Mutagenetix > Incidental Mutation

Incidental Mutation 'R7640:Sema3f'

628329

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

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7640 (G1)

Quality Score

52.0072

Status

Validated

Chromosome

Chromosomal Location

107681500-107710475 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 107683575 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 644 (S644R)

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 benign
Transcript: ENSMUST00000080560
AA Change: S613R

PolyPhen 2 Score 0.434 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000079400
Gene: ENSMUSG00000034684
AA Change: S613R

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 benign
Transcript: ENSMUST00000192727
AA Change: S644R

PolyPhen 2 Score 0.196 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000141865
Gene: ENSMUSG00000034684
AA Change: S644R

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: 99.2%

Validation Efficiency

99% (68/69)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700013G24Rik	A	T	4: 137,454,594	N20I	probably damaging	Het
1700020D05Rik	T	A	19: 5,503,007	S249C	probably damaging	Het
4930558K02Rik	A	G	1: 161,957,149	S74P	probably benign	Het
4932415D10Rik	T	A	10: 82,294,656	N840I	probably damaging	Het
Abcb6	A	T	1: 75,174,845		probably null	Het
Adamts14	C	A	10: 61,246,057	A234S	probably benign	Het
Ankrd42	A	G	7: 92,619,635	S167P	probably benign	Het
Ap3m1	T	C	14: 21,038,175	I272V	probably benign	Het
Armt1	T	C	10: 4,453,572	F219S	probably damaging	Het
Atr	T	G	9: 95,907,293		probably null	Het
Cep72	G	A	13: 74,058,488	Q72*	probably null	Het
Clock	G	T	5: 76,248,378	L175M	possibly damaging	Het
Cnmd	T	A	14: 79,661,534	Y26F	possibly damaging	Het
Col6a6	A	T	9: 105,785,744	M198K	possibly damaging	Het
Cuta	C	T	17: 26,938,422	V135I	probably benign	Het
Ddx41	A	T	13: 55,534,239	M241K	possibly damaging	Het
Dnajc22	A	G	15: 99,101,114	N60S	probably damaging	Het
Drc3	A	G	11: 60,388,904	M432V	probably benign	Het
Eef1d	C	A	15: 75,902,707	G368C	probably damaging	Het
En2	A	T	5: 28,170,166	K236*	probably null	Het
Fas	A	G	19: 34,307,164	T24A	possibly damaging	Het
Gm13078	T	C	4: 143,726,706	V128A	probably benign	Het
Golga2	T	C	2: 32,306,239	V930A	probably benign	Het
Gprin2	G	T	14: 34,195,753	A20D	probably benign	Het
Ighv14-4	A	T	12: 114,176,444	C115*	probably null	Het
Impdh2	T	C	9: 108,565,181	Y459H	possibly damaging	Het
Klhdc7b	G	T	15: 89,387,260	V124L	possibly damaging	Het
L2hgdh	A	T	12: 69,721,357	Y122*	probably null	Het
Lamc2	A	T	1: 153,136,804	I708N	possibly damaging	Het
Large2	T	C	2: 92,374,705	M1V	probably null	Het
Lrit2	T	C	14: 37,072,124	W382R	probably damaging	Het
Mcee	T	A	7: 64,411,968	V173E	probably damaging	Het
Mcph1	T	A	8: 18,632,326	V493E	probably benign	Het
Mfap4	A	G	11: 61,487,087	N118D	probably damaging	Het
Mknk2	T	C	10: 80,668,566	S301G	probably benign	Het
Mlf1	G	A	3: 67,392,933	M94I	possibly damaging	Het
Mrc2	T	A	11: 105,332,295	S455T	possibly damaging	Het
Mrgprb5	T	G	7: 48,168,259	I243L	probably benign	Het
Muc4	C	A	16: 32,760,105	P360T		Het
Nat10	G	A	2: 103,743,090	A354V	probably damaging	Het
Nts	T	C	10: 102,490,304	Q7R	possibly damaging	Het
Oas1b	T	C	5: 120,821,414	L288P	probably damaging	Het
Olfr1076	A	G	2: 86,508,943	I161M	possibly damaging	Het
Olfr1131	A	G	2: 87,629,092	I94V	probably benign	Het
Olfr1196	T	A	2: 88,700,886	I148L	probably benign	Het
Olfr633	A	T	7: 103,946,943	I126F	probably damaging	Het
Otoa	A	G	7: 121,145,626	E869G	probably damaging	Het
Pcdhac2	T	C	18: 37,144,525	L186P	probably damaging	Het
Plekhh2	A	G	17: 84,610,776	E1271G	possibly damaging	Het
Pmepa1	C	T	2: 173,276,163	A8T	probably benign	Het
Rc3h2	A	G	2: 37,377,849		probably null	Het
Rlf	T	A	4: 121,146,801	M1771L	possibly damaging	Het
Rpap1	G	A	2: 119,764,410	P1372L	possibly damaging	Het
Rragd	A	T	4: 32,983,527	D22V	probably benign	Het
Sp110	G	A	1: 85,579,092	R417C	probably benign	Het
Specc1l	T	A	10: 75,257,869	N717K	probably damaging	Het
Sphkap	C	T	1: 83,278,928	D367N	possibly damaging	Het
Tbc1d21	C	T	9: 58,361,261	V272M	probably damaging	Het
Tmem132c	A	G	5: 127,563,006	D747G	probably damaging	Het
Tmem56	A	G	3: 121,235,041		probably null	Het
Trim2	C	A	3: 84,190,906	V372F	probably benign	Het
Ttc34	A	G	4: 154,861,384	T292A	probably benign	Het
Ube3b	A	G	5: 114,415,323	T919A	probably benign	Het
Wdr34	T	G	2: 30,031,768	D527A	probably benign	Het
Zfhx4	T	C	3: 5,412,480	I3385T	probably benign	Het
Zfp423	T	C	8: 87,781,277	K813R	probably damaging	Het
Zfp850	T	C	7: 27,989,209	T525A	probably benign	Het
Zfp873	T	C	10: 82,060,275	I280T	possibly damaging	Het
Zkscan7	A	G	9: 122,896,056	T697A	possibly damaging	Het

Other mutations in Sema3f

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00945:Sema3f	APN	9	107685522	missense	probably benign	0.44
IGL01940:Sema3f	APN	9	107683697	unclassified	probably benign
IGL02070:Sema3f	APN	9	107692241	missense	probably damaging	1.00
IGL02381:Sema3f	APN	9	107692395	missense	probably damaging	1.00
IGL02472:Sema3f	APN	9	107687736	missense	probably damaging	1.00
IGL02557:Sema3f	APN	9	107687212	missense	probably damaging	1.00
IGL02614:Sema3f	APN	9	107682511	missense	probably benign	0.28
IGL02660:Sema3f	APN	9	107683984	missense	probably benign	0.05
R1468:Sema3f	UTSW	9	107687572	unclassified	probably benign
R1905:Sema3f	UTSW	9	107684376	missense	probably damaging	1.00
R4728:Sema3f	UTSW	9	107705440	missense	probably benign	0.00
R4772:Sema3f	UTSW	9	107689720	nonsense	probably null
R4786:Sema3f	UTSW	9	107682682	missense	probably benign	0.45
R4845:Sema3f	UTSW	9	107685501	missense	probably damaging	1.00
R5418:Sema3f	UTSW	9	107692621	missense	probably damaging	1.00
R5780:Sema3f	UTSW	9	107682589	missense	probably damaging	0.98
R5849:Sema3f	UTSW	9	107682616	missense	probably damaging	0.98
R5929:Sema3f	UTSW	9	107692193	missense	probably damaging	1.00
R6968:Sema3f	UTSW	9	107691449	critical splice acceptor site	probably null
R7043:Sema3f	UTSW	9	107691400	missense	possibly damaging	0.91
R7449:Sema3f	UTSW	9	107684036	missense	probably damaging	1.00
R7526:Sema3f	UTSW	9	107689728	missense	probably damaging	0.96
R7559:Sema3f	UTSW	9	107684578	missense	possibly damaging	0.52
R7771:Sema3f	UTSW	9	107692426	missense	possibly damaging	0.89
R7789:Sema3f	UTSW	9	107705432	missense	probably benign	0.00
R8058:Sema3f	UTSW	9	107682601	missense	probably benign	0.42
R8113:Sema3f	UTSW	9	107688076	missense	possibly damaging	0.95
R9574:Sema3f	UTSW	9	107689773	missense	possibly damaging	0.50
R9641:Sema3f	UTSW	9	107688255	missense	unknown
R9674:Sema3f	UTSW	9	107689748	missense	possibly damaging	0.69
R9799:Sema3f	UTSW	9	107685363	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGGTATAACCCCGACAGAGTAC -3'
(R):5'- AGGAAGCCACCTCAATGGAG -3'

Sequencing Primer
(F):5'- GAACTTGCTCTGTAGACCAGACTG -3'
(R):5'- TCAATGGAGAGTCACCCAGCG -3'

Posted On

2020-03-06