Mutagenetix > Incidental Mutations

Incidental Mutation 'R4903:Sema3d'

377932

Institutional Source

Beutler Lab

Gene Symbol

Sema3d

Ensembl Gene

ENSMUSG00000040254

Gene Name

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

Synonyms

4631426B19Rik

MMRRC Submission

042506-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.247) question?

Stock #

R4903 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

12383385-12588948 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 12563158 bp

Zygosity

Heterozygous

Amino Acid Change

Lysine to Glutamic Acid at position 401 (K401E)

Ref Sequence

ENSEMBL: ENSMUSP00000142453 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030868] [ENSMUST00000197927]

Predicted Effect

probably benign
Transcript: ENSMUST00000030868
AA Change: K401E

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: K401E

Domain	Start	End	E-Value	Type
transmembrane domain	16	35	N/A	INTRINSIC
Sema	70	515	2.97e-207	SMART
PSI	533	585	2.03e-13	SMART
IG	598	682	1.39e-2	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196618

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196982

Predicted Effect

probably benign
Transcript: ENSMUST00000197927
AA Change: K401E

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: K401E

Domain	Start	End	E-Value	Type
signal peptide	1	37	N/A	INTRINSIC
Sema	70	515	1e-209	SMART
PSI	533	585	8.5e-16	SMART
Blast:Sema	590	622	1e-9	BLAST

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 95.8%
20x: 90.8%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit pulmonary vein connection to the right atrium and atrial septal defect. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9130019O22Rik	T	A	7: 127,385,406	T175S	probably benign	Het
A430033K04Rik	G	T	5: 138,646,857	E335*	probably null	Het
Abca9	A	G	11: 110,147,001	Y508H	probably damaging	Het
Abcc9	A	T	6: 142,600,965	L1347H	probably damaging	Het
Acox3	A	G	5: 35,589,736	N166D	probably damaging	Het
Adam5	T	C	8: 24,786,232	Y473C	probably damaging	Het
Agbl2	A	G	2: 90,797,473	I207M	possibly damaging	Het
Akna	C	A	4: 63,374,037	R1130S	probably damaging	Het
Alg12	A	T	15: 88,814,540	I194N	probably damaging	Het
Alk	T	A	17: 71,869,563	H1582L	probably damaging	Het
Atn1	G	C	6: 124,743,257		probably benign	Het
Carhsp1	T	C	16: 8,661,000	T130A	probably damaging	Het
Chrna3	T	C	9: 55,015,526	T333A	probably benign	Het
Ctsr	T	A	13: 61,163,131	I34L	probably benign	Het
Cxcl16	A	G	11: 70,455,693	V208A	probably benign	Het
Dars2	G	C	1: 161,051,371	P362R	probably benign	Het
Dnah10	A	G	5: 124,817,748	E3459G	probably damaging	Het
Dus2	G	A	8: 106,044,805	D188N	probably benign	Het
Ece2	C	T	16: 20,631,222	R189*	probably null	Het
Egfr	A	T	11: 16,908,949	D976V	probably damaging	Het
Egr2	T	A	10: 67,538,333	I51N	probably damaging	Het
Exoc3l4	A	G	12: 111,428,721	H591R	probably benign	Het
G2e3	A	G	12: 51,371,630	I603V	probably benign	Het
Gm11564	A	C	11: 99,815,032	C191G	unknown	Het
Gpatch8	A	G	11: 102,480,133	S860P	unknown	Het
Gprin1	C	G	13: 54,737,929	W844S	probably damaging	Het
Hhipl2	T	A	1: 183,426,790	Y252*	probably null	Het
Hormad1	T	A	3: 95,585,220		probably null	Het
Hrg	A	G	16: 22,961,151		probably benign	Het
Hsh2d	C	T	8: 72,193,528	A23V	probably benign	Het
Ints6	A	G	14: 62,702,462	L593P	probably damaging	Het
Jak2	A	G	19: 29,275,036	S129G	probably benign	Het
Kif1a	C	T	1: 93,021,734	E1579K	probably damaging	Het
Lhcgr	A	T	17: 88,742,361	I579N	probably damaging	Het
Lrig3	A	T	10: 125,996,613		probably null	Het
Man2c1	C	A	9: 57,138,956	Q465K	probably benign	Het
Map3k5	T	A	10: 20,118,489	L1043Q	probably null	Het
Map4k1	A	T	7: 28,983,002	H16L	probably benign	Het
Mapk8ip3	A	G	17: 24,901,209	S946P	probably benign	Het
Mrpl50	T	C	4: 49,514,488	Y61C	probably damaging	Het
Myf5	A	T	10: 107,485,872	C20*	probably null	Het
Nek11	T	C	9: 105,314,722	K163R	possibly damaging	Het
Olfr1202	A	T	2: 88,817,998	I276L	probably benign	Het
Olfr364-ps1	A	T	2: 37,146,371	H53L	probably benign	Het
Pcdhga9	C	A	18: 37,739,005	T629K	probably damaging	Het
Pglyrp1	A	G	7: 18,890,203	N137S	probably benign	Het
Pip5k1a	T	C	3: 95,070,783	I275V	probably benign	Het
Pitpnm2	T	A	5: 124,152,605	Y6F	probably damaging	Het
Pkd1	T	G	17: 24,572,002	V1057G	probably benign	Het
Plcb3	C	A	19: 6,955,843	R970L	probably damaging	Het
Plekha5	T	A	6: 140,586,367	M586K	probably damaging	Het
Ppp4r4	T	A	12: 103,590,771		probably null	Het
Rasal3	C	T	17: 32,397,383	C278Y	probably damaging	Het
Rbm34	T	C	8: 126,951,337	D269G	possibly damaging	Het
Rnf32	G	A	5: 29,198,578	R7H	probably benign	Het
Sema7a	T	C	9: 57,955,095	Y194H	probably benign	Het
Senp5	A	T	16: 31,983,299	Y585N	probably damaging	Het
Serpinb9	T	A	13: 33,008,864	W135R	probably damaging	Het
Shbg	C	T	11: 69,615,086	S365N	probably benign	Het
Slc39a6	A	T	18: 24,597,868	S65T	probably damaging	Het
Stk3	T	C	15: 34,959,066	E320G	probably damaging	Het
Syk	T	A	13: 52,611,081	H81Q	probably damaging	Het
Tet1	A	G	10: 62,822,658	W1470R	probably damaging	Het
Thada	C	A	17: 84,252,400	V1450L	possibly damaging	Het
Tmem241	A	G	18: 12,104,119	S87P	probably damaging	Het
Trdv1	T	A	14: 53,881,918		probably benign	Het
Trim40	T	C	17: 36,883,225	E192G	possibly damaging	Het
Trip11	A	T	12: 101,886,806		probably null	Het
Trmt2a	T	A	16: 18,249,554	C30*	probably null	Het
Tshr	A	G	12: 91,401,188	D35G	probably benign	Het
Tssc4	T	C	7: 143,070,585	V210A	probably damaging	Het
Ttk	T	A	9: 83,865,148	I680N	probably benign	Het
Ttn	A	T	2: 76,811,243	L5176Q	possibly damaging	Het
Txnl4a	T	C	18: 80,207,278	F30L	probably damaging	Het
Ubac2	G	T	14: 121,994,238	C192F	probably benign	Het
Vmn1r12	A	G	6: 57,159,517	T156A	possibly damaging	Het

Other mutations in Sema3d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00559:Sema3d	APN	5	12563222	missense	probably benign	0.01
IGL00582:Sema3d	APN	5	12585195	missense	probably damaging	1.00
IGL00661:Sema3d	APN	5	12505839	missense	probably damaging	1.00
IGL00780:Sema3d	APN	5	12524326	missense	probably damaging	1.00
IGL01531:Sema3d	APN	5	12541080	missense	probably benign
IGL01957:Sema3d	APN	5	12563315	missense	probably damaging	1.00
IGL02100:Sema3d	APN	5	12584991	missense	probably benign	0.29
IGL02676:Sema3d	APN	5	12570978	missense	probably benign	0.38
IGL02749:Sema3d	APN	5	12563145	splice site	probably benign
IGL02827:Sema3d	APN	5	12585118	missense	probably benign	0.04
IGL03325:Sema3d	APN	5	12463222	missense	probably damaging	0.99
R0050:Sema3d	UTSW	5	12584953	missense	probably benign	0.00
R0085:Sema3d	UTSW	5	12570986	missense	probably benign	0.00
R0095:Sema3d	UTSW	5	12563347	missense	probably damaging	1.00
R0157:Sema3d	UTSW	5	12508137	missense	possibly damaging	0.95
R0328:Sema3d	UTSW	5	12448075	missense	possibly damaging	0.48
R0924:Sema3d	UTSW	5	12463216	missense	possibly damaging	0.69
R0930:Sema3d	UTSW	5	12463216	missense	possibly damaging	0.69
R1609:Sema3d	UTSW	5	12541056	missense	probably damaging	1.00
R1657:Sema3d	UTSW	5	12584974	missense	possibly damaging	0.82
R1669:Sema3d	UTSW	5	12508084	splice site	probably benign
R1795:Sema3d	UTSW	5	12584887	missense	probably benign	0.02
R1861:Sema3d	UTSW	5	12497603	missense	probably benign	0.00
R1889:Sema3d	UTSW	5	12485021	splice site	probably null
R1895:Sema3d	UTSW	5	12573843	missense	probably damaging	1.00
R1946:Sema3d	UTSW	5	12573843	missense	probably damaging	1.00
R1975:Sema3d	UTSW	5	12563318	missense	probably damaging	1.00
R1975:Sema3d	UTSW	5	12584998	missense	probably benign
R2117:Sema3d	UTSW	5	12563273	missense	probably benign
R2148:Sema3d	UTSW	5	12484959	missense	probably damaging	0.99
R2276:Sema3d	UTSW	5	12542582	missense	possibly damaging	0.63
R3761:Sema3d	UTSW	5	12571037	missense	probably damaging	1.00
R4063:Sema3d	UTSW	5	12585124	missense	probably benign	0.25
R4428:Sema3d	UTSW	5	12448120	missense	probably benign	0.32
R4999:Sema3d	UTSW	5	12508087	splice site	probably null
R5000:Sema3d	UTSW	5	12448038	missense	probably benign	0.01
R5022:Sema3d	UTSW	5	12584956	missense	probably damaging	1.00
R5186:Sema3d	UTSW	5	12584908	missense	probably benign
R5584:Sema3d	UTSW	5	12566008	missense	possibly damaging	0.49
R5584:Sema3d	UTSW	5	12570987	missense	possibly damaging	0.73
R6270:Sema3d	UTSW	5	12448107	missense	probably benign
R6368:Sema3d	UTSW	5	12571013	missense	probably damaging	1.00
R6426:Sema3d	UTSW	5	12563264	missense	probably damaging	1.00
R6750:Sema3d	UTSW	5	12585100	nonsense	probably null
R7403:Sema3d	UTSW	5	12497584	missense	probably damaging	0.97
R7450:Sema3d	UTSW	5	12584934	nonsense	probably null
R7470:Sema3d	UTSW	5	12508185	missense	probably damaging	1.00
R7548:Sema3d	UTSW	5	12577816	missense	unknown
R7593:Sema3d	UTSW	5	12508145	missense	probably benign	0.02
R7683:Sema3d	UTSW	5	12573856	nonsense	probably null
R8155:Sema3d	UTSW	5	12448181	critical splice donor site	probably null
R8442:Sema3d	UTSW	5	12542641	missense	probably damaging	0.99
Z1176:Sema3d	UTSW	5	12585059	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- CTCGAGAAATCTTGGAAAATTCAGG -3'
(R):5'- TGGTCTGATCATACCTGTTCCG -3'

Sequencing Primer
(F):5'- TCTTGGAAAATTCAGGTAAAGTCAC -3'
(R):5'- GTCTGATCATACCTGTTCCGAGAAAC -3'

Posted On

2016-04-15