Mutagenetix > Incidental Mutation

Incidental Mutation 'R7448:Sema3b'

577485

Institutional Source

Beutler Lab

Gene Symbol

Sema3b

Ensembl Gene

ENSMUSG00000057969

Gene Name

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

Synonyms

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

MMRRC Submission

045523-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.321) question?

Stock #

R7448 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

107474873-107486428 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 107480162 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 192 (D192V)

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: D192V

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

SMART Domains

Protein: ENSMUSP00000073152
Gene: ENSMUSG00000057969
AA Change: D192V

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: D192V

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

SMART Domains

Protein: ENSMUSP00000099588
Gene: ENSMUSG00000057969
AA Change: D192V

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: D192V

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

SMART Domains

Protein: ENSMUSP00000099589
Gene: ENSMUSG00000057969
AA Change: D192V

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: D192V

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

SMART Domains

Protein: ENSMUSP00000099590
Gene: ENSMUSG00000057969
AA Change: D192V

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: D192V

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

SMART Domains

Protein: ENSMUSP00000099591
Gene: ENSMUSG00000057969
AA Change: D192V

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: D192V

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

SMART Domains

Protein: ENSMUSP00000137952
Gene: ENSMUSG00000057969
AA Change: D192V

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

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

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

probably benign
Transcript: ENSMUST00000195057

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 98.9%

Validation Efficiency

100% (117/117)

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: 119 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acss2	T	C	2: 155,360,186 (GRCm39)	S54P	probably damaging	Het
Ahnak2	T	C	12: 112,746,605 (GRCm39)	K1242E		Het
Alpi	T	A	1: 87,029,257 (GRCm39)	M1L	possibly damaging	Het
Atp2c1	C	T	9: 105,329,982 (GRCm39)	A283T	probably damaging	Het
Atp8b5	T	G	4: 43,366,021 (GRCm39)	M764R	probably benign	Het
B4galnt2	T	A	11: 95,760,193 (GRCm39)	H278L	probably damaging	Het
Bcl9l	G	T	9: 44,420,634 (GRCm39)	A1347S	probably benign	Het
Bicd2	A	G	13: 49,533,427 (GRCm39)	E671G	probably damaging	Het
Bmp3	A	T	5: 99,020,077 (GRCm39)	I167F	probably damaging	Het
Bpifb5	T	A	2: 154,072,105 (GRCm39)	C271S	possibly damaging	Het
Camsap2	T	A	1: 136,198,644 (GRCm39)	H793L		Het
Casp8ap2	T	A	4: 32,643,974 (GRCm39)	S1016T	possibly damaging	Het
Castor1	A	G	11: 4,171,897 (GRCm39)	S325G	not run	Het
Ccdc134	T	A	15: 82,025,149 (GRCm39)	I216N	possibly damaging	Het
Ccdc63	G	T	5: 122,246,245 (GRCm39)	R559S	probably benign	Het
Cd276	T	C	9: 58,442,895 (GRCm39)	T187A	probably benign	Het
Ciao1	C	T	2: 127,087,678 (GRCm39)	R219H	probably damaging	Het
Clmn	T	C	12: 104,751,687 (GRCm39)	D256G	possibly damaging	Het
Cobl	A	C	11: 12,206,225 (GRCm39)	M550R	possibly damaging	Het
Cracr2b	A	T	7: 141,044,118 (GRCm39)	T117S	probably benign	Het
Cx3cr1	G	A	9: 119,881,282 (GRCm39)	A40V	probably benign	Het
Cxcl14	A	G	13: 56,440,344 (GRCm39)	C72R	probably damaging	Het
Dab2	T	A	15: 6,451,747 (GRCm39)	I121N	probably damaging	Het
Dapk1	A	G	13: 60,898,990 (GRCm39)	Y820C	probably damaging	Het
Dele1	A	G	18: 38,390,319 (GRCm39)	N256D	probably damaging	Het
Ech1	T	A	7: 28,525,623 (GRCm39)	C91S	probably damaging	Het
Exosc5	T	G	7: 25,358,734 (GRCm39)	V25G	probably benign	Het
Fbp1	A	C	13: 63,020,564 (GRCm39)	D122E	possibly damaging	Het
Fbxw13	A	G	9: 109,014,471 (GRCm39)	Y101H	unknown	Het
Fcsk	C	T	8: 111,616,963 (GRCm39)	G396S	possibly damaging	Het
Fhip1a	G	A	3: 85,579,871 (GRCm39)	S778L	probably benign	Het
Fmnl1	T	A	11: 103,077,453 (GRCm39)	V271E	probably damaging	Het
Galnt1	T	A	18: 24,417,866 (GRCm39)	S545T	probably benign	Het
Galnt13	G	A	2: 54,406,576 (GRCm39)	V9M	possibly damaging	Het
Gm7995	A	T	14: 42,132,302 (GRCm39)	I45F		Het
Gpr137	C	T	19: 6,917,726 (GRCm39)	R134Q	possibly damaging	Het
Gpr22	T	G	12: 31,759,514 (GRCm39)	I203L	probably benign	Het
H2-Q10	T	C	17: 35,784,457 (GRCm39)	Y324H	not run	Het
Hcn4	G	A	9: 58,751,582 (GRCm39)	E403K	unknown	Het
Hddc2	T	A	10: 31,189,412 (GRCm39)	M1K	probably null	Het
Hps3	A	G	3: 20,089,329 (GRCm39)	F34S	probably damaging	Het
Ift56	T	A	6: 38,381,422 (GRCm39)	Y319*	probably null	Het
Igdcc4	G	T	9: 65,031,276 (GRCm39)	V405L	possibly damaging	Het
Itpr2	C	A	6: 146,231,006 (GRCm39)	V1215L	probably damaging	Het
Kif26b	T	C	1: 178,742,339 (GRCm39)	S812P	probably damaging	Het
Lgi1	T	A	19: 38,289,713 (GRCm39)	C260S	probably damaging	Het
Lhfpl6	A	G	3: 53,168,020 (GRCm39)	Y198C	probably damaging	Het
Lrp5	T	C	19: 3,699,439 (GRCm39)	D282G	probably benign	Het
Lrpprc	T	C	17: 85,079,567 (GRCm39)	T230A	probably damaging	Het
Lrtm2	A	G	6: 119,297,784 (GRCm39)	W86R	probably benign	Het
Maco1	A	T	4: 134,555,590 (GRCm39)	N294K	possibly damaging	Het
Magi2	G	A	5: 20,563,954 (GRCm39)	G199D	probably damaging	Het
Map1b	C	T	13: 99,644,648 (GRCm39)	R85Q	probably damaging	Het
Marchf7	T	A	2: 60,077,858 (GRCm39)		probably null	Het
Morc1	A	G	16: 48,251,708 (GRCm39)	D2G	probably damaging	Het
Mpp7	A	T	18: 7,351,079 (GRCm39)	F539L	probably damaging	Het
Muc13	A	T	16: 33,634,951 (GRCm39)	I502F	probably damaging	Het
Myh13	A	G	11: 67,255,286 (GRCm39)		probably null	Het
Nat10	C	G	2: 103,578,390 (GRCm39)	L238F	probably damaging	Het
Nckap1	G	A	2: 80,354,885 (GRCm39)	T679I	probably damaging	Het
Npy6r	T	A	18: 44,409,260 (GRCm39)	I227N	probably damaging	Het
Nudt18	A	T	14: 70,815,389 (GRCm39)	M1L	unknown	Het
Or13d1	T	A	4: 52,971,207 (GRCm39)	N195K	probably damaging	Het
Or14a257	G	A	7: 86,138,417 (GRCm39)	T114I	probably damaging	Het
Or4f14	T	A	2: 111,742,637 (GRCm39)	I213L	probably benign	Het
Or8d1	C	A	9: 38,766,412 (GRCm39)	T18K	probably damaging	Het
Or8u8	T	C	2: 86,011,678 (GRCm39)	Y259C	probably damaging	Het
Pcdha3	T	A	18: 37,079,266 (GRCm39)	F3I	probably benign	Het
Pcdhga3	T	A	18: 37,808,917 (GRCm39)	Y457N	possibly damaging	Het
Pclo	A	T	5: 14,719,631 (GRCm39)	Q1256L	unknown	Het
Piezo2	C	T	18: 63,157,543 (GRCm39)	R2389H	probably damaging	Het
Pml	G	T	9: 58,154,496 (GRCm39)	Q126K	probably benign	Het
Ppef2	A	G	5: 92,376,563 (GRCm39)	Y655H	probably damaging	Het
Ppp4r1	T	C	17: 66,147,936 (GRCm39)	V926A	probably damaging	Het
Psg29	A	G	7: 16,945,648 (GRCm39)	D406G	possibly damaging	Het
Ptprf	T	C	4: 118,092,864 (GRCm39)	D517G	probably benign	Het
Ptprg	G	A	14: 12,142,461 (GRCm38)	E371K	probably benign	Het
Pttg1ip2	T	C	5: 5,505,952 (GRCm39)	I110V	probably benign	Het
Rasgrp1	T	C	2: 117,118,424 (GRCm39)	I522V	probably damaging	Het
Rasgrp1	T	A	2: 117,122,178 (GRCm39)	D404V	possibly damaging	Het
Rb1cc1	T	A	1: 6,315,727 (GRCm39)	F541I	probably damaging	Het
Rgsl1	C	A	1: 153,719,847 (GRCm39)		probably null	Het
Rhobtb2	C	T	14: 70,033,397 (GRCm39)	W524*	probably null	Het
Rhox4d	G	A	X: 36,700,645 (GRCm39)	G191E	unknown	Het
Rims1	A	G	1: 22,474,699 (GRCm39)	S211P		Het
Ripor2	A	T	13: 24,854,054 (GRCm39)	Q54L	possibly damaging	Het
Rnf213	A	G	11: 119,372,117 (GRCm39)	I4903V		Het
Robo3	T	A	9: 37,336,111 (GRCm39)	I452F	possibly damaging	Het
Rpl27rt	A	G	18: 34,870,580 (GRCm39)	K38R	probably damaging	Het
Seh1l	C	T	18: 67,916,988 (GRCm39)	H56Y	probably damaging	Het
Sidt1	A	T	16: 44,106,763 (GRCm39)	C222*	probably null	Het
Skor1	A	G	9: 63,053,385 (GRCm39)	F195L	probably damaging	Het
Slc44a2	A	C	9: 21,259,642 (GRCm39)	K596N	possibly damaging	Het
Smgc	A	G	15: 91,729,696 (GRCm39)	K217E	probably benign	Het
Socs7	C	A	11: 97,267,917 (GRCm39)	H349Q	possibly damaging	Het
Speer4f2	A	G	5: 17,581,540 (GRCm39)	T161A		Het
Spg11	T	C	2: 121,924,026 (GRCm39)		probably null	Het
Ssb	A	G	2: 69,693,624 (GRCm39)	T11A	probably benign	Het
Sun1	A	G	5: 139,232,589 (GRCm39)	S837G	probably damaging	Het
Szt2	A	C	4: 118,220,668 (GRCm39)	S3385A	unknown	Het
Tapbp	T	C	17: 34,139,391 (GRCm39)	V129A	possibly damaging	Het
Thsd1	T	C	8: 22,733,349 (GRCm39)	I132T	possibly damaging	Het
Tm6sf2	T	A	8: 70,530,589 (GRCm39)	V223E	possibly damaging	Het
Tm9sf4	T	A	2: 153,036,267 (GRCm39)	M343K	probably benign	Het
Trank1	C	A	9: 111,195,417 (GRCm39)	P1147Q	probably benign	Het
Trip4	G	A	9: 65,773,757 (GRCm39)	T275M	probably damaging	Het
Tsen34	T	C	7: 3,698,834 (GRCm39)		probably null	Het
Ttn	T	C	2: 76,680,422 (GRCm39)	E1086G	unknown	Het
Ubr4	A	T	4: 139,189,778 (GRCm39)	M853L	unknown	Het
Ubxn11	A	T	4: 133,852,466 (GRCm39)	R352W	probably damaging	Het
Vmn1r35	G	A	6: 66,656,219 (GRCm39)		probably benign	Het
Vmn2r107	C	T	17: 20,595,994 (GRCm39)	T849I	probably benign	Het
Vmn2r93	C	A	17: 18,546,248 (GRCm39)	L707I	probably benign	Het
Wwc1	G	A	11: 35,766,533 (GRCm39)	T574I	probably benign	Het
Zfp143	A	G	7: 109,669,705 (GRCm39)	M45V	probably benign	Het
Zfp518a	T	A	19: 40,902,601 (GRCm39)	N843K	possibly damaging	Het
Zfp87	A	T	13: 67,665,163 (GRCm39)	M433K	probably benign	Het
Zfp873	C	A	10: 81,896,461 (GRCm39)	H397Q	probably damaging	Het
Zscan21	A	T	5: 138,116,110 (GRCm39)		probably benign	Het

Other mutations in Sema3b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00674:Sema3b	APN	9	107,481,240 (GRCm39)	critical splice donor site	probably null
IGL02750:Sema3b	APN	9	107,480,363 (GRCm39)	missense	probably benign	0.02
IGL02878:Sema3b	APN	9	107,478,192 (GRCm39)	missense	probably damaging	0.97
IGL03004:Sema3b	APN	9	107,480,114 (GRCm39)	missense	possibly damaging	0.72
IGL03026:Sema3b	APN	9	107,479,262 (GRCm39)	missense	probably damaging	1.00
IGL03129:Sema3b	APN	9	107,476,995 (GRCm39)	unclassified	probably benign
IGL03334:Sema3b	APN	9	107,481,276 (GRCm39)	missense	probably damaging	1.00
R0373:Sema3b	UTSW	9	107,480,117 (GRCm39)	missense	probably benign	0.05
R0384:Sema3b	UTSW	9	107,478,165 (GRCm39)	missense	probably damaging	1.00
R0883:Sema3b	UTSW	9	107,481,355 (GRCm39)	missense	possibly damaging	0.77
R3916:Sema3b	UTSW	9	107,477,657 (GRCm39)	missense	probably damaging	1.00
R3971:Sema3b	UTSW	9	107,477,567 (GRCm39)	missense	probably benign
R4212:Sema3b	UTSW	9	107,480,597 (GRCm39)	missense	probably damaging	1.00
R4647:Sema3b	UTSW	9	107,476,250 (GRCm39)	missense	possibly damaging	0.79
R4694:Sema3b	UTSW	9	107,482,201 (GRCm39)	missense	probably benign	0.03
R4791:Sema3b	UTSW	9	107,481,012 (GRCm39)	missense	probably damaging	1.00
R4853:Sema3b	UTSW	9	107,479,266 (GRCm39)	splice site	probably null
R5305:Sema3b	UTSW	9	107,480,536 (GRCm39)	missense	probably null	1.00
R5487:Sema3b	UTSW	9	107,478,161 (GRCm39)	missense	probably damaging	1.00
R5745:Sema3b	UTSW	9	107,478,628 (GRCm39)	missense	probably damaging	0.98
R5751:Sema3b	UTSW	9	107,476,913 (GRCm39)	missense	probably benign
R6086:Sema3b	UTSW	9	107,478,047 (GRCm39)	missense	probably damaging	1.00
R6306:Sema3b	UTSW	9	107,478,119 (GRCm39)	missense	possibly damaging	0.88
R6594:Sema3b	UTSW	9	107,476,025 (GRCm39)	missense	probably benign	0.01
R6816:Sema3b	UTSW	9	107,477,549 (GRCm39)	missense	probably benign	0.08
R6833:Sema3b	UTSW	9	107,480,515 (GRCm39)	missense	probably benign	0.04
R7320:Sema3b	UTSW	9	107,478,141 (GRCm39)	missense	probably benign
R7687:Sema3b	UTSW	9	107,481,013 (GRCm39)	missense	probably damaging	1.00
R8839:Sema3b	UTSW	9	107,478,552 (GRCm39)	unclassified	probably benign
R9090:Sema3b	UTSW	9	107,476,154 (GRCm39)	missense	probably damaging	1.00
R9123:Sema3b	UTSW	9	107,478,173 (GRCm39)	missense	possibly damaging	0.64
R9271:Sema3b	UTSW	9	107,476,154 (GRCm39)	missense	probably damaging	1.00
R9442:Sema3b	UTSW	9	107,478,957 (GRCm39)	critical splice donor site	probably null
R9682:Sema3b	UTSW	9	107,481,013 (GRCm39)	missense	probably damaging	1.00
R9755:Sema3b	UTSW	9	107,478,784 (GRCm39)	missense	probably damaging	1.00
Z1088:Sema3b	UTSW	9	107,476,233 (GRCm39)	splice site	probably null
Z1176:Sema3b	UTSW	9	107,476,838 (GRCm39)	missense	possibly damaging	0.89

Predicted Primers

PCR Primer
(F):5'- GCCTCTGGCTCAGGGATTATAG -3'
(R):5'- CTCCTTATGACCCAAGGCATCG -3'

Sequencing Primer
(F):5'- TACATGGAGAGACTTCAATGTGGCTC -3'
(R):5'- GCTGAGTACCCCTTTGT -3'

Posted On

2019-10-07