Mutagenetix > Incidental Mutation

Incidental Mutation 'R5327:Sema3a'

422029

Institutional Source

Beutler Lab

Gene Symbol

Sema3a

Ensembl Gene

ENSMUSG00000028883

Gene Name

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

Synonyms

Semad, collapsin-1, SemD, sema III, semaphorin III

MMRRC Submission

042910-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.949) question?

Stock #

R5327 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

13175381-13652533 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 13649357 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 702 (V702A)

Ref Sequence

ENSEMBL: ENSMUSP00000092621 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030714] [ENSMUST00000095012] [ENSMUST00000137798]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000030714
AA Change: V702A

PolyPhen 2 Score 0.252 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000030714
Gene: ENSMUSG00000028883
AA Change: V702A

Domain	Start	End	E-Value	Type
Sema	57	498	4.09e-219	SMART
PSI	516	568	3.03e-12	SMART
IG	583	669	3.54e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000095012
AA Change: V702A

PolyPhen 2 Score 0.252 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000092621
Gene: ENSMUSG00000028883
AA Change: V702A

Domain	Start	End	E-Value	Type
Sema	57	498	4.09e-219	SMART
PSI	516	568	3.03e-12	SMART
IG	583	669	3.54e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000137798

SMART Domains

Protein: ENSMUSP00000128153
Gene: ENSMUSG00000028883

Domain	Start	End	E-Value	Type
Sema	57	498	4.09e-219	SMART
PSI	516	568	3.03e-12	SMART
IG	583	669	3.54e-4	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000200088

Meta Mutation Damage Score

0.0848

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.9%

Validation Efficiency

100% (101/101)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the semaphorin family and encodes a protein with an Ig-like C2-type (immunoglobulin-like) domain, a PSI domain and a Sema domain. This secreted protein can function as either a chemorepulsive agent, inhibiting axonal outgrowth, or as a chemoattractive agent, stimulating the growth of apical dendrites. In both cases, the protein is vital for normal neuronal pattern development. Increased expression of this protein is associated with schizophrenia and is seen in a variety of human tumor cell lines. Also, aberrant release of this protein is associated with the progression of Alzheimer's disease. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations exhibit patterning abnormalities of sensory and sympathetic neurons, abnormal embryonic bones and cartilaginous structures, cardiac defects, and high postnatal mortality. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
AA986860	A	G	1: 130,668,740 (GRCm39)	S36G	probably damaging	Het
Aarsd1	T	C	11: 101,301,203 (GRCm39)	N280D	probably benign	Het
Abca2	T	A	2: 25,335,686 (GRCm39)	M2099K	probably damaging	Het
Abcb5	T	A	12: 118,875,278 (GRCm39)	E631D	probably benign	Het
Acss2	T	A	2: 155,415,149 (GRCm39)	L682Q	probably null	Het
Adamts14	G	A	10: 61,034,267 (GRCm39)	P1207L	probably benign	Het
Adora1	G	A	1: 134,130,748 (GRCm39)	R308*	probably null	Het
Arcn1	A	T	9: 44,668,444 (GRCm39)	V264E	probably benign	Het
B3galt1	G	A	2: 67,949,112 (GRCm39)	G276S	probably damaging	Het
Bms1	A	T	6: 118,382,179 (GRCm39)	M453K	possibly damaging	Het
Bnip3l	T	C	14: 67,225,180 (GRCm39)	Y218C	probably damaging	Het
Cacna2d2	A	G	9: 107,390,805 (GRCm39)	E379G	probably null	Het
Cacng6	G	A	7: 3,483,376 (GRCm39)	G235R	probably damaging	Het
Capn8	A	T	1: 182,456,169 (GRCm39)	T640S	probably benign	Het
Ccdc106	T	C	7: 5,063,159 (GRCm39)		probably benign	Het
Ccdc33	A	T	9: 57,993,860 (GRCm39)	N95K	probably benign	Het
Celsr3	T	A	9: 108,719,907 (GRCm39)		probably benign	Het
Cemip	A	T	7: 83,604,509 (GRCm39)	N844K	probably damaging	Het
Chrdl2	A	T	7: 99,677,948 (GRCm39)	T284S	probably damaging	Het
Ckm	A	G	7: 19,154,090 (GRCm39)	Y279C	probably damaging	Het
Clvs1	A	T	4: 9,424,261 (GRCm39)	I236F	probably damaging	Het
Col9a1	T	C	1: 24,234,620 (GRCm39)		probably null	Het
Csmd1	T	C	8: 17,266,728 (GRCm39)	E66G	possibly damaging	Het
Ctdsp2	A	G	10: 126,831,923 (GRCm39)	D26G	probably damaging	Het
Ctsll3	C	A	13: 60,946,721 (GRCm39)		probably null	Het
Cyp2d12	A	T	15: 82,439,423 (GRCm39)	M26L	probably benign	Het
Cyp8b1	C	T	9: 121,743,950 (GRCm39)	D461N	probably damaging	Het
Dbt	A	T	3: 116,322,220 (GRCm39)		probably benign	Het
Dnah7c	A	G	1: 46,704,728 (GRCm39)	D2247G	probably benign	Het
Dsg1c	A	G	18: 20,400,994 (GRCm39)	I166V	possibly damaging	Het
Duoxa1	T	A	2: 122,134,361 (GRCm39)	E252D	probably damaging	Het
Ezr	T	A	17: 7,020,448 (GRCm39)	K211M	probably damaging	Het
Faap100	T	A	11: 120,268,458 (GRCm39)	E105V	possibly damaging	Het
Fahd2a	T	C	2: 127,283,878 (GRCm39)	D54G	possibly damaging	Het
Fbxo9	A	T	9: 78,003,146 (GRCm39)		probably null	Het
Fndc1	A	G	17: 7,991,540 (GRCm39)	S719P	unknown	Het
Gas7	G	T	11: 67,552,916 (GRCm39)	G159C	probably damaging	Het
Gba2	T	C	4: 43,574,063 (GRCm39)	D130G	probably damaging	Het
Gli3	T	G	13: 15,723,092 (GRCm39)	S78A	probably damaging	Het
Gtpbp6	A	G	5: 110,254,770 (GRCm39)	F101S	probably damaging	Het
Gzme	G	A	14: 56,355,224 (GRCm39)	H236Y	probably benign	Het
Hira	T	C	16: 18,773,508 (GRCm39)	Y943H	probably damaging	Het
Hmbox1	G	A	14: 65,134,144 (GRCm39)	S152L	possibly damaging	Het
Ibtk	A	G	9: 85,619,519 (GRCm39)		probably null	Het
Jade1	T	C	3: 41,568,413 (GRCm39)	I827T	possibly damaging	Het
Jakmip3	A	T	7: 138,627,164 (GRCm39)	E389D	possibly damaging	Het
Klhdc8b	A	T	9: 108,326,241 (GRCm39)		probably benign	Het
Lama2	T	C	10: 27,014,942 (GRCm39)	T1589A	probably benign	Het
Lbx2	A	C	6: 83,064,784 (GRCm39)	K107T	probably damaging	Het
Ldha	A	G	7: 46,503,522 (GRCm39)	M259V	probably benign	Het
Lrrtm4	A	G	6: 79,999,620 (GRCm39)	K344R	probably damaging	Het
Ltb	A	T	17: 35,414,935 (GRCm39)	E245V	probably damaging	Het
Macf1	GCCCCC	GCCCCCC	4: 123,244,784 (GRCm39)		probably null	Het
Map3k13	T	A	16: 21,740,397 (GRCm39)	S575T	possibly damaging	Het
Mcpt2	A	T	14: 56,280,833 (GRCm39)	I74F	probably damaging	Het
Mpeg1	T	A	19: 12,439,013 (GRCm39)	V157D	probably damaging	Het
Mrpl21	A	T	19: 3,337,009 (GRCm39)		probably null	Het
Nagpa	T	C	16: 5,017,877 (GRCm39)	T99A	possibly damaging	Het
Nphs1	A	T	7: 30,163,250 (GRCm39)	I469F	probably benign	Het
Nyap2	A	G	1: 81,169,756 (GRCm39)	E171G	possibly damaging	Het
Oas1e	A	G	5: 120,930,006 (GRCm39)	Y171H	probably damaging	Het
Or10ag59	T	A	2: 87,406,043 (GRCm39)	V205D	probably damaging	Het
Or2y1f	T	C	11: 49,184,493 (GRCm39)	L115P	probably damaging	Het
Or5ac23	T	C	16: 59,149,461 (GRCm39)	K137R	probably benign	Het
Or5h26	T	C	16: 58,987,983 (GRCm39)	I174M	possibly damaging	Het
Otud7b	C	A	3: 96,063,055 (GRCm39)	Q765K	probably benign	Het
Pdzd7	A	G	19: 45,017,216 (GRCm39)	V851A	probably benign	Het
Pi4ka	T	G	16: 17,143,277 (GRCm39)	K794T	probably damaging	Het
Pkhd1l1	T	A	15: 44,410,258 (GRCm39)	N2588K	probably damaging	Het
Pla2g6	A	T	15: 79,186,837 (GRCm39)	M471K	probably benign	Het
Plagl2	T	C	2: 153,077,759 (GRCm39)	H74R	possibly damaging	Het
Prf1	T	A	10: 61,136,037 (GRCm39)	N104K	probably benign	Het
Ptprf	A	T	4: 118,093,586 (GRCm39)	I358N	probably damaging	Het
Rcsd1	A	G	1: 165,482,872 (GRCm39)		probably null	Het
Rev1	G	A	1: 38,147,532 (GRCm39)	R3*	probably null	Het
Rp1	T	C	1: 4,419,583 (GRCm39)		probably null	Het
Rrp12	G	A	19: 41,881,035 (GRCm39)	T132I	probably damaging	Het
Serpinb12	A	G	1: 106,884,174 (GRCm39)	N307D	probably damaging	Het
Slc35d1	A	G	4: 103,070,383 (GRCm39)	L103P	probably damaging	Het
Smyd4	T	C	11: 75,281,765 (GRCm39)	C413R	probably damaging	Het
Stab1	G	A	14: 30,883,793 (GRCm39)	Q255*	probably null	Het
Synpo	T	A	18: 60,736,918 (GRCm39)	I343F	possibly damaging	Het
Tcirg1	A	G	19: 3,952,342 (GRCm39)		probably null	Het
Tmem132c	A	G	5: 127,640,816 (GRCm39)	T996A	possibly damaging	Het
Trim10	A	G	17: 37,181,081 (GRCm39)	E104G	probably damaging	Het
Trpc1	T	C	9: 95,603,524 (GRCm39)		probably null	Het
Tspo2	A	T	17: 48,756,887 (GRCm39)		probably benign	Het
Ugt2a3	A	T	5: 87,479,174 (GRCm39)	I258N	probably damaging	Het
Usp34	T	C	11: 23,418,846 (GRCm39)	L2998P	probably damaging	Het
Vmn1r45	A	C	6: 89,910,123 (GRCm39)	D162E	possibly damaging	Het
Vmn2r117	A	T	17: 23,696,848 (GRCm39)	Y186*	probably null	Het
Vmn2r67	A	G	7: 84,785,698 (GRCm39)	F769S	probably damaging	Het
Zbtb17	A	G	4: 141,192,942 (GRCm39)	I514V	probably benign	Het
Zfp329	A	C	7: 12,545,421 (GRCm39)	D34E	probably benign	Het

Other mutations in Sema3a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01022:Sema3a	APN	5	13,523,433 (GRCm39)	missense	probably damaging	1.00
IGL01783:Sema3a	APN	5	13,611,767 (GRCm39)	missense	probably damaging	1.00
IGL02423:Sema3a	APN	5	13,615,776 (GRCm39)	missense	probably damaging	1.00
IGL02728:Sema3a	APN	5	13,615,881 (GRCm39)	missense	probably damaging	1.00
IGL02739:Sema3a	APN	5	13,501,128 (GRCm39)	missense	probably damaging	1.00
IGL02987:Sema3a	APN	5	13,615,863 (GRCm39)	missense	probably damaging	1.00
IGL03106:Sema3a	APN	5	13,649,456 (GRCm39)	missense	probably damaging	1.00
R0055:Sema3a	UTSW	5	13,450,004 (GRCm39)	missense	possibly damaging	0.92
R0334:Sema3a	UTSW	5	13,607,268 (GRCm39)	missense	probably damaging	0.99
R0684:Sema3a	UTSW	5	13,606,494 (GRCm39)	critical splice acceptor site	probably null
R0750:Sema3a	UTSW	5	13,607,092 (GRCm39)	critical splice donor site	probably null
R1204:Sema3a	UTSW	5	13,573,142 (GRCm39)	critical splice donor site	probably benign
R1221:Sema3a	UTSW	5	13,566,190 (GRCm39)	missense	probably benign
R1484:Sema3a	UTSW	5	13,523,407 (GRCm39)	missense	probably damaging	1.00
R1663:Sema3a	UTSW	5	13,607,092 (GRCm39)	critical splice donor site	probably null
R2079:Sema3a	UTSW	5	13,501,098 (GRCm39)	missense	possibly damaging	0.95
R4165:Sema3a	UTSW	5	13,523,364 (GRCm39)	critical splice acceptor site	probably null
R4596:Sema3a	UTSW	5	13,620,125 (GRCm39)	missense	probably damaging	1.00
R4867:Sema3a	UTSW	5	13,501,208 (GRCm39)	missense	probably benign	0.05
R4904:Sema3a	UTSW	5	13,631,066 (GRCm39)	missense	probably damaging	1.00
R5107:Sema3a	UTSW	5	13,627,572 (GRCm39)	nonsense	probably null
R5343:Sema3a	UTSW	5	13,523,373 (GRCm39)	missense	probably damaging	1.00
R5430:Sema3a	UTSW	5	13,615,730 (GRCm39)	missense	probably damaging	0.97
R5604:Sema3a	UTSW	5	13,523,487 (GRCm39)	critical splice donor site	probably null
R5774:Sema3a	UTSW	5	13,573,131 (GRCm39)	missense	probably damaging	1.00
R6057:Sema3a	UTSW	5	13,615,832 (GRCm39)	missense	probably damaging	1.00
R6110:Sema3a	UTSW	5	13,630,969 (GRCm39)	missense	probably damaging	1.00
R6132:Sema3a	UTSW	5	13,573,142 (GRCm39)	critical splice donor site	probably null
R6310:Sema3a	UTSW	5	13,606,986 (GRCm39)	missense	probably damaging	1.00
R6754:Sema3a	UTSW	5	13,649,243 (GRCm39)	missense	possibly damaging	0.94
R6788:Sema3a	UTSW	5	13,647,584 (GRCm39)	missense	possibly damaging	0.95
R6878:Sema3a	UTSW	5	13,505,511 (GRCm39)	missense	possibly damaging	0.88
R7411:Sema3a	UTSW	5	13,566,230 (GRCm39)	nonsense	probably null
R7501:Sema3a	UTSW	5	13,607,008 (GRCm39)	missense	probably damaging	1.00
R7514:Sema3a	UTSW	5	13,573,093 (GRCm39)	missense	probably benign	0.03
R7531:Sema3a	UTSW	5	13,615,805 (GRCm39)	missense	probably damaging	1.00
R7538:Sema3a	UTSW	5	13,611,787 (GRCm39)	missense	probably benign	0.42
R7970:Sema3a	UTSW	5	13,649,375 (GRCm39)	missense	possibly damaging	0.93
R8121:Sema3a	UTSW	5	13,649,215 (GRCm39)	missense	probably damaging	1.00
R8283:Sema3a	UTSW	5	13,450,030 (GRCm39)	missense	probably damaging	0.98
R8434:Sema3a	UTSW	5	13,523,487 (GRCm39)	critical splice donor site	probably null
R8918:Sema3a	UTSW	5	13,573,099 (GRCm39)	missense	probably damaging	1.00
R9500:Sema3a	UTSW	5	13,615,854 (GRCm39)	missense	possibly damaging	0.88
X0064:Sema3a	UTSW	5	13,631,066 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGGCAATTACCTGTGTCACG -3'
(R):5'- ACCCGGTTGAACTTCCCATC -3'

Sequencing Primer
(F):5'- TACCTGTGTCACGCTGTGGAAC -3'
(R):5'- CGGTTGAACTTCCCATCATTGTAAAC -3'

Posted On

2016-08-04