Mutagenetix > Incidental Mutation

Incidental Mutation 'R4855:Sema3e'

373875

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

042466-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.509) question?

Stock #

R4855 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

14075290-14306703 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 14280144 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glutamic Acid at position 341 (V341E)

Ref Sequence

ENSEMBL: ENSMUSP00000073612 (fasta)

Gene Model

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

AlphaFold

P70275

Predicted Effect

probably damaging
Transcript: ENSMUST00000073957
AA Change: V341E

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000073612
Gene: ENSMUSG00000063531
AA Change: V341E

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199698

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.5%

Validation Efficiency

98% (93/95)

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700049A03Rik	G	T	12: 71,211,320 (GRCm39)	E685*	probably null	Het
2700049A03Rik	A	T	12: 71,211,321 (GRCm39)	E685V	possibly damaging	Het
Ablim2	C	T	5: 35,959,766 (GRCm39)	R73C	possibly damaging	Het
Adad1	G	T	3: 37,139,260 (GRCm39)	L443F	probably damaging	Het
Amph	T	A	13: 19,268,378 (GRCm39)	M70K	probably damaging	Het
Ankra2	T	A	13: 98,409,919 (GRCm39)	L306H	probably damaging	Het
Arc	A	C	15: 74,543,592 (GRCm39)	D210E	probably benign	Het
Arhgap10	A	G	8: 78,159,367 (GRCm39)		probably null	Het
Atp8b5	T	A	4: 43,344,449 (GRCm39)	N445K	probably benign	Het
C1qc	G	T	4: 136,617,746 (GRCm39)	Q117K	probably benign	Het
Cadps	T	A	14: 12,822,449 (GRCm38)	E97V	unknown	Het
Capn13	GCA	G	17: 73,658,501 (GRCm39)		probably null	Het
Cdk13	A	T	13: 17,895,868 (GRCm39)	W1014R	probably damaging	Het
Cltb	C	T	13: 54,746,908 (GRCm39)	E23K	probably damaging	Het
Clvs2	A	T	10: 33,498,642 (GRCm39)	I96N	probably damaging	Het
Cwf19l1	A	G	19: 44,103,006 (GRCm39)	V403A	probably damaging	Het
Ddr2	A	T	1: 169,816,066 (GRCm39)	L547Q	possibly damaging	Het
Ebf1	A	T	11: 44,863,735 (GRCm39)	K354*	probably null	Het
Fat4	A	G	3: 38,942,466 (GRCm39)	Q453R	probably benign	Het
Gas2l3	CACTCGTCATACT	CACT	10: 89,266,820 (GRCm39)		probably benign	Het
Gata6	A	G	18: 11,054,497 (GRCm39)	E142G	possibly damaging	Het
Gm14221	T	C	2: 160,416,600 (GRCm39)		noncoding transcript	Het
Gm42791	C	A	5: 148,896,247 (GRCm39)		probably benign	Het
Gm6370	G	T	5: 146,430,621 (GRCm39)	V269L	probably benign	Het
Gphn	G	A	12: 78,673,984 (GRCm39)	V526M	probably damaging	Het
Gpt	A	T	15: 76,583,485 (GRCm39)	E206V	probably damaging	Het
Grm3	G	A	5: 9,620,047 (GRCm39)	A399V	probably damaging	Het
Helq	A	T	5: 100,931,025 (GRCm39)	V575E	possibly damaging	Het
Herc4	A	G	10: 63,151,437 (GRCm39)		probably null	Het
Ifi207	A	T	1: 173,557,381 (GRCm39)	N452K	probably damaging	Het
Ikbke	A	G	1: 131,184,848 (GRCm39)		probably null	Het
Kbtbd2	A	G	6: 56,756,687 (GRCm39)	F350L	probably benign	Het
Kmt2c	A	G	5: 25,519,555 (GRCm39)	V2185A	probably benign	Het
Lgi2	T	C	5: 52,695,849 (GRCm39)	Q362R	probably damaging	Het
Lrit1	G	A	14: 36,783,773 (GRCm39)	G367E	possibly damaging	Het
Lrp1	G	A	10: 127,446,311 (GRCm39)	H78Y	probably benign	Het
Matk	A	G	10: 81,098,720 (GRCm39)		probably benign	Het
Med21	G	A	6: 146,549,690 (GRCm39)	G24S	probably damaging	Het
Met	G	T	6: 17,558,796 (GRCm39)	L1141F	probably damaging	Het
Mroh3	A	T	1: 136,128,677 (GRCm39)		probably null	Het
Mrpl15	T	C	1: 4,844,683 (GRCm39)	I203V	probably benign	Het
Naip1	T	C	13: 100,559,728 (GRCm39)		probably null	Het
Ndufa9	A	C	6: 126,804,505 (GRCm39)	Y298*	probably null	Het
Neb	T	C	2: 52,188,906 (GRCm39)	E808G	probably damaging	Het
Nol4l	C	T	2: 153,253,726 (GRCm39)	G616S	probably benign	Het
Oprm1	T	A	10: 6,788,468 (GRCm39)	C408S	probably benign	Het
Or2ag18	T	C	7: 106,405,463 (GRCm39)	M69V	probably benign	Het
Or4f14	A	G	2: 111,742,444 (GRCm39)	V277A	probably benign	Het
Or4k42	T	G	2: 111,320,293 (GRCm39)	D70A	probably damaging	Het
Or52e7	T	A	7: 104,684,858 (GRCm39)	I151N	probably damaging	Het
Or5ak20	T	C	2: 85,183,793 (GRCm39)	N159S	possibly damaging	Het
Paqr3	A	G	5: 97,256,053 (GRCm39)	I107T	possibly damaging	Het
Pex5l	G	A	3: 33,196,989 (GRCm39)		probably benign	Het
Phf8-ps	C	T	17: 33,285,713 (GRCm39)	S363N	probably benign	Het
Pik3ap1	T	C	19: 41,316,284 (GRCm39)	D326G	probably benign	Het
Plaa	G	T	4: 94,474,645 (GRCm39)	D252E	probably damaging	Het
Plxna2	G	A	1: 194,480,040 (GRCm39)	V1404I	probably benign	Het
Ppargc1a	G	A	5: 51,631,564 (GRCm39)	A355V	possibly damaging	Het
Primpol	A	G	8: 47,039,726 (GRCm39)	S350P	probably benign	Het
Prlr	T	C	15: 10,328,883 (GRCm39)	S453P	probably benign	Het
Psmd5	T	C	2: 34,742,564 (GRCm39)		probably benign	Het
Robo2	A	T	16: 73,768,079 (GRCm39)	V571E	probably damaging	Het
Sbspon	A	T	1: 15,929,264 (GRCm39)	S176T	possibly damaging	Het
Scyl2	G	A	10: 89,476,325 (GRCm39)		probably benign	Het
Serpinb3b	A	T	1: 107,082,270 (GRCm39)	F331L	possibly damaging	Het
Setd2	A	G	9: 110,401,022 (GRCm39)	H1736R	probably benign	Het
Sidt2	A	T	9: 45,863,327 (GRCm39)	D180E	probably benign	Het
Skint9	A	T	4: 112,248,208 (GRCm39)	Y179N	probably benign	Het
Slc27a5	T	C	7: 12,722,560 (GRCm39)	N638S	probably benign	Het
Slc6a4	T	A	11: 76,904,135 (GRCm39)	W197R	probably damaging	Het
Spag17	A	T	3: 99,970,649 (GRCm39)	M1278L	probably benign	Het
Sptbn1	T	A	11: 30,092,353 (GRCm39)	I471F	probably damaging	Het
Tasor2	A	T	13: 3,616,680 (GRCm39)		probably null	Het
Teddm1a	A	G	1: 153,768,382 (GRCm39)	Q282R	probably benign	Het
Tex35	A	G	1: 156,927,295 (GRCm39)	L160P	probably damaging	Het
Tfap2c	T	C	2: 172,393,438 (GRCm39)	Y118H	probably damaging	Het
Tpp1	T	C	7: 105,395,930 (GRCm39)	Q533R	probably benign	Het
Ttc13	C	T	8: 125,401,174 (GRCm39)	D730N	probably damaging	Het
Ufc1	A	G	1: 171,122,375 (GRCm39)		probably benign	Het
Vcpip1	A	G	1: 9,817,589 (GRCm39)	W265R	probably damaging	Het
Wdr11	C	G	7: 129,202,158 (GRCm39)		probably null	Het
Xirp2	A	G	2: 67,341,408 (GRCm39)	I1216M	possibly damaging	Het
Zswim2	A	G	2: 83,747,187 (GRCm39)		probably null	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
R4884:Sema3e	UTSW	5	14,275,579 (GRCm39)	missense	probably damaging	1.00
R4960:Sema3e	UTSW	5	14,302,646 (GRCm39)	missense	possibly damaging	0.93
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'- AGGAGTGATAAAGTCTTTCGGTC -3'
(R):5'- GCAGCTCTTTACCGTTTGAACATTC -3'

Sequencing Primer
(F):5'- GTGATAAAGTCTTTCGGTCTCATTAC -3'
(R):5'- ACTGTAAAGTAAGACAGAACACATG -3'

Posted On

2016-03-01