Mutagenetix > Incidental Mutation

Incidental Mutation 'R7687:Sema3b'

593156

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

Essential gene?

Possibly non essential (E-score: 0.319) question?

Stock #

R7687 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

107597674-107609229 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 107603814 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 108 (D108G)

Ref Sequence

ENSEMBL: ENSMUSP00000073152 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000073448
AA Change: D108G

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

SMART Domains

Protein: ENSMUSP00000073152
Gene: ENSMUSG00000057969
AA Change: D108G

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: D108G

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

SMART Domains

Protein: ENSMUSP00000099588
Gene: ENSMUSG00000057969
AA Change: D108G

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: D108G

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

SMART Domains

Protein: ENSMUSP00000099589
Gene: ENSMUSG00000057969
AA Change: D108G

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: D108G

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

SMART Domains

Protein: ENSMUSP00000099590
Gene: ENSMUSG00000057969
AA Change: D108G

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: D108G

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

SMART Domains

Protein: ENSMUSP00000099591
Gene: ENSMUSG00000057969
AA Change: D108G

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: D108G

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000137952
Gene: ENSMUSG00000057969
AA Change: D108G

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000193180
AA Change: D108G

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

SMART Domains

Protein: ENSMUSP00000141726
Gene: ENSMUSG00000057969
AA Change: D108G

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000194433
AA Change: D108G

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

SMART Domains

Protein: ENSMUSP00000141403
Gene: ENSMUSG00000057969
AA Change: D108G

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

probably benign
Transcript: ENSMUST00000195057

Predicted Effect

probably damaging
Transcript: ENSMUST00000195662
AA Change: D108G

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

SMART Domains

Protein: ENSMUSP00000141614
Gene: ENSMUSG00000057969
AA Change: D108G

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca12	T	C	1: 71,258,182	K2383R	probably benign	Het
Acly	C	T	11: 100,504,854		probably null	Het
Baiap3	T	A	17: 25,249,337	I276F	possibly damaging	Het
Cdc14b	A	T	13: 64,209,193	D419E	probably benign	Het
Celsr2	G	T	3: 108,397,769	P2165T	probably benign	Het
Clk4	A	G	11: 51,281,398	D476G	probably benign	Het
Dera	A	G	6: 137,836,880	T10A		Het
Dip2c	A	T	13: 9,604,581	T742S	probably benign	Het
Dohh	C	A	10: 81,387,806	A231E	probably benign	Het
Dot1l	T	G	10: 80,789,368	S1150A	possibly damaging	Het
Eea1	T	A	10: 96,026,598	I794N	probably benign	Het
En2	T	C	5: 28,170,289	S277P	probably damaging	Het
Erich1	A	G	8: 14,030,691	L276P	probably damaging	Het
Flnb	A	G	14: 7,924,224	N1779S	probably damaging	Het
Frzb	T	A	2: 80,424,635	T186S	probably benign	Het
Gdf7	T	A	12: 8,298,257	R347*	probably null	Het
Ighv9-4	T	C	12: 114,300,263	I17V	not run	Het
Ipo13	G	A	4: 117,911,891	P235S	probably benign	Het
Itga2	C	A	13: 114,866,260	G565C	probably damaging	Het
Kcnc4	CCCGCCGCCGCCGCCGCCGCCGC	CCCGCCGCCGCCGCCGCCGCCGCCGC	3: 107,458,609		probably benign	Het
Kcnk10	A	G	12: 98,435,096	I440T	probably damaging	Het
Kdm3a	T	A	6: 71,599,492	K779N	possibly damaging	Het
Kmt2d	C	T	15: 98,862,120	D1086N	unknown	Het
Kntc1	A	G	5: 123,759,089	I172V	probably benign	Het
Maip1	A	G	1: 57,411,844	E215G	probably damaging	Het
Mms19	A	T	19: 41,955,168	M417K	possibly damaging	Het
Mslnl	T	C	17: 25,743,183	V185A	probably damaging	Het
Naa11	A	T	5: 97,391,789	V170E	probably benign	Het
Ncapg	C	T	5: 45,699,885	P980S	probably benign	Het
Olfr170	T	C	16: 19,605,735	N310S	probably benign	Het
Pbxip1	A	G	3: 89,448,199	D675G	probably damaging	Het
Pdlim5	A	G	3: 142,277,847	S382P	probably benign	Het
Pkd1l1	T	A	11: 8,854,390	I2184F		Het
Plau	A	G	14: 20,839,798	Y237C	probably damaging	Het
Ppl	T	C	16: 5,097,942	T586A	probably benign	Het
Rapgef6	T	G	11: 54,661,075	I923S	possibly damaging	Het
Rbfox2	C	T	15: 77,306,494	G17D	unknown	Het
Slc6a20a	A	G	9: 123,656,266	I297T	probably damaging	Het
Slit1	A	G	19: 41,650,689	F261L	probably benign	Het
Tcp10a	T	A	17: 7,345,108	V433D	probably damaging	Het
Tktl2	A	G	8: 66,513,101	E437G	probably damaging	Het
Tll1	G	T	8: 64,121,492	Y109*	probably null	Het
Tmem79	A	G	3: 88,332,581	V274A	probably damaging	Het
Tnfrsf23	G	A	7: 143,681,462	S55L	probably benign	Het
Ubd	T	C	17: 37,193,974		probably null	Het
Ubl3	C	A	5: 148,506,175	R105L	possibly damaging	Het
Ubl7	A	T	9: 57,914,584	D72V	probably damaging	Het
Wdr55	T	C	18: 36,762,023	S81P	probably damaging	Het
Wtip	T	C	7: 34,116,619	Y344C	probably damaging	Het
Zfp488	A	G	14: 33,970,400	S269P	possibly damaging	Het
Zkscan2	A	C	7: 123,499,862	S36A	probably benign	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
R3916:Sema3b	UTSW	9	107600458	missense	probably damaging	1.00
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
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'- ACCTTCACAGGGTAACTACATGAG -3'
(R):5'- TAGGGTCCCAATCCAGTCTG -3'

Sequencing Primer
(F):5'- TCCCCCTGTGACTCAGAG -3'
(R):5'- GTCTAGACTCTAGAGAATCTCCAAGG -3'

Posted On

2019-11-12