Mutagenetix > Incidental Mutation

Incidental Mutation 'R4960:Sema3e'

382258

Institutional Source

Beutler Lab

Gene Symbol

Sema3e

Ensembl Gene

ENSMUSG00000063531

Gene Name

sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E

Synonyms

Semah

MMRRC Submission

042557-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.560) question?

Stock #

R4960 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

14075290-14306703 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 14302646 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glycine at position 724 (R724G)

Ref Sequence

ENSEMBL: ENSMUSP00000073612 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000073957]

AlphaFold

P70275

Predicted Effect

possibly damaging
Transcript: ENSMUST00000073957
AA Change: R724G

PolyPhen 2 Score 0.933 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000073612
Gene: ENSMUSG00000063531
AA Change: R724G

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Sema	58	500	1.85e-194	SMART
PSI	518	573	1.81e-10	SMART
IG	587	673	5.75e-4	SMART
low complexity region	737	750	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130116

Coding Region Coverage

1x: 99.3%
3x: 98.5%
10x: 96.8%
20x: 93.8%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Semaphorins are a large family of conserved secreted and membrane associated proteins which possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Based on sequence and structural similarities, semaphorins are put into eight classes: invertebrates contain classes 1 and 2, viruses have class V, and vertebrates contain classes 3-7. Semaphorins serve as axon guidance ligands via multimeric receptor complexes, some (if not all) containing plexin proteins. This gene encodes a class 4 semaphorin. This gene encodes a class 3 semaphorin. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]
PHENOTYPE: Homozygous null mice display abnormal intersomitic vacular development and loss of the normal segmented somite pattern. Homozygous mutants for another allele have Bergmeister papillae on the surface of the optic disc. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 102 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc9	A	T	6: 142,566,509 (GRCm39)		probably null	Het
Abtb3	A	C	10: 85,487,526 (GRCm39)	N998T	probably benign	Het
Adamts20	T	C	15: 94,277,655 (GRCm39)	H269R	probably benign	Het
Adamtsl1	C	T	4: 86,342,410 (GRCm39)	Q1642*	probably null	Het
Adamtsl3	A	C	7: 82,216,185 (GRCm39)	T863P	probably damaging	Het
Adcy3	G	T	12: 4,184,896 (GRCm39)	V191L	probably benign	Het
Akap9	G	T	5: 4,007,664 (GRCm39)	R244L	probably benign	Het
Anapc1	C	T	2: 128,526,514 (GRCm39)	V95M	probably benign	Het
Arhgap17	G	T	7: 122,886,149 (GRCm39)		probably benign	Het
Art2b	T	A	7: 101,229,437 (GRCm39)	Y154F	probably damaging	Het
Atrn	C	T	2: 130,836,967 (GRCm39)	R1144*	probably null	Het
Atxn3	T	C	12: 101,914,638 (GRCm39)	S29G	possibly damaging	Het
Batf3	C	T	1: 190,830,707 (GRCm39)	P18S	probably benign	Het
Bmal1	T	A	7: 112,898,642 (GRCm39)		probably null	Het
Bmpr1b	A	T	3: 141,576,546 (GRCm39)	C96S	probably damaging	Het
Bola1	A	G	3: 96,104,370 (GRCm39)	S75P	probably benign	Het
Cela3a	G	A	4: 137,129,959 (GRCm39)	R221*	probably null	Het
Chat	A	G	14: 32,142,771 (GRCm39)	V406A	possibly damaging	Het
Chd1	T	A	17: 15,962,493 (GRCm39)	M750K	probably damaging	Het
Clip1	T	A	5: 123,792,066 (GRCm39)	K35*	probably null	Het
Cnr2	G	A	4: 135,644,918 (GRCm39)	G332D	probably benign	Het
Cnrip1	A	G	11: 17,002,228 (GRCm39)	D20G	probably damaging	Het
Col2a1	T	C	15: 97,874,030 (GRCm39)	Y1384C	unknown	Het
Col6a3	T	A	1: 90,731,940 (GRCm39)	I831F	probably damaging	Het
Cp	G	A	3: 20,027,961 (GRCm39)	V456I	probably damaging	Het
Cspp1	T	A	1: 10,196,688 (GRCm39)	N900K	probably damaging	Het
Ctbp2	T	C	7: 132,615,967 (GRCm39)	I323V	probably benign	Het
Ctnna2	C	T	6: 77,630,094 (GRCm39)	R120H	probably damaging	Het
Cyp2a12	A	G	7: 26,733,575 (GRCm39)	H318R	probably benign	Het
Cyp2c66	A	T	19: 39,151,766 (GRCm39)		probably null	Het
Cyp2j8	T	C	4: 96,395,614 (GRCm39)	T4A	probably benign	Het
Cyp4v3	A	G	8: 45,773,674 (GRCm39)	V165A	possibly damaging	Het
D5Ertd579e	G	A	5: 36,773,571 (GRCm39)	R275*	probably null	Het
Deup1	G	T	9: 15,512,264 (GRCm39)	Q160K	possibly damaging	Het
Dhx36	A	T	3: 62,404,280 (GRCm39)	I221K	probably damaging	Het
Dnah7b	T	A	1: 46,272,886 (GRCm39)	M2338K	probably benign	Het
Dync2li1	T	G	17: 84,940,969 (GRCm39)	L62V	probably benign	Het
Ephb3	A	G	16: 21,039,245 (GRCm39)	K367R	probably benign	Het
Etv3	A	G	3: 87,435,368 (GRCm39)	K80E	probably damaging	Het
Flacc1	T	A	1: 58,706,965 (GRCm39)	E234V	probably damaging	Het
Gdap1l1	T	C	2: 163,295,779 (GRCm39)	F346L	probably benign	Het
Gm4787	C	T	12: 81,426,090 (GRCm39)	V23M	probably damaging	Het
Greb1l	T	A	18: 10,547,306 (GRCm39)	I1508N	probably damaging	Het
Heatr5b	G	A	17: 79,139,013 (GRCm39)	T43I	probably benign	Het
Hephl1	T	C	9: 14,997,586 (GRCm39)	Y360C	probably damaging	Het
Itgam	A	C	7: 127,715,012 (GRCm39)	T865P	possibly damaging	Het
Kcnma1	T	C	14: 24,054,186 (GRCm39)		probably benign	Het
Kidins220	T	A	12: 25,042,259 (GRCm39)	C185*	probably null	Het
Klhl35	G	T	7: 99,118,275 (GRCm39)	G273V	probably damaging	Het
Lama5	A	G	2: 179,850,045 (GRCm39)		probably null	Het
Lamc3	A	G	2: 31,805,966 (GRCm39)	Q689R	probably benign	Het
Lnx2	C	T	5: 146,955,850 (GRCm39)	V649I	probably benign	Het
Lrrc43	A	G	5: 123,637,675 (GRCm39)	I281V	probably benign	Het
Ly6g6d	C	A	17: 35,290,730 (GRCm39)	A67S	probably benign	Het
Map1b	A	G	13: 99,568,720 (GRCm39)	S1334P	probably benign	Het
Mast1	T	A	8: 85,644,500 (GRCm39)	T810S	probably benign	Het
Matcap1	G	T	8: 106,009,843 (GRCm39)	R369S	probably damaging	Het
Mbnl1	A	G	3: 60,503,117 (GRCm39)	M1V	probably null	Het
Mc5r	T	G	18: 68,471,890 (GRCm39)	M83R	possibly damaging	Het
Mkln1	T	C	6: 31,435,941 (GRCm39)	F300S	probably damaging	Het
Mrgpre	A	T	7: 143,335,088 (GRCm39)	C138*	probably null	Het
Mtarc2	T	A	1: 184,566,116 (GRCm39)	M186L	probably benign	Het
Ncbp1	C	T	4: 46,165,273 (GRCm39)	Q529*	probably null	Het
Nherf1	A	G	11: 115,067,289 (GRCm39)	D180G	probably benign	Het
Nrcam	A	G	12: 44,613,082 (GRCm39)	D591G	probably benign	Het
Nrxn3	A	T	12: 88,761,971 (GRCm39)	H6L	possibly damaging	Het
Nsmaf	T	A	4: 6,423,342 (GRCm39)	D342V	probably damaging	Het
Oip5	TGAGAAA	T	2: 119,448,342 (GRCm39)		probably benign	Het
Omt2a	T	A	9: 78,220,305 (GRCm39)	E31D	possibly damaging	Het
Or4f62	A	G	2: 111,986,697 (GRCm39)	T134A	probably benign	Het
Or52n2b	A	G	7: 104,565,915 (GRCm39)	I196T	probably benign	Het
Or5ac20	A	G	16: 59,104,348 (GRCm39)	S171P	probably benign	Het
Or6c88	A	C	10: 129,406,895 (GRCm39)	I124L	probably damaging	Het
Or9a2	C	A	6: 41,749,003 (GRCm39)	V77F	probably damaging	Het
Phyhipl	A	G	10: 70,404,815 (GRCm39)	V131A	probably benign	Het
Pik3r5	A	G	11: 68,384,464 (GRCm39)	M619V	probably benign	Het
Pramel19	T	C	4: 101,798,661 (GRCm39)	Y211H	probably benign	Het
Ptprg	A	T	14: 12,237,837 (GRCm38)	E1431D	probably benign	Het
Rnf20	A	G	4: 49,638,029 (GRCm39)	T85A	probably damaging	Het
Rtn3	A	T	19: 7,433,886 (GRCm39)	I683K	probably damaging	Het
Rwdd3	A	G	3: 120,952,470 (GRCm39)	F174L	probably damaging	Het
Ryr1	T	C	7: 28,778,208 (GRCm39)	Q2096R	possibly damaging	Het
Scrn1	T	C	6: 54,511,407 (GRCm39)	D111G	probably damaging	Het
She	A	G	3: 89,741,544 (GRCm39)	M232V	possibly damaging	Het
Skic3	T	A	13: 76,333,275 (GRCm39)	V1508E	possibly damaging	Het
Slc25a54	A	T	3: 109,020,132 (GRCm39)	N382I	possibly damaging	Het
Slc26a2	T	C	18: 61,331,875 (GRCm39)	M519V	probably damaging	Het
Slc9a1	T	A	4: 133,097,967 (GRCm39)	L38H	probably damaging	Het
Snap47	A	T	11: 59,319,369 (GRCm39)	D256E	probably damaging	Het
Tacc3	A	G	5: 33,829,326 (GRCm39)	T610A	probably benign	Het
Tbc1d30	G	A	10: 121,103,121 (GRCm39)	T637M	probably benign	Het
Tbcd	T	A	11: 121,464,681 (GRCm39)	M572K	probably benign	Het
Thoc7	A	T	14: 13,953,460 (GRCm38)	D68E	probably benign	Het
Tmpo	G	A	10: 90,989,171 (GRCm39)	T250M	probably damaging	Het
Tmtc1	TGTCCGCCAGGCCCTTGCCCCAGAAGTC	TGTC	6: 148,345,445 (GRCm39)		probably benign	Het
Tnfaip1	A	T	11: 78,418,396 (GRCm39)	C224S	possibly damaging	Het
Tshz1	T	C	18: 84,032,987 (GRCm39)	T474A	probably benign	Het
Tspoap1	C	T	11: 87,657,222 (GRCm39)	Q345*	probably null	Het
Ttc21a	A	G	9: 119,774,067 (GRCm39)	E258G	possibly damaging	Het
Ttyh1	T	C	7: 4,131,225 (GRCm39)	L232P	probably damaging	Het
Usp2	T	A	9: 43,987,110 (GRCm39)	L136Q	probably damaging	Het
Usp31	T	C	7: 121,247,868 (GRCm39)	S1192G	probably damaging	Het

Other mutations in Sema3e

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00503:Sema3e	APN	5	14,290,586 (GRCm39)	missense	probably damaging	1.00
IGL01068:Sema3e	APN	5	14,283,732 (GRCm39)	critical splice donor site	probably null
IGL01128:Sema3e	APN	5	14,282,129 (GRCm39)	missense	probably damaging	1.00
IGL01134:Sema3e	APN	5	14,302,784 (GRCm39)	missense	probably damaging	1.00
IGL02013:Sema3e	APN	5	14,280,207 (GRCm39)	missense	probably damaging	1.00
IGL02051:Sema3e	APN	5	14,274,324 (GRCm39)	missense	possibly damaging	0.77
IGL02309:Sema3e	APN	5	14,274,404 (GRCm39)	missense	probably damaging	0.98
IGL02636:Sema3e	APN	5	14,275,670 (GRCm39)	missense	probably benign
IGL02702:Sema3e	APN	5	14,283,740 (GRCm39)	splice site	probably benign
IGL03001:Sema3e	APN	5	14,291,057 (GRCm39)	missense	probably benign	0.19
R0011:Sema3e	UTSW	5	14,194,025 (GRCm39)	nonsense	probably null
R0098:Sema3e	UTSW	5	14,302,446 (GRCm39)	missense	possibly damaging	0.52
R0098:Sema3e	UTSW	5	14,302,446 (GRCm39)	missense	possibly damaging	0.52
R0220:Sema3e	UTSW	5	14,214,167 (GRCm39)	missense	possibly damaging	0.56
R0564:Sema3e	UTSW	5	14,286,099 (GRCm39)	critical splice donor site	probably null
R1079:Sema3e	UTSW	5	14,275,669 (GRCm39)	missense	probably benign	0.12
R1187:Sema3e	UTSW	5	14,282,098 (GRCm39)	missense	probably damaging	1.00
R1670:Sema3e	UTSW	5	14,212,199 (GRCm39)	splice site	probably benign
R1736:Sema3e	UTSW	5	14,260,390 (GRCm39)	missense	probably damaging	1.00
R3433:Sema3e	UTSW	5	14,302,728 (GRCm39)	missense	probably benign	0.00
R3831:Sema3e	UTSW	5	14,276,496 (GRCm39)	missense	probably damaging	1.00
R4094:Sema3e	UTSW	5	14,283,704 (GRCm39)	missense	probably benign	0.12
R4580:Sema3e	UTSW	5	14,283,717 (GRCm39)	missense	probably damaging	1.00
R4828:Sema3e	UTSW	5	14,276,654 (GRCm39)	missense	probably damaging	1.00
R4855:Sema3e	UTSW	5	14,280,144 (GRCm39)	missense	probably damaging	0.99
R4884:Sema3e	UTSW	5	14,275,579 (GRCm39)	missense	probably damaging	1.00
R5264:Sema3e	UTSW	5	14,276,662 (GRCm39)	missense	probably damaging	1.00
R5389:Sema3e	UTSW	5	14,286,099 (GRCm39)	critical splice donor site	probably benign
R5512:Sema3e	UTSW	5	14,280,194 (GRCm39)	missense	probably damaging	1.00
R5642:Sema3e	UTSW	5	14,212,257 (GRCm39)	missense	probably damaging	1.00
R5647:Sema3e	UTSW	5	14,275,567 (GRCm39)	missense	probably damaging	0.99
R5814:Sema3e	UTSW	5	14,275,680 (GRCm39)	missense	probably benign	0.01
R5993:Sema3e	UTSW	5	14,274,307 (GRCm39)	missense	probably damaging	1.00
R6076:Sema3e	UTSW	5	14,291,100 (GRCm39)	missense	probably benign	0.01
R6906:Sema3e	UTSW	5	14,290,601 (GRCm39)	missense	probably damaging	1.00
R7432:Sema3e	UTSW	5	14,274,404 (GRCm39)	missense	probably damaging	0.98
R8738:Sema3e	UTSW	5	14,214,169 (GRCm39)	missense	possibly damaging	0.95
R8849:Sema3e	UTSW	5	14,302,673 (GRCm39)	missense	probably damaging	1.00
R8879:Sema3e	UTSW	5	14,282,108 (GRCm39)	missense	probably benign	0.16
R8935:Sema3e	UTSW	5	14,282,127 (GRCm39)	missense	probably damaging	0.97
R9071:Sema3e	UTSW	5	14,282,154 (GRCm39)	missense	probably benign	0.00
R9100:Sema3e	UTSW	5	14,282,208 (GRCm39)	missense	probably damaging	1.00
R9367:Sema3e	UTSW	5	14,291,084 (GRCm39)	missense	probably benign	0.00
R9444:Sema3e	UTSW	5	14,302,625 (GRCm39)	missense	possibly damaging	0.63
R9478:Sema3e	UTSW	5	14,286,386 (GRCm39)	missense	probably damaging	1.00
R9601:Sema3e	UTSW	5	14,302,397 (GRCm39)	missense	possibly damaging	0.95
R9671:Sema3e	UTSW	5	14,212,217 (GRCm39)	missense	probably benign	0.00
X0064:Sema3e	UTSW	5	14,280,156 (GRCm39)	missense	probably benign	0.05
Z1088:Sema3e	UTSW	5	14,276,470 (GRCm39)	missense	probably damaging	0.97
Z1177:Sema3e	UTSW	5	14,075,725 (GRCm39)	start gained	probably benign

Predicted Primers

PCR Primer
(F):5'- GTGCGTAAAATCACCTTGGAGG -3'
(R):5'- AAGAGACTGCATGCTTTCAGTC -3'

Sequencing Primer
(F):5'- CCTTGGAGGTGGTCGAAGAG -3'
(R):5'- AAAAATGTTTCCATCCTAGGTTCCTC -3'

Posted On

2016-04-27