Mutagenetix > Incidental Mutation

Incidental Mutation 'R9641:Sema3f'

725998

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

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9641 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

107558699-107587674 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 107565454 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 213 (I213T)

Ref Sequence

ENSEMBL: ENSMUSP00000141668 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000080560] [ENSMUST00000192727] [ENSMUST00000192783] [ENSMUST00000193108] [ENSMUST00000194039]

AlphaFold

O88632

Predicted Effect

silent
Transcript: ENSMUST00000080560

SMART Domains

Protein: ENSMUSP00000079400
Gene: ENSMUSG00000034684

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

silent
Transcript: ENSMUST00000192727

SMART Domains

Protein: ENSMUSP00000141865
Gene: ENSMUSG00000034684

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

unknown
Transcript: ENSMUST00000192783
AA Change: I213T

SMART Domains

Protein: ENSMUSP00000141668
Gene: ENSMUSG00000034684
AA Change: I213T

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

Predicted Effect

probably benign
Transcript: ENSMUST00000195023

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.8%
20x: 99.3%

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017N19Rik	T	C	10: 100,430,498 (GRCm39)	F52L	possibly damaging	Het
Abca16	T	C	7: 120,126,308 (GRCm39)	C1156R	possibly damaging	Het
Abcg3	A	C	5: 105,084,483 (GRCm39)	S571A	probably benign	Het
Abi3	C	A	11: 95,724,503 (GRCm39)	L259F	unknown	Het
Adam19	A	T	11: 46,027,149 (GRCm39)	D594V	probably damaging	Het
Adam34	C	T	8: 44,104,076 (GRCm39)	S523N	probably damaging	Het
Adam6b	G	T	12: 113,454,176 (GRCm39)	C331F	probably benign	Het
Adamts14	A	T	10: 61,106,829 (GRCm39)	V97E	probably damaging	Het
Adipor1	T	C	1: 134,355,878 (GRCm39)	Y226H	probably damaging	Het
Alox12e	T	C	11: 70,212,261 (GRCm39)	Y139C	probably damaging	Het
Ankrd53	A	G	6: 83,740,692 (GRCm39)	D160G	possibly damaging	Het
Ap1m1	A	T	8: 73,003,606 (GRCm39)	Y94F	probably damaging	Het
Arhgef28	A	C	13: 98,078,983 (GRCm39)	D1314E	probably benign	Het
Bicc1	A	G	10: 70,863,772 (GRCm39)	I90T	probably benign	Het
Celf6	A	G	9: 59,485,833 (GRCm39)	D58G	probably damaging	Het
Cfap74	T	C	4: 155,549,054 (GRCm39)	S38P	unknown	Het
Cps1	A	G	1: 67,234,342 (GRCm39)	I910V	probably benign	Het
Cracdl	C	T	1: 37,663,592 (GRCm39)	A769T	possibly damaging	Het
Crybg2	C	T	4: 133,816,620 (GRCm39)	Q1353*	probably null	Het
Cyp4f39	T	C	17: 32,705,982 (GRCm39)	Y358H	probably damaging	Het
Dcp1a	T	A	14: 30,241,132 (GRCm39)	I314N	probably damaging	Het
Dgki	A	C	6: 37,126,489 (GRCm39)	W164G	probably damaging	Het
Dnah8	A	G	17: 30,932,029 (GRCm39)	I1466V	probably benign	Het
Efcab6	T	A	15: 83,763,676 (GRCm39)	R1219W	probably damaging	Het
Faap24	A	T	7: 35,094,494 (GRCm39)	F102Y	probably damaging	Het
Fam186a	T	C	15: 99,838,244 (GRCm39)	T2667A	probably benign	Het
Frem1	C	T	4: 82,877,653 (GRCm39)	G1308D	probably damaging	Het
Hectd1	T	C	12: 51,816,047 (GRCm39)	T1347A	probably benign	Het
Hipk3	A	T	2: 104,267,376 (GRCm39)	H620Q	probably benign	Het
Hpd	A	G	5: 123,310,052 (GRCm39)	S391P	probably benign	Het
Ino80	A	G	2: 119,275,965 (GRCm39)	V437A	probably benign	Het
Itgax	G	T	7: 127,741,152 (GRCm39)	G785C	probably damaging	Het
Kcnk18	C	T	19: 59,223,266 (GRCm39)	T137I	probably damaging	Het
Kif16b	A	G	2: 142,542,589 (GRCm39)	F236L	probably benign	Het
Lamb1	T	C	12: 31,337,457 (GRCm39)	M396T	probably damaging	Het
Lrfn5	C	A	12: 61,886,540 (GRCm39)	N109K	probably damaging	Het
Lrrc15	T	A	16: 30,093,006 (GRCm39)	N111I	probably damaging	Het
Lrrk2	A	T	15: 91,671,251 (GRCm39)	I2011F	possibly damaging	Het
Lsr	A	G	7: 30,658,285 (GRCm39)	I336T	probably damaging	Het
Mettl21e	T	A	1: 44,250,351 (GRCm39)	R18S	probably benign	Het
Mrpl22	T	C	11: 58,068,047 (GRCm39)	L115P	probably damaging	Het
N4bp2	T	A	5: 65,948,035 (GRCm39)	S222T	probably benign	Het
Nat2	A	G	8: 67,954,522 (GRCm39)	T211A	probably benign	Het
Nbeal1	T	A	1: 60,350,247 (GRCm39)	I2432N	probably damaging	Het
Neb	A	G	2: 52,112,783 (GRCm39)	I1158T		Het
Nrip3	C	T	7: 109,362,793 (GRCm39)	E164K	probably damaging	Het
Obox6	G	A	7: 15,568,742 (GRCm39)	Q45*	probably null	Het
Ola1	T	C	2: 73,033,784 (GRCm39)	N44D	probably benign	Het
Or1x6	C	T	11: 50,939,207 (GRCm39)	T91M	probably benign	Het
Or2y1c	T	C	11: 49,361,509 (GRCm39)	F177S	probably damaging	Het
Or5b111	A	T	19: 13,291,100 (GRCm39)	M183K	probably damaging	Het
Or5d39	A	T	2: 87,980,255 (GRCm39)	I36N	possibly damaging	Het
Or5p81	A	T	7: 108,267,516 (GRCm39)	N298Y	probably damaging	Het
Or6ae1	A	G	7: 139,742,771 (GRCm39)	F31L	probably benign	Het
Or8b51	T	A	9: 38,568,915 (GRCm39)	M258L	probably benign	Het
Pde10a	A	G	17: 9,197,816 (GRCm39)	K753R		Het
Phldb1	T	C	9: 44,627,839 (GRCm39)	D202G	probably damaging	Het
Pik3cb	T	C	9: 98,955,789 (GRCm39)	N376S	probably benign	Het
Plekhh2	A	G	17: 84,874,130 (GRCm39)	N472D	probably damaging	Het
Ppp4r4	T	A	12: 103,567,811 (GRCm39)	F708Y	probably benign	Het
Rnf157	A	G	11: 116,303,576 (GRCm39)	V12A	probably benign	Het
Saa3	T	C	7: 46,364,494 (GRCm39)	I11V	probably benign	Het
Sall2	T	C	14: 52,550,882 (GRCm39)	E771G	probably damaging	Het
Sar1b	C	T	11: 51,670,573 (GRCm39)	T39I	probably damaging	Het
Scn10a	A	T	9: 119,445,869 (GRCm39)	L1428Q	possibly damaging	Het
Serpina3m	C	T	12: 104,360,085 (GRCm39)	Q386*	probably null	Het
Sh3gl3	G	A	7: 81,909,370 (GRCm39)	G26R	probably damaging	Het
Shq1	T	C	6: 100,550,633 (GRCm39)	E435G	probably damaging	Het
Sidt2	G	T	9: 45,864,495 (GRCm39)	A78E	probably benign	Het
Sin3b	A	G	8: 73,477,187 (GRCm39)	Y818C	probably damaging	Het
Smarca2	C	T	19: 26,656,498 (GRCm39)	L825F	possibly damaging	Het
Srgn	T	A	10: 62,330,884 (GRCm39)	M74L	probably benign	Het
Tbc1d22b	A	C	17: 29,813,747 (GRCm39)	D360A	possibly damaging	Het
Tbx4	A	G	11: 85,803,128 (GRCm39)	R335G	probably damaging	Het
Tmem144	T	C	3: 79,734,200 (GRCm39)	N168D	probably benign	Het
Trip11	G	A	12: 101,859,957 (GRCm39)	Q307*	probably null	Het
Ttyh2	T	C	11: 114,598,516 (GRCm39)	Y296H	probably damaging	Het
Vmn1r236	G	T	17: 21,507,043 (GRCm39)	V54F	probably benign	Het
Xrra1	A	C	7: 99,561,088 (GRCm39)	H443P	probably benign	Het
Zc3h12a	T	C	4: 125,014,852 (GRCm39)	T211A	probably damaging	Het
Zfp386	T	G	12: 116,023,330 (GRCm39)	D349E	probably benign	Het
Zkscan16	T	A	4: 58,956,577 (GRCm39)	H286Q	probably benign	Het
Znrf2	C	T	6: 54,861,788 (GRCm39)	P233L	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
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
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
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'- GGGATGAGCTCAGCATGTATG -3'
(R):5'- AGATAGGATCTGGCCCTGTG -3'

Sequencing Primer
(F):5'- CTCAGCATGTATGAAGGAAGGATCTG -3'
(R):5'- CCCCAGGGCATCTTGAAGGAAG -3'

Posted On

2022-09-12