Mutagenetix > Incidental Mutation

Incidental Mutation 'R3916:Sema3b'

309755

Institutional Source

Beutler Lab

Gene Symbol

Sema3b

Ensembl Gene

ENSMUSG00000057969

Gene Name

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

Synonyms

SemA, sema5, semaV, Semaa, LUCA-1, SemA

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.410) question?

Stock #

R3916 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

107597674-107609229 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 107600458 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Serine at position 482 (F482S)

Ref Sequence

ENSEMBL: ENSMUSP00000137952 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000073448] [ENSMUST00000102529] [ENSMUST00000102530] [ENSMUST00000102531] [ENSMUST00000102532] [ENSMUST00000123926] [ENSMUST00000193180] [ENSMUST00000194433] [ENSMUST00000194606] [ENSMUST00000195662] [ENSMUST00000195057]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000073448
AA Change: F482S

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

SMART Domains

Protein: ENSMUSP00000073152
Gene: ENSMUSG00000057969
AA Change: F482S

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Sema	55	497	6.37e-207	SMART
PSI	515	567	1.77e-13	SMART
IG	577	660	7.7e-5	SMART
low complexity region	665	683	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000102529
AA Change: F482S

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

SMART Domains

Protein: ENSMUSP00000099588
Gene: ENSMUSG00000057969
AA Change: F482S

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Sema	55	497	6.37e-207	SMART
PSI	515	567	1.77e-13	SMART
IG	577	660	7.7e-5	SMART
low complexity region	665	683	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000102530
AA Change: F482S

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

SMART Domains

Protein: ENSMUSP00000099589
Gene: ENSMUSG00000057969
AA Change: F482S

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Sema	55	497	6.37e-207	SMART
PSI	515	567	1.77e-13	SMART
IG	577	660	7.7e-5	SMART
low complexity region	665	683	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000102531
AA Change: F482S

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

SMART Domains

Protein: ENSMUSP00000099590
Gene: ENSMUSG00000057969
AA Change: F482S

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Sema	55	497	6.37e-207	SMART
PSI	515	567	1.77e-13	SMART
IG	577	660	7.7e-5	SMART
low complexity region	665	683	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000102532
AA Change: F482S

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

SMART Domains

Protein: ENSMUSP00000099591
Gene: ENSMUSG00000057969
AA Change: F482S

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Sema	55	497	6.37e-207	SMART
PSI	515	567	1.77e-13	SMART
IG	577	660	7.7e-5	SMART
low complexity region	665	683	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000123926
AA Change: F482S

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

SMART Domains

Protein: ENSMUSP00000137952
Gene: ENSMUSG00000057969
AA Change: F482S

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Sema	55	497	6.37e-207	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000191791

Predicted Effect

probably benign
Transcript: ENSMUST00000193180

SMART Domains

Protein: ENSMUSP00000141726
Gene: ENSMUSG00000057969

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Pfam:Sema	55	148	8.2e-31	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000193234

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000193551

Predicted Effect

probably benign
Transcript: ENSMUST00000194433

SMART Domains

Protein: ENSMUSP00000141403
Gene: ENSMUSG00000057969

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Pfam:Sema	55	172	3.5e-36	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000194606

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000195472

Predicted Effect

probably benign
Transcript: ENSMUST00000195662

SMART Domains

Protein: ENSMUSP00000141614
Gene: ENSMUSG00000057969

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Pfam:Sema	55	137	8.4e-26	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000195057

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.4%

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a secreted protein that belongs to the class 3 semaphorin/collapsin family. Members of this family play a role in growth cone guidance during neurogenesis. The encoded protein inhibits axonal extension. This protein is thought to be an osteoblast protein that regulates bone mass and affects skeletal homeostasis. A similar gene in humans functions as a tumor suppressor gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]
PHENOTYPE: Mice homozygous for one knock-out allele are viable and fertile with no obvious pathological abnormalities. Mice homozygous for a second knock-out allele exhibit improper positioning of a major brain commissural projection, the anterior commissure. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932414N04Rik	T	G	2: 68,731,985	F319V	possibly damaging	Het
Acad12	A	G	5: 121,599,214	V498A	probably damaging	Het
Adam19	A	G	11: 46,060,935	E37G	probably benign	Het
Anks3	A	G	16: 4,947,279	Y423H	probably damaging	Het
Arfgef1	A	T	1: 10,189,443	V600D	probably benign	Het
Arhgef18	T	C	8: 3,454,197	F939L	probably benign	Het
Arhgef2	A	G	3: 88,633,033	N127S	probably damaging	Het
Arid1b	A	G	17: 5,342,653	S2100G	probably benign	Het
Atp1b2	A	G	11: 69,603,075	V93A	probably damaging	Het
Atrnl1	T	C	19: 57,935,652	V1283A	possibly damaging	Het
Bpifb5	A	C	2: 154,228,181	K184Q	probably benign	Het
Cadps	C	T	14: 12,457,702	A1060T	probably benign	Het
Cant1	A	G	11: 118,408,746	V259A	probably damaging	Het
Ccdc89	A	G	7: 90,426,825	D81G	probably damaging	Het
Cd109	CATTTATTTATTTATTTATTTATTTATTTATTTAT	CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT	9: 78,712,500		probably benign	Het
Cntnap4	C	G	8: 112,875,533	P1190A	probably benign	Het
Colgalt2	T	A	1: 152,508,611	Y567*	probably null	Het
Cyp4f18	A	T	8: 71,996,037	F256Y	probably benign	Het
Ddx41	G	A	13: 55,534,480	R205W	possibly damaging	Het
Dopey1	G	A	9: 86,521,133	R1462H	probably damaging	Het
Dync1i2	A	G	2: 71,249,372	T377A	probably damaging	Het
F2	G	A	2: 91,625,488	T600M	probably damaging	Het
Fam91a1	C	T	15: 58,430,734	H308Y	probably damaging	Het
Fkbp2	C	A	19: 6,978,557		probably null	Het
Gabarapl2	T	A	8: 111,952,396	F115L	probably benign	Het
Heatr3	T	G	8: 88,150,371		probably null	Het
Ifi204	T	G	1: 173,755,775	K292N	possibly damaging	Het
Itpkc	A	T	7: 27,228,303	I62N	probably benign	Het
Kcnab1	G	A	3: 65,304,164		probably null	Het
Krt88	G	A	15: 101,452,928		probably null	Het
Larp4	C	T	15: 99,990,403	T107I	probably benign	Het
Lmo7	T	C	14: 101,929,342		probably benign	Het
Lrrc37a	T	C	11: 103,455,518	Y3174C	possibly damaging	Het
Lyzl4	T	A	9: 121,583,035	D105V	probably damaging	Het
Mst1	A	G	9: 108,084,295	I575V	probably benign	Het
Myh7	C	A	14: 54,974,046	E1555D	probably damaging	Het
Nwd1	T	A	8: 72,667,811	C608*	probably null	Het
Obox3	C	A	7: 15,627,226	C38F	probably benign	Het
P4ha2	A	G	11: 54,126,248	D441G	probably benign	Het
Pcdhb14	A	T	18: 37,448,545	I235F	possibly damaging	Het
Rasgrf2	A	G	13: 92,030,788	V259A	probably damaging	Het
Scn1a	T	C	2: 66,277,613	T1590A	probably damaging	Het
Sdk1	T	A	5: 142,051,244	D817E	probably damaging	Het
Slc35a5	G	C	16: 45,158,158		probably benign	Het
Slc6a3	A	G	13: 73,562,308	I346V	probably benign	Het
Slu7	G	T	11: 43,440,684		probably null	Het
Spns1	A	T	7: 126,371,539		probably null	Het
Supv3l1	T	C	10: 62,449,420	D89G	possibly damaging	Het
Taf1c	G	A	8: 119,600,505	R412W	probably damaging	Het
Tctn3	T	A	19: 40,607,649	T305S	possibly damaging	Het
Tekt1	A	G	11: 72,345,748	I296T	possibly damaging	Het
Tet2	T	C	3: 133,486,055	K873E	possibly damaging	Het
Thada	G	A	17: 84,441,782	A587V	possibly damaging	Het
Tmprss15	T	A	16: 78,985,996	N712Y	probably damaging	Het
Tnks	A	G	8: 34,853,361	S719P	probably damaging	Het
Tnrc6a	A	C	7: 123,181,384	Q1332H	probably damaging	Het
Trpv3	A	G	11: 73,283,734	D309G	possibly damaging	Het
Tti2	A	G	8: 31,153,519	K221E	possibly damaging	Het
Uba5	A	T	9: 104,054,190	C227S	probably damaging	Het
Ugcg	C	T	4: 59,207,798	P46S	probably benign	Het
Unc80	T	C	1: 66,677,495	C2925R	probably benign	Het
Vmn2r83	G	A	10: 79,478,910	G331R	probably benign	Het
Xirp2	G	T	2: 67,511,422	V1336F	probably benign	Het
Zbed5	T	C	5: 129,902,277	Y356H	possibly damaging	Het

Other mutations in Sema3b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00674:Sema3b	APN	9	107604041	critical splice donor site	probably null
IGL02750:Sema3b	APN	9	107603164	missense	probably benign	0.02
IGL02878:Sema3b	APN	9	107600993	missense	probably damaging	0.97
IGL03004:Sema3b	APN	9	107602915	missense	possibly damaging	0.72
IGL03026:Sema3b	APN	9	107602063	missense	probably damaging	1.00
IGL03129:Sema3b	APN	9	107599796	unclassified	probably benign
IGL03334:Sema3b	APN	9	107604077	missense	probably damaging	1.00
R0373:Sema3b	UTSW	9	107602918	missense	probably benign	0.05
R0384:Sema3b	UTSW	9	107600966	missense	probably damaging	1.00
R0883:Sema3b	UTSW	9	107604156	missense	possibly damaging	0.77
R3971:Sema3b	UTSW	9	107600368	missense	probably benign
R4212:Sema3b	UTSW	9	107603398	missense	probably damaging	1.00
R4647:Sema3b	UTSW	9	107599051	missense	possibly damaging	0.79
R4694:Sema3b	UTSW	9	107605002	missense	probably benign	0.03
R4791:Sema3b	UTSW	9	107603813	missense	probably damaging	1.00
R4853:Sema3b	UTSW	9	107602067	splice site	probably null
R5305:Sema3b	UTSW	9	107603337	missense	probably null	1.00
R5487:Sema3b	UTSW	9	107600962	missense	probably damaging	1.00
R5745:Sema3b	UTSW	9	107601429	missense	probably damaging	0.98
R5751:Sema3b	UTSW	9	107599714	missense	probably benign
R6086:Sema3b	UTSW	9	107600848	missense	probably damaging	1.00
R6306:Sema3b	UTSW	9	107600920	missense	possibly damaging	0.88
R6594:Sema3b	UTSW	9	107598826	missense	probably benign	0.01
R6816:Sema3b	UTSW	9	107600350	missense	probably benign	0.08
R6833:Sema3b	UTSW	9	107603316	missense	probably benign	0.04
R7320:Sema3b	UTSW	9	107600942	missense	probably benign
R7448:Sema3b	UTSW	9	107602963	missense	probably damaging	1.00
R7687:Sema3b	UTSW	9	107603814	missense	probably damaging	1.00
R8839:Sema3b	UTSW	9	107601353	unclassified	probably benign
R9090:Sema3b	UTSW	9	107598955	missense	probably damaging	1.00
R9123:Sema3b	UTSW	9	107600974	missense	possibly damaging	0.64
R9271:Sema3b	UTSW	9	107598955	missense	probably damaging	1.00
R9442:Sema3b	UTSW	9	107601758	critical splice donor site	probably null
R9682:Sema3b	UTSW	9	107603814	missense	probably damaging	1.00
R9755:Sema3b	UTSW	9	107601585	missense	probably damaging	1.00
Z1088:Sema3b	UTSW	9	107599034	splice site	probably null
Z1176:Sema3b	UTSW	9	107599639	missense	possibly damaging	0.89

Predicted Primers

PCR Primer
(F):5'- CGGGGCTTTGAAAACCAAGG -3'
(R):5'- CCCAATCATGATGATGGTGGAG -3'

Sequencing Primer
(F):5'- CTTTGAAAACCAAGGAGAAGCTAGAC -3'
(R):5'- CAATCATGATGATGGTGGAGACAGG -3'

Posted On

2015-04-17