Mutagenetix > Incidental Mutation

Incidental Mutation 'R6057:Sema3a'

482956

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

Accession Numbers

Essential gene?

Probably essential (E-score: 0.949) question?

Stock #

R6057 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

13175381-13652533 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 13615832 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 419 (R419C)

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: R419C

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

SMART Domains

Protein: ENSMUSP00000030714
Gene: ENSMUSG00000028883
AA Change: R419C

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: R419C

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

SMART Domains

Protein: ENSMUSP00000092621
Gene: ENSMUSG00000028883
AA Change: R419C

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: R419C

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

SMART Domains

Protein: ENSMUSP00000128153
Gene: ENSMUSG00000028883
AA Change: R419C

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

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 97.9%
20x: 93.6%

Validation Efficiency

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: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5730596B20Rik	A	G	6: 52,156,500 (GRCm39)		probably benign	Het
Acan	A	G	7: 78,749,530 (GRCm39)	S11G	probably null	Het
Ankrd13d	A	C	19: 4,332,256 (GRCm39)	V56G	probably damaging	Het
Arl15	A	G	13: 114,104,151 (GRCm39)	Y76C	probably damaging	Het
Aspg	G	A	12: 112,087,432 (GRCm39)	C296Y	probably damaging	Het
Astl	T	A	2: 127,187,889 (GRCm39)	D101E	probably benign	Het
Bmpr2	A	G	1: 59,881,977 (GRCm39)	N202S	probably benign	Het
Borcs7	T	C	19: 46,690,003 (GRCm39)	*106Q	probably null	Het
Brip1	A	G	11: 85,955,865 (GRCm39)	S883P	possibly damaging	Het
Cacng2	A	T	15: 78,002,991 (GRCm39)	L34Q	probably damaging	Het
Catip	A	C	1: 74,402,077 (GRCm39)	D84A	probably damaging	Het
Ccdc162	A	G	10: 41,510,037 (GRCm39)	L856S	possibly damaging	Het
Ccdc38	A	G	10: 93,417,608 (GRCm39)	K500E	probably damaging	Het
Ccser2	T	C	14: 36,663,122 (GRCm39)	K21E	probably damaging	Het
Cd93	A	T	2: 148,283,439 (GRCm39)	Y636N	probably damaging	Het
Cep128	A	T	12: 91,262,998 (GRCm39)	N300K	possibly damaging	Het
Cfap44	A	G	16: 44,269,460 (GRCm39)	T1155A	probably benign	Het
Clec16a	T	C	16: 10,447,951 (GRCm39)	L550P	probably damaging	Het
Csmd3	T	C	15: 47,618,787 (GRCm39)	Y1867C	probably damaging	Het
Cul3	A	T	1: 80,249,249 (GRCm39)	I674N	probably damaging	Het
Cybb	C	G	X: 9,316,989 (GRCm39)	D246H	probably benign	Het
Cyp2d34	T	C	15: 82,500,552 (GRCm39)	H429R	probably benign	Het
Dab2ip	T	A	2: 35,582,267 (GRCm39)	C4*	probably null	Het
Dcaf1	A	G	9: 106,731,446 (GRCm39)	E641G	probably damaging	Het
Dda1	T	A	8: 71,927,276 (GRCm39)		probably benign	Het
Dmgdh	C	T	13: 93,888,960 (GRCm39)	T866I	probably benign	Het
Ect2l	T	C	10: 18,037,250 (GRCm39)	T383A	probably benign	Het
Ets2	A	G	16: 95,515,416 (GRCm39)	N181D	probably benign	Het
Ezh2	A	G	6: 47,529,357 (GRCm39)	F222L	probably damaging	Het
Frem3	T	C	8: 81,342,216 (GRCm39)	L1503P	probably damaging	Het
Fsip2	C	A	2: 82,809,777 (GRCm39)	A2032E	probably damaging	Het
Gm1818	C	T	12: 48,602,346 (GRCm39)		noncoding transcript	Het
Gm9493	A	G	19: 23,597,106 (GRCm39)	S1G	probably damaging	Het
Grin2b	A	G	6: 135,710,942 (GRCm39)	I868T	possibly damaging	Het
Ift22	A	T	5: 136,939,987 (GRCm39)	T17S	possibly damaging	Het
Il4ra	T	C	7: 125,170,735 (GRCm39)	W216R	probably damaging	Het
Kcnj6	A	T	16: 94,633,236 (GRCm39)	W274R	probably damaging	Het
Kctd19	G	A	8: 106,123,082 (GRCm39)	H111Y	probably damaging	Het
Kremen2	A	G	17: 23,961,679 (GRCm39)	V276A	probably benign	Het
Lig1	C	A	7: 13,022,598 (GRCm39)	Q143K	probably damaging	Het
Lrp1	A	T	10: 127,403,359 (GRCm39)	D2071E	probably damaging	Het
Macf1	C	T	4: 123,404,536 (GRCm39)	M475I	probably damaging	Het
Mbtd1	G	A	11: 93,820,485 (GRCm39)	A427T	probably damaging	Het
Myof	A	G	19: 37,915,429 (GRCm39)		probably null	Het
Nbeal2	T	C	9: 110,470,945 (GRCm39)	D308G	possibly damaging	Het
Ncdn	T	C	4: 126,638,824 (GRCm39)	Q665R	probably benign	Het
Nkd1	T	C	8: 89,316,442 (GRCm39)		probably null	Het
Nktr	G	A	9: 121,577,455 (GRCm39)		probably benign	Het
Npc1l1	A	T	11: 6,167,806 (GRCm39)	M995K	possibly damaging	Het
Or10ag59	C	A	2: 87,406,363 (GRCm39)	R312S	probably benign	Het
Or11g7	A	T	14: 50,691,201 (GRCm39)	R231*	probably null	Het
Or14n1-ps1	T	A	7: 86,092,397 (GRCm39)	C69*	probably null	Het
Padi4	T	C	4: 140,487,351 (GRCm39)	T184A	probably damaging	Het
Pgm2l1	C	T	7: 99,915,881 (GRCm39)	P409S	probably benign	Het
Pgpep1	G	A	8: 71,105,101 (GRCm39)	T53M	probably damaging	Het
Pgr	T	C	9: 8,902,006 (GRCm39)	L513P	probably damaging	Het
Pikfyve	T	A	1: 65,311,730 (GRCm39)	I1989N	probably damaging	Het
Prrc2a	T	C	17: 35,371,716 (GRCm39)	T1806A	probably benign	Het
Psd	T	C	19: 46,311,753 (GRCm39)	E309G	possibly damaging	Het
Qtrt1	C	T	9: 21,323,299 (GRCm39)	T50I	probably damaging	Het
Rims2	A	C	15: 39,538,416 (GRCm39)	T1320P	probably damaging	Het
Scn11a	T	G	9: 119,594,514 (GRCm39)	N1293T	probably damaging	Het
Scn8a	T	C	15: 100,872,548 (GRCm39)	F529S	possibly damaging	Het
Sec14l4	A	T	11: 3,985,142 (GRCm39)	D25V	possibly damaging	Het
Slc12a1	T	C	2: 125,032,133 (GRCm39)	Y595H	probably damaging	Het
Slc25a28	A	T	19: 43,655,364 (GRCm39)	H170Q	possibly damaging	Het
Slc26a1	T	A	5: 108,821,631 (GRCm39)	Q86L	probably damaging	Het
Slc48a1	T	A	15: 97,687,798 (GRCm39)	W51R	probably damaging	Het
Sptlc3	T	A	2: 139,423,533 (GRCm39)	V309D	probably damaging	Het
Srcap	G	A	7: 127,140,528 (GRCm39)	S1375N	probably damaging	Het
Tanc1	C	A	2: 59,647,837 (GRCm39)	H986Q	possibly damaging	Het
Tbc1d4	A	G	14: 101,727,353 (GRCm39)	V486A	probably damaging	Het
Tceanc2	T	C	4: 107,004,776 (GRCm39)	D124G	probably damaging	Het
Tdrd9	A	G	12: 111,979,720 (GRCm39)	M402V	possibly damaging	Het
Tmem132d	T	C	5: 127,861,934 (GRCm39)	D729G	probably damaging	Het
Tmem62	T	A	2: 120,807,943 (GRCm39)	I55N	probably damaging	Het
Tnfrsf21	A	T	17: 43,350,606 (GRCm39)	N257Y	possibly damaging	Het
Trappc3	T	C	4: 126,167,834 (GRCm39)	L131P	probably damaging	Het
Vmn2r25	A	T	6: 123,799,900 (GRCm39)	M814K	possibly damaging	Het
Vmn2r87	T	C	10: 130,308,226 (GRCm39)	I671V	probably benign	Het
Vwa8	A	T	14: 79,320,313 (GRCm39)	D1108V	probably benign	Het
Xrcc4	C	G	13: 90,139,198 (GRCm39)	A241P	possibly damaging	Het
Xylt1	T	A	7: 117,191,135 (GRCm39)	D310E	probably benign	Het
Zfp27	T	G	7: 29,594,444 (GRCm39)	H507P	possibly damaging	Het
Zfp341	C	T	2: 154,466,954 (GRCm39)	P108S	probably benign	Het
Zfp641	T	C	15: 98,190,816 (GRCm39)	N76S	probably benign	Het
Zfp936	T	C	7: 42,839,787 (GRCm39)	V418A	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
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
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'- TGCGACTAAACAGCAATTAACATGG -3'
(R):5'- AGAACTTGGCCTTGGTTCTCAG -3'

Posted On

2017-07-14