Mutagenetix > Incidental Mutation

Incidental Mutation 'R4728:Sema3f'

358613

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

042020-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4728 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

107558699-107587674 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 107582639 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 35 (S35P)

Ref Sequence

ENSEMBL: ENSMUSP00000142221 (fasta)

Gene Model

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

AlphaFold

O88632

Predicted Effect

probably benign
Transcript: ENSMUST00000080560
AA Change: S35P

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000079400
Gene: ENSMUSG00000034684
AA Change: S35P

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: ENSMUST00000192727
AA Change: S35P

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000141865
Gene: ENSMUSG00000034684
AA Change: S35P

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: ENSMUST00000193108
AA Change: S35P

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000141878
Gene: ENSMUSG00000034684
AA Change: S35P

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
AA Change: S35P

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000142221
Gene: ENSMUSG00000034684
AA Change: S35P

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

Meta Mutation Damage Score

0.1381

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.3%

Validation Efficiency

94% (73/78)

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Bicc1	C	T	10: 70,771,661 (GRCm39)		probably null	Het
Bpifc	T	A	10: 85,827,063 (GRCm39)	H162L	possibly damaging	Het
Ccdc163	C	T	4: 116,566,209 (GRCm39)		probably benign	Het
Cldn12	A	G	5: 5,558,385 (GRCm39)	F14S	probably damaging	Het
Cyth4	G	A	15: 78,486,913 (GRCm39)	G14R	probably benign	Het
Ddhd2	C	T	8: 26,242,294 (GRCm39)	V194I	probably damaging	Het
Ddx23	A	T	15: 98,548,106 (GRCm39)	V433E	probably damaging	Het
Defb34	A	G	8: 19,176,434 (GRCm39)	N42D	possibly damaging	Het
Dennd6a	A	G	14: 26,348,575 (GRCm39)	E313G	probably null	Het
Dhx30	A	G	9: 109,916,718 (GRCm39)	F570S	probably damaging	Het
Dnah3	T	C	7: 119,658,589 (GRCm39)	E864G	probably damaging	Het
Eps8	G	A	6: 137,486,160 (GRCm39)	Q451*	probably null	Het
Fmo9	A	T	1: 166,490,880 (GRCm39)	Y533N	possibly damaging	Het
Fut8	T	A	12: 77,521,973 (GRCm39)	D537E	probably damaging	Het
Gm5407	T	C	16: 49,117,283 (GRCm39)		noncoding transcript	Het
Gm9916	A	G	3: 118,228,690 (GRCm39)		noncoding transcript	Het
Grm5	T	A	7: 87,624,496 (GRCm39)	F354L	probably damaging	Het
Hira	C	T	16: 18,741,654 (GRCm39)	A353V	probably damaging	Het
Ifna4	C	A	4: 88,760,519 (GRCm39)	T141K	probably benign	Het
Igf1r	T	C	7: 67,839,372 (GRCm39)	L628P	probably damaging	Het
Kcnh5	A	T	12: 75,054,555 (GRCm39)	I463N	probably damaging	Het
Kcnh8	C	A	17: 53,032,898 (GRCm39)	Q62K	probably damaging	Het
Kif3c	A	T	12: 3,415,873 (GRCm39)		probably benign	Het
Kmo	A	G	1: 175,484,329 (GRCm39)	D353G	possibly damaging	Het
Lrp1	T	C	10: 127,399,606 (GRCm39)	T2301A	probably damaging	Het
Lrrc7	GAAGTTGTTTGGAGATTCTTATCTTA	GA	3: 158,024,045 (GRCm39)		probably benign	Het
Map3k9	C	T	12: 81,769,147 (GRCm39)	R967Q	probably damaging	Het
Mcm8	A	G	2: 132,674,774 (GRCm39)	H414R	probably damaging	Het
Mier1	A	G	4: 102,997,402 (GRCm39)	E145G	probably damaging	Het
Mlc1	A	T	15: 88,862,234 (GRCm39)		probably null	Het
Napb	T	C	2: 148,551,245 (GRCm39)	D96G	probably damaging	Het
Nbas	T	A	12: 13,338,740 (GRCm39)	S193R	probably damaging	Het
Nlrp4a	T	C	7: 26,174,515 (GRCm39)	V967A	probably benign	Het
Nlrp4e	T	A	7: 23,020,989 (GRCm39)	I492K	probably benign	Het
Notch4	A	G	17: 34,789,179 (GRCm39)	T497A	probably benign	Het
Npdc1	G	A	2: 25,298,957 (GRCm39)	D284N	probably damaging	Het
Ogdh	T	A	11: 6,292,549 (GRCm39)	Y417N	probably damaging	Het
Or5w19	T	C	2: 87,698,779 (GRCm39)	V148A	probably benign	Het
Ovol1	A	T	19: 5,603,690 (GRCm39)	Y70*	probably null	Het
P2ry1	A	G	3: 60,911,641 (GRCm39)	Y260C	probably damaging	Het
Pcx	G	T	19: 4,653,124 (GRCm39)	R263L	probably damaging	Het
Pla2g4f	T	A	2: 120,131,402 (GRCm39)	T774S	probably benign	Het
Prdm15	T	G	16: 97,622,986 (GRCm39)	K289Q	probably benign	Het
Prl7c1	A	T	13: 27,960,268 (GRCm39)	H91Q	probably benign	Het
Prmt5	C	T	14: 54,745,364 (GRCm39)	R601H	probably benign	Het
Prrc2b	T	A	2: 32,120,637 (GRCm39)	D2192E	probably damaging	Het
Ptdss2	A	G	7: 140,734,372 (GRCm39)	I299V	probably benign	Het
Rbm28	A	G	6: 29,143,591 (GRCm39)	V354A	probably damaging	Het
Rps6kb1	G	C	11: 86,435,484 (GRCm39)		probably null	Het
Serpina3n	A	T	12: 104,375,422 (GRCm39)	T165S	probably benign	Het
Serpinb13	C	T	1: 106,910,574 (GRCm39)	S66L	probably damaging	Het
Sh2d4b	T	A	14: 40,564,389 (GRCm39)	R267*	probably null	Het
Slc5a12	A	T	2: 110,474,769 (GRCm39)	K554*	probably null	Het
Snrnp200	T	C	2: 127,059,334 (GRCm39)	L409P	probably damaging	Het
Snrnp200	T	A	2: 127,069,798 (GRCm39)	V981E	possibly damaging	Het
Spon2	T	A	5: 33,374,682 (GRCm39)	R41S	probably benign	Het
Sptb	A	T	12: 76,630,153 (GRCm39)	M2279K	probably benign	Het
Srcap	T	G	7: 127,140,096 (GRCm39)		probably null	Het
Tctn3	A	G	19: 40,594,186 (GRCm39)	V409A	probably damaging	Het
Tg	A	C	15: 66,554,676 (GRCm39)	Q697P	probably damaging	Het
Tmem181a	A	G	17: 6,340,874 (GRCm39)	D141G	probably benign	Het
Tmem82	A	G	4: 141,341,963 (GRCm39)	S334P	probably benign	Het
Ubr4	A	G	4: 139,151,190 (GRCm39)	Y1875C	probably damaging	Het
Vmn1r63	C	A	7: 5,806,362 (GRCm39)	R90L	probably damaging	Het
Zfp330	A	C	8: 83,497,475 (GRCm39)	Y56D	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
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
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'- AGGACCCTCTCTCAAAATATCTCAG -3'
(R):5'- GCTGCATACGGAAATGGCTC -3'

Sequencing Primer
(F):5'- TCAAAATATCTCAGTCCTCAGTGC -3'
(R):5'- GAAATGGCTCACACATTCCAACTTTG -3'

Posted On

2015-11-11