Mutagenetix > Incidental Mutation

Incidental Mutation 'R7449:Sema3f'

577571

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

045524-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7449 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

107558699-107587674 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 107561235 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Glycine at position 584 (S584G)

Ref Sequence

ENSEMBL: ENSMUSP00000141865 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000010205] [ENSMUST00000080560] [ENSMUST00000192271] [ENSMUST00000192727] [ENSMUST00000192783] [ENSMUST00000193108] [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 damaging
Transcript: ENSMUST00000080560
AA Change: S553G

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

SMART Domains

Protein: ENSMUSP00000079400
Gene: ENSMUSG00000034684
AA Change: S553G

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

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 damaging
Transcript: ENSMUST00000192727
AA Change: S584G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000141865
Gene: ENSMUSG00000034684
AA Change: S584G

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

probably benign
Transcript: ENSMUST00000192783

SMART Domains

Protein: ENSMUSP00000141668
Gene: ENSMUSG00000034684

Domain	Start	End	E-Value	Type
Sema	1	276	3.6e-7	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000193108

SMART Domains

Protein: ENSMUSP00000141878
Gene: ENSMUSG00000034684

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
Pfam:Sema	57	191	9.9e-46	PFAM

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: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca16	T	A	7: 120,035,131 (GRCm39)	Y306N	possibly damaging	Het
Adgrv1	A	T	13: 81,647,192 (GRCm39)	V3116D	probably damaging	Het
Adss1	A	T	12: 112,600,585 (GRCm39)	T185S	probably damaging	Het
Ago2	G	A	15: 73,018,348 (GRCm39)	P30L	probably damaging	Het
Arb2a	A	G	13: 77,907,561 (GRCm39)	I41V	probably damaging	Het
Atp5pf	C	T	16: 84,628,251 (GRCm39)	V44M	probably benign	Het
Atp7b	T	A	8: 22,501,865 (GRCm39)	I833F	probably damaging	Het
Birc6	T	A	17: 75,009,336 (GRCm39)	N4869K	probably benign	Het
Cacna1c	C	T	6: 118,579,310 (GRCm39)	D1796N		Het
Ccng2	C	G	5: 93,421,202 (GRCm39)	S237R	probably benign	Het
Cnga1	A	G	5: 72,762,647 (GRCm39)	I289T	probably benign	Het
Crybg1	C	A	10: 43,880,515 (GRCm39)	E224D	probably benign	Het
Dysf	T	C	6: 84,114,362 (GRCm39)	L1217P	possibly damaging	Het
Ebf2	T	A	14: 67,647,469 (GRCm39)	N339K	probably damaging	Het
Eva1c	T	C	16: 90,673,081 (GRCm39)		probably null	Het
Fam184a	T	C	10: 53,574,730 (GRCm39)	E293G	probably damaging	Het
Folh1	G	A	7: 86,380,956 (GRCm39)	P506S	probably benign	Het
Ftcd	A	T	10: 76,415,997 (GRCm39)	K210N	probably benign	Het
Gdf6	T	A	4: 9,844,494 (GRCm39)	V6D	possibly damaging	Het
Ghitm	C	A	14: 36,853,538 (GRCm39)	G101C	probably damaging	Het
Gimap5	T	A	6: 48,729,838 (GRCm39)	V136D	probably damaging	Het
Grm4	C	T	17: 27,654,345 (GRCm39)	G535D	probably damaging	Het
Gse1	T	C	8: 120,956,450 (GRCm39)	S314P	unknown	Het
Hnrnpdl	A	G	5: 100,185,014 (GRCm39)	I279T	probably damaging	Het
Idi2l	T	A	13: 8,993,340 (GRCm39)	H51L	probably damaging	Het
Itpr1	T	C	6: 108,366,345 (GRCm39)	S923P	probably damaging	Het
Krt39	C	A	11: 99,408,887 (GRCm39)	C303F	probably benign	Het
Lrrn1	T	C	6: 107,545,482 (GRCm39)	S427P	possibly damaging	Het
Lrrn3	T	A	12: 41,503,487 (GRCm39)	R277W	probably damaging	Het
Ltb4r1	T	C	14: 56,005,375 (GRCm39)	L226P	probably damaging	Het
Map1b	C	T	13: 99,644,648 (GRCm39)	R85Q	probably damaging	Het
Mcoln1	T	C	8: 3,557,285 (GRCm39)	L125P	probably damaging	Het
Nid1	T	G	13: 13,656,636 (GRCm39)	V589G	probably damaging	Het
Nlrp5	T	G	7: 23,116,951 (GRCm39)	F225C	probably benign	Het
Notch3	C	T	17: 32,376,940 (GRCm39)	A322T	probably damaging	Het
Or14c43	A	G	7: 86,115,063 (GRCm39)	H148R	probably benign	Het
Or52a5b	G	T	7: 103,417,026 (GRCm39)	Q193K	probably benign	Het
Or7g34	T	A	9: 19,478,162 (GRCm39)	T173S	probably benign	Het
Otogl	A	G	10: 107,639,524 (GRCm39)	C1363R	probably damaging	Het
Ovol1	T	A	19: 5,603,625 (GRCm39)	D92V	probably benign	Het
Pigt	T	C	2: 164,344,419 (GRCm39)	L356P	probably damaging	Het
Plekhg3	A	G	12: 76,612,996 (GRCm39)	Q434R	probably damaging	Het
Plekhh1	T	C	12: 79,126,326 (GRCm39)	F1344L	probably benign	Het
Polr1has	A	G	17: 37,275,275 (GRCm39)	D16G	probably damaging	Het
Psmd3	T	A	11: 98,586,377 (GRCm39)	L515Q	probably damaging	Het
Pus1	A	G	5: 110,922,452 (GRCm39)	L405P	probably damaging	Het
Qtrt2	T	A	16: 43,701,395 (GRCm39)	H55L	probably benign	Het
Rasgrp1	T	C	2: 117,118,424 (GRCm39)	I522V	probably damaging	Het
Raver2	T	A	4: 100,959,860 (GRCm39)	H113Q	probably damaging	Het
Recql4	T	C	15: 76,589,765 (GRCm39)	D760G	unknown	Het
Rhobtb3	C	T	13: 76,058,860 (GRCm39)	V313M	probably benign	Het
Rhox4d	G	A	X: 36,700,645 (GRCm39)	G191E	unknown	Het
Rictor	C	T	15: 6,801,635 (GRCm39)	S441L	probably benign	Het
Rnf185	T	C	11: 3,376,578 (GRCm39)	Q135R	probably benign	Het
Sh3pxd2a	T	A	19: 47,256,091 (GRCm39)	T904S	probably benign	Het
Slc4a10	T	C	2: 62,134,290 (GRCm39)	V1002A	probably benign	Het
Taf1b	T	C	12: 24,554,992 (GRCm39)	I55T	probably benign	Het
Tchh	CTCCGCCGGGAGCAAGAGCTCCGCCGGGAGCAAGAGTTCCGCCGGGAGCAAGAGCTCCGCCGGGAGCAAGAGTTCCGCCGGGAGCAAGAGCTCCGCC	CTCCGCCGGGAGCAAGAGCTCCGCCGGGAGCAAGAGTTCCGCCGGGAGCAAGAGCTCCGCC	3: 93,354,015 (GRCm39)		probably benign	Het
Tenm4	A	T	7: 96,523,420 (GRCm39)	D1654V	possibly damaging	Het
Tgfb1	G	A	7: 25,404,263 (GRCm39)	V357M	probably damaging	Het
Tnxb	C	T	17: 34,922,335 (GRCm39)	P2383S	possibly damaging	Het
Trpm1	A	T	7: 63,858,723 (GRCm39)	M382L	probably benign	Het
Trrap	A	G	5: 144,788,019 (GRCm39)	Y3516C	probably damaging	Het
Txnrd1	T	A	10: 82,721,067 (GRCm39)	Y494*	probably null	Het
Ubr2	C	T	17: 47,275,714 (GRCm39)	E811K	probably damaging	Het
Ubxn4	T	A	1: 128,172,280 (GRCm39)	F25I	possibly damaging	Het
Vmn2r117	A	G	17: 23,678,869 (GRCm39)	M785T	probably damaging	Het
Vmn2r99	G	A	17: 19,599,407 (GRCm39)	D364N	probably benign	Het
Vps45	C	A	3: 95,954,448 (GRCm39)		probably null	Het
Wdr25	A	C	12: 108,992,367 (GRCm39)	H426P	probably damaging	Het
Wdr83	A	T	8: 85,806,310 (GRCm39)	W136R	probably damaging	Het
Xylt1	A	C	7: 117,191,232 (GRCm39)	I343L	possibly damaging	Het
Zscan4b	T	C	7: 10,637,985 (GRCm39)	Q53R	possibly 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
R4786:Sema3f	UTSW	9	107,559,881 (GRCm39)	missense	probably benign	0.45
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
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'- CTCTCCATTGAGGTGGCTTC -3'
(R):5'- GCCAGAACCTCGGGATTCTATC -3'

Sequencing Primer
(F):5'- ATTGAGGTGGCTTCCTAATCCCAG -3'
(R):5'- GATTCTATCCAAAGCCCTGGGAG -3'

Posted On

2019-10-07