Mutagenetix > Incidental Mutation

Incidental Mutation 'R9100:Sema3e'

691605

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

068914-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.509) question?

Stock #

R9100 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

14075290-14306703 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 14282208 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 448 (Y448C)

Ref Sequence

ENSEMBL: ENSMUSP00000073612 (fasta)

Gene Model

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

AlphaFold

P70275

Predicted Effect

probably damaging
Transcript: ENSMUST00000073957
AA Change: Y448C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000073612
Gene: ENSMUSG00000063531
AA Change: Y448C

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

Meta Mutation Damage Score

0.8896

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

96% (75/78)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc4	A	G	14: 118,853,800 (GRCm39)	V444A	possibly damaging	Het
Add1	T	A	5: 34,770,622 (GRCm39)		probably benign	Het
Adgrg3	A	G	8: 95,762,891 (GRCm39)		probably benign	Het
Adgrl3	A	C	5: 81,842,299 (GRCm39)	Q809P	possibly damaging	Het
Ankmy2	T	C	12: 36,236,806 (GRCm39)	C205R	probably damaging	Het
Atp6v1b2	A	G	8: 69,541,476 (GRCm39)	N11S		Het
B3gnt6	T	A	7: 97,843,958 (GRCm39)	M1L	not run	Het
Bltp1	A	G	3: 37,098,907 (GRCm39)	K1256R		Het
Ccdc88b	T	C	19: 6,833,213 (GRCm39)	E278G	probably damaging	Het
Cdca8	T	C	4: 124,830,238 (GRCm39)	T45A	probably benign	Het
Ces2b	C	A	8: 105,558,221 (GRCm39)		probably benign	Het
Clip4	G	A	17: 72,117,884 (GRCm39)	G310R	probably damaging	Het
Cmklr1	G	C	5: 113,752,043 (GRCm39)	H319Q	probably benign	Het
Cnot3	A	G	7: 3,661,192 (GRCm39)	D567G	probably benign	Het
Cnot6l	T	C	5: 96,230,875 (GRCm39)	D364G	probably damaging	Het
Cpped1	A	G	16: 11,646,419 (GRCm39)	V111A		Het
Cstdc4	T	A	16: 36,008,285 (GRCm39)	M57K	possibly damaging	Het
Cyp11b2	T	C	15: 74,722,995 (GRCm39)	K468E	probably damaging	Het
Dpp4	T	G	2: 62,204,733 (GRCm39)	T245P	possibly damaging	Het
Efcab15	T	C	11: 103,090,893 (GRCm39)	T151A	probably benign	Het
Fat2	A	G	11: 55,153,347 (GRCm39)	W3622R	probably damaging	Het
Fat4	A	C	3: 39,064,803 (GRCm39)	K4920Q		Het
Frmpd2	A	G	14: 33,252,407 (GRCm39)	I656M	probably benign	Het
Gck	A	G	11: 5,856,516 (GRCm39)	Y214H	probably damaging	Het
Gde1	C	T	7: 118,294,305 (GRCm39)	R166H	probably benign	Het
Gdf7	A	T	12: 8,348,652 (GRCm39)	F215Y	unknown	Het
Gdpgp1	A	G	7: 79,888,282 (GRCm39)	I104M	probably benign	Het
Gldc	A	G	19: 30,077,314 (GRCm39)	S953P	possibly damaging	Het
Golga3	C	T	5: 110,337,544 (GRCm39)	H411Y	probably benign	Het
Gpn1	G	T	5: 31,655,740 (GRCm39)	R101I	probably damaging	Het
Itgb5	T	A	16: 33,740,551 (GRCm39)	S554T	possibly damaging	Het
Klhl1	G	A	14: 96,584,364 (GRCm39)	L289F	probably damaging	Het
Klhl13	C	T	X: 23,113,733 (GRCm39)	R95Q	probably benign	Het
Kmt2d	G	C	15: 98,747,832 (GRCm39)	T3164R	unknown	Het
Knl1	T	C	2: 118,899,469 (GRCm39)	V390A	probably benign	Het
Krtap5-2	GCCACAGCCTCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACCACAGCCCCCACAGGAACTACA	GCCACAGCCCCCACAGGAACTACA	7: 141,728,836 (GRCm39)		probably benign	Het
Lamtor4	G	A	5: 138,254,595 (GRCm39)		probably benign	Het
Lonrf1	AGGCGGCGGCGGCGG	AGGCGGCGGCGG	8: 36,715,919 (GRCm39)		probably benign	Het
Ltbp1	C	T	17: 75,622,102 (GRCm39)	L829F	probably benign	Het
Ltbp1	T	A	17: 75,622,103 (GRCm39)	L829H	probably damaging	Het
Mrgpra1	C	T	7: 46,984,732 (GRCm39)	E316K	probably damaging	Het
Muc16	T	A	9: 18,556,966 (GRCm39)	H3109L	unknown	Het
Nck1	T	C	9: 100,377,561 (GRCm39)	E368G	probably damaging	Het
Nox4	G	A	7: 87,025,448 (GRCm39)	R525Q	probably benign	Het
Nus1	A	T	10: 52,305,287 (GRCm39)		probably null	Het
Nxph2	T	C	2: 23,289,780 (GRCm39)	V44A	probably benign	Het
Or1e30	A	G	11: 73,678,687 (GRCm39)	K308E	probably benign	Het
Or4f56	A	G	2: 111,703,606 (GRCm39)	M198T	possibly damaging	Het
Or4k35	A	G	2: 111,100,094 (GRCm39)	L206P	probably benign	Het
Or4z4	G	T	19: 12,076,254 (GRCm39)	H250N	probably benign	Het
Or5d35	T	C	2: 87,855,330 (GRCm39)	I88T	probably benign	Het
Or5m11b	A	G	2: 85,806,096 (GRCm39)	K170E	probably benign	Het
Or6d13	A	T	6: 116,517,990 (GRCm39)	N192I	possibly damaging	Het
Otof	T	C	5: 30,539,696 (GRCm39)	D1039G	possibly damaging	Het
Parpbp	T	A	10: 87,968,969 (GRCm39)	Q159L	possibly damaging	Het
Per2	A	T	1: 91,351,464 (GRCm39)	L1014Q	possibly damaging	Het
Pik3ap1	C	G	19: 41,312,924 (GRCm39)		silent	Het
Pik3ca	A	G	3: 32,514,168 (GRCm39)	N885D	probably damaging	Het
Pip5k1c	T	C	10: 81,145,056 (GRCm39)	V299A	probably benign	Het
Polr3h	A	T	15: 81,806,717 (GRCm39)		probably benign	Het
Pramel11	T	A	4: 143,623,646 (GRCm39)	N176I	probably benign	Het
Pramel23	T	G	4: 143,425,727 (GRCm39)	N72T	probably benign	Het
Pus3	C	A	9: 35,476,946 (GRCm39)	Q248K	probably benign	Het
Sectm1a	T	A	11: 120,960,569 (GRCm39)	Q82L	possibly damaging	Het
Slc12a4	A	T	8: 106,675,774 (GRCm39)	S584T	probably benign	Het
Slc25a40	T	C	5: 8,499,613 (GRCm39)	F249L	probably benign	Het
St3gal6	T	A	16: 58,306,793 (GRCm39)	N79I		Het
Stxbp4	A	T	11: 90,426,320 (GRCm39)	I496K	possibly damaging	Het
Sulf1	A	G	1: 12,878,118 (GRCm39)	Y202C	probably damaging	Het
Swt1	A	G	1: 151,299,256 (GRCm39)		probably null	Het
Tdrd6	T	C	17: 43,936,305 (GRCm39)	Y1581C	possibly damaging	Het
Tenm4	G	C	7: 96,495,061 (GRCm39)	G1163A	probably damaging	Het
Tlr4	A	G	4: 66,758,518 (GRCm39)	E437G	probably benign	Het
Txnrd2	A	T	16: 18,256,315 (GRCm39)	H101L	probably damaging	Het
Uba3	A	T	6: 97,163,671 (GRCm39)	V306E	probably damaging	Het
Unc5b	T	C	10: 60,604,152 (GRCm39)	Q814R	probably damaging	Het
Vamp5	T	G	6: 72,347,304 (GRCm39)	E5A	possibly damaging	Het
Vmn1r69	T	A	7: 10,314,064 (GRCm39)	R222S	probably damaging	Het
Zfp507	G	A	7: 35,494,446 (GRCm39)	T199I	probably benign	Het
Zfyve19	T	G	2: 119,041,718 (GRCm39)	L95R	probably benign	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
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
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'- CGGAGGCAAGTATGGAACCA -3'
(R):5'- ACAACATGTGACGATTAGTACACATT -3'

Sequencing Primer
(F):5'- ACCAAAGATTACCCCGATGACG -3'
(R):5'- GCAGCTCTAAGGCATGCGAATC -3'

Posted On

2021-12-30