Mutagenetix > Incidental Mutation

Incidental Mutation 'R4786:Sema3f'

367106

Institutional Source

Beutler Lab

Gene Symbol

Sema3f

Ensembl Gene

ENSMUSG00000034684

Gene Name

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

Synonyms

Sema IV, Semak

MMRRC Submission

041995-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4786 (G1)

Quality Score

168

Status

Not validated

Chromosome

Chromosomal Location

107558699-107587674 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 107559881 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 671 (V671A)

Ref Sequence

ENSEMBL: ENSMUSP00000079400 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000010205] [ENSMUST00000080560] [ENSMUST00000192271] [ENSMUST00000192727] [ENSMUST00000194039]

AlphaFold

O88632

Predicted Effect

probably benign
Transcript: ENSMUST00000010205

SMART Domains

Protein: ENSMUSP00000010205
Gene: ENSMUSG00000034837

Domain	Start	End	E-Value	Type
G_alpha	9	349	5.13e-223	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000080560
AA Change: V671A

PolyPhen 2 Score 0.446 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000079400
Gene: ENSMUSG00000034684
AA Change: V671A

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
Sema	57	498	5.46e-206	SMART
PSI	516	568	1.87e-12	SMART
IGc2	586	654	3.79e-4	SMART
low complexity region	673	695	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000192157

Predicted Effect

probably benign
Transcript: ENSMUST00000192271

SMART Domains

Protein: ENSMUSP00000141571
Gene: ENSMUSG00000034837

Domain	Start	End	E-Value	Type
low complexity region	14	27	N/A	INTRINSIC
transmembrane domain	32	49	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000192727
AA Change: V702A

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000141865
Gene: ENSMUSG00000034684
AA Change: V702A

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
Sema	57	529	3.31e-205	SMART
PSI	547	599	1.87e-12	SMART
IGc2	617	685	3.79e-4	SMART
low complexity region	704	726	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000193188

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000193665

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000195129

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000194846

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000194153

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000194146

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000195267

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000194802

Predicted Effect

probably benign
Transcript: ENSMUST00000194039

SMART Domains

Protein: ENSMUSP00000142221
Gene: ENSMUSG00000034684

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
Pfam:Sema	57	185	2e-42	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000194424

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.0%
20x: 94.7%

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 loop and a C-terminal basic domain. This gene is expressed by the endothelial cells where it was found to act in an autocrine fashion to induce apoptosis, inhibit cell proliferation and survival, and function as an anti-tumorigenic agent. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
PHENOTYPE: Inactivation of this locus results in neuronal defects including impaired CNS axon pathfinding, and PNS and limbic system circuitry. Mice homozygous for a knock-out allele exhibit increased lymphatic branching complexity and LEC numbers. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700097O09Rik	A	T	12: 55,106,321 (GRCm39)	I134N	possibly damaging	Het
Acvr1c	T	C	2: 58,170,366 (GRCm39)	Y414C	probably damaging	Het
Adam32	A	C	8: 25,353,509 (GRCm39)	S693R	probably damaging	Het
Aldh2	A	T	5: 121,710,887 (GRCm39)	F314Y	probably benign	Het
Anks1	A	G	17: 28,271,704 (GRCm39)	D874G	possibly damaging	Het
Ap4b1	T	A	3: 103,726,120 (GRCm39)	V372E	probably benign	Het
Aqp12	G	A	1: 92,934,177 (GRCm39)	C18Y	probably damaging	Het
Arap1	T	A	7: 101,034,212 (GRCm39)	I218N	possibly damaging	Het
Arhgap42	C	A	9: 9,238,703 (GRCm39)	E28*	probably null	Het
Asb5	G	A	8: 55,038,874 (GRCm39)	E247K	probably benign	Het
Atg9b	T	C	5: 24,591,087 (GRCm39)	D781G	possibly damaging	Het
Atxn10	A	G	15: 85,271,344 (GRCm39)	H294R	probably benign	Het
Bod1l	G	T	5: 41,976,781 (GRCm39)	T1511K	probably benign	Het
Btnl2	A	T	17: 34,582,322 (GRCm39)	N296I	probably damaging	Het
Camta1	A	T	4: 151,374,496 (GRCm39)	L168H	probably damaging	Het
Cant1	A	T	11: 118,299,665 (GRCm39)	V265E	possibly damaging	Het
Ccdc157	T	C	11: 4,101,861 (GRCm39)	D20G	probably damaging	Het
Cd209c	T	G	8: 3,995,698 (GRCm39)	T35P	possibly damaging	Het
Cdc20b	G	A	13: 113,215,268 (GRCm39)	V279M	probably damaging	Het
Cdh18	T	A	15: 23,410,873 (GRCm39)	W453R	probably null	Het
Cdh24	A	G	14: 54,875,007 (GRCm39)	S333P	possibly damaging	Het
Ceacam11	T	C	7: 17,706,239 (GRCm39)		probably null	Het
Ciz1	C	T	2: 32,267,539 (GRCm39)	P150L	probably damaging	Het
Crip3	C	A	17: 46,741,968 (GRCm39)	Q152K	possibly damaging	Het
Dars2	G	A	1: 160,888,330 (GRCm39)	R197W	probably damaging	Het
Dctn4	A	G	18: 60,688,267 (GRCm39)	D394G	probably damaging	Het
Dido1	T	C	2: 180,312,664 (GRCm39)	Y1077C	possibly damaging	Het
Dnhd1	A	G	7: 105,323,651 (GRCm39)	T641A	probably benign	Het
Egln3	A	T	12: 54,232,367 (GRCm39)	I146N	probably damaging	Het
Eif2ak3	C	T	6: 70,869,602 (GRCm39)	T763M	possibly damaging	Het
Etfbkmt	A	T	6: 149,048,744 (GRCm39)	M1L	probably benign	Het
Fam171a1	A	T	2: 3,226,615 (GRCm39)	I583F	probably damaging	Het
Fbxo38	A	C	18: 62,662,745 (GRCm39)	L249W	probably damaging	Het
Fxyd5	T	C	7: 30,740,907 (GRCm39)		probably benign	Het
Gabrr3	C	A	16: 59,250,463 (GRCm39)	T154K	probably benign	Het
Gm7233	C	A	14: 43,038,347 (GRCm39)	D90E	probably benign	Het
Gm8186	A	G	17: 26,318,014 (GRCm39)	V61A	probably benign	Het
Gnao1	A	G	8: 94,670,931 (GRCm39)	I137V	probably benign	Het
Gnptab	A	G	10: 88,272,044 (GRCm39)	M945V	probably damaging	Het
Gpsm1	G	A	2: 26,212,493 (GRCm39)	A78T	probably benign	Het
Gtf2b	T	C	3: 142,487,230 (GRCm39)	L222P	probably damaging	Het
Hnrnpf	A	G	6: 117,900,857 (GRCm39)	Y47C	probably damaging	Het
Itga6	A	G	2: 71,669,034 (GRCm39)	N608S	possibly damaging	Het
Kdm2b	T	C	5: 123,018,917 (GRCm39)		probably null	Het
Krit1	T	A	5: 3,862,467 (GRCm39)	H207Q	possibly damaging	Het
Ky	A	G	9: 102,419,186 (GRCm39)	N398D	probably benign	Het
Lama1	T	A	17: 68,080,854 (GRCm39)	V1294E	possibly damaging	Het
Lef1	C	T	3: 130,905,173 (GRCm39)	T18I	probably damaging	Het
Lrp2	T	C	2: 69,368,300 (GRCm39)	N178S	probably damaging	Het
Lrrc36	A	G	8: 106,181,910 (GRCm39)	T525A	probably benign	Het
Map3k8	A	T	18: 4,340,647 (GRCm39)	C222*	probably null	Het
Mapre2	G	C	18: 24,011,016 (GRCm39)	S199T	probably benign	Het
Mcm3ap	A	G	10: 76,324,300 (GRCm39)	N911S	probably benign	Het
Mroh4	G	T	15: 74,482,083 (GRCm39)	H722Q	probably benign	Het
Muc21	A	T	17: 35,930,221 (GRCm39)		probably benign	Het
Myo5b	A	C	18: 74,828,451 (GRCm39)	Y701S	probably benign	Het
Myt1l	G	T	12: 29,861,457 (GRCm39)	V80L	unknown	Het
Ncoa7	C	A	10: 30,531,638 (GRCm39)	V24L	probably benign	Het
Nlrp10	A	T	7: 108,524,445 (GRCm39)	V345D	probably damaging	Het
Nmral1	C	A	16: 4,534,288 (GRCm39)	G51V	probably damaging	Het
Npc1	A	G	18: 12,332,554 (GRCm39)	I797T	probably benign	Het
Or4x6	A	T	2: 89,949,351 (GRCm39)	I197N	possibly damaging	Het
Or8g22	T	A	9: 38,958,783 (GRCm39)	R22*	probably null	Het
Or8g34	A	T	9: 39,373,137 (GRCm39)	I134L	probably benign	Het
Pclo	A	T	5: 14,773,281 (GRCm39)	I4419F	unknown	Het
Phf3	C	A	1: 30,855,638 (GRCm39)	E983*	probably null	Het
Pitpnm2	A	T	5: 124,259,806 (GRCm39)	Y1149*	probably null	Het
Sdc3	A	T	4: 130,550,079 (GRCm39)	T430S	probably damaging	Het
Sigirr	T	G	7: 140,671,346 (GRCm39)	S379R	probably benign	Het
Slc25a23	T	A	17: 57,354,326 (GRCm39)	N360I	possibly damaging	Het
Slco6c1	A	T	1: 97,015,720 (GRCm39)	M357K	probably benign	Het
Sox14	C	A	9: 99,757,018 (GRCm39)	M240I	probably benign	Het
Stradb	A	T	1: 59,030,367 (GRCm39)		probably benign	Het
Szt2	A	T	4: 118,256,259 (GRCm39)	M200K	probably benign	Het
Tef	T	C	15: 81,699,453 (GRCm39)	S85P	probably benign	Het
Thada	T	A	17: 84,766,283 (GRCm39)	H41L	possibly damaging	Het
Tinagl1	A	G	4: 130,067,724 (GRCm39)	F90S	probably benign	Het
Tnfaip1	G	A	11: 78,421,045 (GRCm39)	T5I	possibly damaging	Het
Tnfrsf23	A	T	7: 143,233,801 (GRCm39)	V59D	probably damaging	Het
Tnpo3	A	G	6: 29,578,541 (GRCm39)	V311A	probably benign	Het
Trak1	T	A	9: 121,301,560 (GRCm39)	M772K	probably benign	Het
Ubash3a	A	G	17: 31,436,938 (GRCm39)	D185G	probably benign	Het
Vmn2r120	T	C	17: 57,829,048 (GRCm39)	T516A	probably benign	Het
Wdr4	A	C	17: 31,728,785 (GRCm39)	L130R	probably damaging	Het
Zfp12	T	C	5: 143,231,257 (GRCm39)	I528T	probably damaging	Het
Zfp607a	T	C	7: 27,578,838 (GRCm39)	L636P	probably damaging	Het

Other mutations in Sema3f

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00945:Sema3f	APN	9	107,562,721 (GRCm39)	missense	probably benign	0.44
IGL01940:Sema3f	APN	9	107,560,896 (GRCm39)	unclassified	probably benign
IGL02070:Sema3f	APN	9	107,569,440 (GRCm39)	missense	probably damaging	1.00
IGL02381:Sema3f	APN	9	107,569,594 (GRCm39)	missense	probably damaging	1.00
IGL02472:Sema3f	APN	9	107,564,935 (GRCm39)	missense	probably damaging	1.00
IGL02557:Sema3f	APN	9	107,564,411 (GRCm39)	missense	probably damaging	1.00
IGL02614:Sema3f	APN	9	107,559,710 (GRCm39)	missense	probably benign	0.28
IGL02660:Sema3f	APN	9	107,561,183 (GRCm39)	missense	probably benign	0.05
R1468:Sema3f	UTSW	9	107,564,771 (GRCm39)	unclassified	probably benign
R1905:Sema3f	UTSW	9	107,561,575 (GRCm39)	missense	probably damaging	1.00
R4728:Sema3f	UTSW	9	107,582,639 (GRCm39)	missense	probably benign	0.00
R4772:Sema3f	UTSW	9	107,566,919 (GRCm39)	nonsense	probably null
R4845:Sema3f	UTSW	9	107,562,700 (GRCm39)	missense	probably damaging	1.00
R5418:Sema3f	UTSW	9	107,569,820 (GRCm39)	missense	probably damaging	1.00
R5780:Sema3f	UTSW	9	107,559,788 (GRCm39)	missense	probably damaging	0.98
R5849:Sema3f	UTSW	9	107,559,815 (GRCm39)	missense	probably damaging	0.98
R5929:Sema3f	UTSW	9	107,569,392 (GRCm39)	missense	probably damaging	1.00
R6968:Sema3f	UTSW	9	107,568,648 (GRCm39)	critical splice acceptor site	probably null
R7043:Sema3f	UTSW	9	107,568,599 (GRCm39)	missense	possibly damaging	0.91
R7449:Sema3f	UTSW	9	107,561,235 (GRCm39)	missense	probably damaging	1.00
R7526:Sema3f	UTSW	9	107,566,927 (GRCm39)	missense	probably damaging	0.96
R7559:Sema3f	UTSW	9	107,561,777 (GRCm39)	missense	possibly damaging	0.52
R7640:Sema3f	UTSW	9	107,560,774 (GRCm39)	missense	probably benign	0.20
R7771:Sema3f	UTSW	9	107,569,625 (GRCm39)	missense	possibly damaging	0.89
R7789:Sema3f	UTSW	9	107,582,631 (GRCm39)	missense	probably benign	0.00
R8058:Sema3f	UTSW	9	107,559,800 (GRCm39)	missense	probably benign	0.42
R8113:Sema3f	UTSW	9	107,565,275 (GRCm39)	missense	possibly damaging	0.95
R9574:Sema3f	UTSW	9	107,566,972 (GRCm39)	missense	possibly damaging	0.50
R9641:Sema3f	UTSW	9	107,565,454 (GRCm39)	missense	unknown
R9674:Sema3f	UTSW	9	107,566,947 (GRCm39)	missense	possibly damaging	0.69
R9799:Sema3f	UTSW	9	107,562,562 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TTCAGGAGGCCTAAGTGCTC -3'
(R):5'- ACAAACGTGGTGGTCTCAC -3'

Sequencing Primer
(F):5'- AGGCCTAAGTGCTCCTGGC -3'
(R):5'- TCTCACCTGGAAGCTGGCTAG -3'

Posted On

2015-12-29