*	probably null	Het
Zfp518a	T	A	19: 40,904,000 (GRCm39)	F1310I	probably benign	Het
Zswim1	A	G	2: 164,667,320 (GRCm39)	I191V	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
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'- TTAAACCATCTTCAACTATGGCTG -3'
(R):5'- CTGAAGTTCGGGCTGCTAAG -3'

Sequencing Primer
(F):5'- CCATCTTCAACTATGGCTGACAATG -3'
(R):5'- GTGACTCAGCCAACAGATCCTTG -3'

Posted On

2014-06-23