Mutagenetix > Incidental Mutation

Incidental Mutation 'R1484:Sema3a'

163298

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

039537-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.947) question?

Stock #

R1484 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

13175381-13652533 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 13523407 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 125 (N125K)

Ref Sequence

ENSEMBL: ENSMUSP00000128153 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000030714
AA Change: N125K

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

SMART Domains

Protein: ENSMUSP00000030714
Gene: ENSMUSG00000028883
AA Change: N125K

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 damaging
Transcript: ENSMUST00000095012
AA Change: N125K

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

SMART Domains

Protein: ENSMUSP00000092621
Gene: ENSMUSG00000028883
AA Change: N125K

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 damaging
Transcript: ENSMUST00000137798
AA Change: N125K

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

SMART Domains

Protein: ENSMUSP00000128153
Gene: ENSMUSG00000028883
AA Change: N125K

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: ENSMUST00000195907

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000200073

Meta Mutation Damage Score

0.7216

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.5%
20x: 93.4%

Validation Efficiency

97% (85/88)

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930584F24Rik	A	T	5: 26,684,776 (GRCm39)		noncoding transcript	Het
Acvr1	A	T	2: 58,369,901 (GRCm39)	V36E	probably damaging	Het
Aldh4a1	A	G	4: 139,370,758 (GRCm39)	I414V	probably benign	Het
Alox5	C	T	6: 116,431,128 (GRCm39)	C100Y	probably damaging	Het
Ano5	T	A	7: 51,216,068 (GRCm39)	D348E	probably damaging	Het
Arhgap30	G	A	1: 171,230,839 (GRCm39)	V199M	probably damaging	Het
Arl13b	T	A	16: 62,626,999 (GRCm39)	Q234L	probably benign	Het
Atxn1	C	A	13: 45,711,052 (GRCm39)	E627*	probably null	Het
Bend3	T	C	10: 43,386,197 (GRCm39)	F197L	probably benign	Het
Brca1	A	T	11: 101,420,638 (GRCm39)	V190E	possibly damaging	Het
Brpf1	T	C	6: 113,292,096 (GRCm39)	W381R	probably damaging	Het
Brwd1	A	C	16: 95,829,491 (GRCm39)		probably null	Het
C1s2	T	C	6: 124,602,604 (GRCm39)	I530V	possibly damaging	Het
C2cd3	C	T	7: 100,089,397 (GRCm39)	R1638W	probably damaging	Het
Capns1	T	A	7: 29,893,511 (GRCm39)		probably benign	Het
Cd109	CATTTATTTATTTATTTATTTATTTATTTATTTAT	CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT	9: 78,619,782 (GRCm39)		probably benign	Het
Cep126	G	A	9: 8,100,554 (GRCm39)	T660I	possibly damaging	Het
Cep295	A	C	9: 15,246,080 (GRCm39)	I744R	probably damaging	Het
Chd3	T	C	11: 69,250,725 (GRCm39)	E668G	probably benign	Het
Chek2	A	G	5: 110,996,553 (GRCm39)	T172A	probably damaging	Het
Col6a4	A	G	9: 105,890,501 (GRCm39)		probably null	Het
Coq3	G	A	4: 21,900,291 (GRCm39)	V173I	probably benign	Het
Cyp4x1	A	T	4: 114,970,098 (GRCm39)	I343N	probably damaging	Het
Dnah7b	T	A	1: 46,176,703 (GRCm39)	D774E	probably benign	Het
Dnai3	T	C	3: 145,802,996 (GRCm39)	D65G	probably benign	Het
Ecm1	G	A	3: 95,643,275 (GRCm39)	R342C	probably damaging	Het
Esrra	T	C	19: 6,890,197 (GRCm39)	Y209C	probably damaging	Het
Gpr149	A	T	3: 62,502,592 (GRCm39)	D421E	probably benign	Het
Gpr15	T	C	16: 58,538,937 (GRCm39)	N51D	probably damaging	Het
Gpr156	T	C	16: 37,812,558 (GRCm39)	V298A	probably damaging	Het
Hmcn2	G	A	2: 31,236,507 (GRCm39)	G350D	probably damaging	Het
Ifih1	A	T	2: 62,440,902 (GRCm39)	N421K	probably benign	Het
Ilvbl	C	A	10: 78,412,564 (GRCm39)	T95K	probably damaging	Het
Itgb4	T	A	11: 115,890,625 (GRCm39)	D1104E	probably benign	Het
Katnip	C	A	7: 125,415,743 (GRCm39)		probably benign	Het
Lipf	A	T	19: 33,942,180 (GRCm39)	M37L	probably benign	Het
Lyst	T	A	13: 13,852,775 (GRCm39)	N2258K	probably benign	Het
Moxd1	A	G	10: 24,099,758 (GRCm39)	Y86C	probably damaging	Het
Muc5ac	T	C	7: 141,367,629 (GRCm39)		probably null	Het
Myo16	G	A	8: 10,610,145 (GRCm39)	R1162H	probably damaging	Het
Myo5c	A	T	9: 75,208,092 (GRCm39)	N1609Y	probably damaging	Het
Nbeal1	T	C	1: 60,240,098 (GRCm39)	F155L	probably damaging	Het
Nek4	A	T	14: 30,704,290 (GRCm39)	M602L	possibly damaging	Het
Nek9	A	G	12: 85,348,622 (GRCm39)	S971P	probably damaging	Het
Nfya	A	T	17: 48,700,570 (GRCm39)		probably benign	Het
Nrxn3	A	T	12: 89,221,547 (GRCm39)	N442I	probably damaging	Het
Nup42	A	C	5: 24,383,075 (GRCm39)	K200N	probably benign	Het
Or1e26	T	A	11: 73,480,187 (GRCm39)	I126L	possibly damaging	Het
Or4c111	G	A	2: 88,843,713 (GRCm39)	R232*	probably null	Het
Or7g32	G	A	9: 19,389,423 (GRCm39)	T38I	probably damaging	Het
Pcdh15	T	A	10: 74,126,833 (GRCm39)	I304N	probably damaging	Het
Pigo	G	C	4: 43,024,779 (GRCm39)	P107A	probably damaging	Het
Plce1	C	T	19: 38,693,783 (GRCm39)	Q769*	probably null	Het
Plin2	C	T	4: 86,575,481 (GRCm39)	R356H	probably benign	Het
Ppp1r9a	G	T	6: 5,113,712 (GRCm39)	E739*	probably null	Het
Ppp3cc	G	T	14: 70,478,397 (GRCm39)	N268K	probably damaging	Het
Prkag3	T	A	1: 74,779,919 (GRCm39)	D472V	probably damaging	Het
Ptch2	A	T	4: 116,968,046 (GRCm39)	D846V	probably damaging	Het
Rhob	A	T	12: 8,549,388 (GRCm39)	M82K	probably damaging	Het
Rps6kc1	T	A	1: 190,531,672 (GRCm39)	R777W	possibly damaging	Het
Sap130	T	A	18: 31,844,380 (GRCm39)	V850E	probably damaging	Het
Sema5a	A	G	15: 32,460,431 (GRCm39)	D64G	probably damaging	Het
Sgo2b	T	A	8: 64,384,507 (GRCm39)	D163V	possibly damaging	Het
Slc15a1	A	T	14: 121,728,651 (GRCm39)	Y31*	probably null	Het
Smchd1	A	T	17: 71,685,252 (GRCm39)	M1392K	probably benign	Het
Sobp	T	A	10: 43,036,827 (GRCm39)	N37I	probably damaging	Het
Spock3	G	T	8: 63,673,739 (GRCm39)	C142F	probably damaging	Het
Stx6	A	C	1: 155,053,650 (GRCm39)	S86R	probably benign	Het
Sult2a4	C	A	7: 13,643,726 (GRCm39)	M280I	probably benign	Het
Synm	A	T	7: 67,386,080 (GRCm39)	D527E	probably damaging	Het
Tax1bp1	C	T	6: 52,710,305 (GRCm39)	R195W	probably damaging	Het
Themis2	A	T	4: 132,519,796 (GRCm39)	N76K	possibly damaging	Het
Tmem8b	A	G	4: 43,690,234 (GRCm39)	T890A	probably benign	Het
Traf7	T	A	17: 24,730,785 (GRCm39)	H366L	possibly damaging	Het
Trim30c	A	T	7: 104,032,459 (GRCm39)	V289D	probably benign	Het
Tsr1	T	A	11: 74,792,914 (GRCm39)	D407E	probably damaging	Het
Ubap2	G	T	4: 41,235,593 (GRCm39)	A33E	probably damaging	Het
Unc13d	C	A	11: 115,964,701 (GRCm39)	R255L	possibly damaging	Het
Ush2a	G	T	1: 188,542,534 (GRCm39)	G3367*	probably null	Het
Vmn1r229	T	C	17: 21,034,791 (GRCm39)	L12P	probably damaging	Het
Vmn2r27	C	A	6: 124,177,474 (GRCm39)	G510V	probably damaging	Het
Vps4b	T	C	1: 106,707,712 (GRCm39)	E257G	probably damaging	Het
Vps72	T	C	3: 95,026,462 (GRCm39)	S136P	probably damaging	Het
Wdr36	T	C	18: 32,976,938 (GRCm39)	I181T	possibly damaging	Het
Wfikkn1	C	T	17: 26,096,765 (GRCm39)	A520T	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
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
R5327:Sema3a	UTSW	5	13,649,357 (GRCm39)	missense	probably benign	0.25
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'- CCCATGATTACTGGCAACCCAGAAC -3'
(R):5'- ATGAGCTGAAGGAATCAGCAATGAACT -3'

Sequencing Primer
(F):5'- ggacccttccctatcaatcac -3'
(R):5'- TGTTTAAACCGGAAGGAGCC -3'

Posted On

2014-03-28