Mutagenetix > Incidental Mutation

Incidental Mutation 'R5022:Sema3d'

389236

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

042613-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.210) question?

Stock #

R5022 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

12383385-12588948 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 12584956 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Serine at position 663 (Y663S)

Ref Sequence

ENSEMBL: ENSMUSP00000030868 (fasta)

Gene Model

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

AlphaFold

Q8BH34

Predicted Effect

probably damaging
Transcript: ENSMUST00000030868
AA Change: Y663S

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: Y663S

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: ENSMUST00000195923

Meta Mutation Damage Score

0.9554

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.4%
20x: 92.6%

Validation Efficiency

99% (110/111)

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: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca1	TCGACTGC	T	4: 53,041,570		probably null	Het
Abca15	T	C	7: 120,346,096	I465T	probably damaging	Het
Abca3	C	T	17: 24,374,300	R224C	probably damaging	Het
Abcb4	T	A	5: 8,909,054		probably null	Het
Acan	T	C	7: 79,092,808		probably null	Het
Aebp2	G	A	6: 140,637,730	R109Q	possibly damaging	Het
Agfg2	A	T	5: 137,660,160		probably null	Het
Ankib1	T	A	5: 3,734,011	I322F	possibly damaging	Het
AW551984	A	T	9: 39,597,965	N293K	probably benign	Het
BC028528	T	A	3: 95,888,823		probably benign	Het
Bicc1	A	G	10: 70,947,883	S393P	possibly damaging	Het
Birc6	A	G	17: 74,692,332	Y4656C	probably damaging	Het
Bmp3	A	G	5: 98,872,824	R369G	probably damaging	Het
C1d	T	A	11: 17,266,674	N135K	probably benign	Het
Ccdc148	G	A	2: 58,827,632	A453V	probably damaging	Het
Cd163	C	T	6: 124,325,288	T937I	probably damaging	Het
Celf2	C	T	2: 6,607,847		probably benign	Het
Chga	T	C	12: 102,562,837	W358R	probably damaging	Het
Clec4b2	A	T	6: 123,200,956	S77C	probably null	Het
Crim1	T	C	17: 78,280,129	V221A	possibly damaging	Het
D630003M21Rik	A	T	2: 158,217,633	S116T	probably damaging	Het
Dlg5	T	C	14: 24,136,622	E1847G	probably damaging	Het
Dmxl1	T	A	18: 49,895,127	I2206K	probably damaging	Het
Dusp7	T	A	9: 106,373,741	L355Q	probably damaging	Het
Exd2	T	A	12: 80,496,790	N582K	probably damaging	Het
Fbln1	G	A	15: 85,237,626	S316N	probably damaging	Het
Fchsd1	A	G	18: 37,964,810	I340T	possibly damaging	Het
Fn1	T	C	1: 71,624,179	Y1050C	probably damaging	Het
Fsip2	A	G	2: 82,979,429	I2031V	probably benign	Het
Gm10803	A	C	2: 93,564,172	L96F	probably damaging	Het
Gm12169	T	A	11: 46,528,532	D58E	probably damaging	Het
Gm14569	T	C	X: 36,430,817	D1413G	probably benign	Het
Gm15455	T	C	1: 33,837,351		noncoding transcript	Het
Gm1818	G	C	12: 48,555,535		noncoding transcript	Het
Gm4907	G	A	X: 23,907,241	G327E	probably damaging	Het
Gm5039	T	C	12: 88,321,301	I61V	probably benign	Het
Gm5420	A	T	10: 21,691,727		noncoding transcript	Het
Gm6803	A	T	12: 88,018,711	S21T	unknown	Het
Gm7104	A	T	12: 88,285,759		noncoding transcript	Het
Gp2	A	G	7: 119,449,114	I427T	probably damaging	Het
Gpc4	G	A	X: 52,074,563	R148C	probably damaging	Het
Gpr142	A	C	11: 114,804,388	S60R	probably benign	Het
Helz2	T	C	2: 181,240,569	R144G	probably benign	Het
Herc1	A	T	9: 66,470,326	K3458M	possibly damaging	Het
Hnf4g	G	T	3: 3,644,587	A144S	probably damaging	Het
Irs2	A	C	8: 10,987,012	*1322G	probably null	Het
Keg1	A	G	19: 12,719,157	N288S	probably damaging	Het
Kif19a	G	A	11: 114,767,227	M37I	probably benign	Het
Klhl1	G	A	14: 96,136,706	P635S	probably benign	Het
Klk14	G	A	7: 43,692,077	C51Y	probably damaging	Het
Lsm11	T	C	11: 45,944,839	D25G	probably damaging	Het
Manea	A	T	4: 26,336,630	Y215*	probably null	Het
Mdga2	C	T	12: 66,470,760	C100Y	possibly damaging	Het
Mthfd1	T	G	12: 76,294,374	V480G	probably damaging	Het
Mthfd1	T	A	12: 76,301,328	M582K	probably damaging	Het
Myh7b	G	C	2: 155,632,373	R1669S	possibly damaging	Het
Nanos1	T	C	19: 60,756,980	Y239H	probably damaging	Het
Nat8	G	A	6: 85,830,857	T98I	possibly damaging	Het
Ndufs3	C	A	2: 90,898,660	A161S	probably benign	Het
Nexmif	A	T	X: 104,087,350	N320K	probably damaging	Het
Olfr1216	A	G	2: 89,014,043	V7A	probably damaging	Het
Olfr1228	C	T	2: 89,249,417	M92I	probably benign	Het
Olfr164	A	T	16: 19,286,059	V228D	probably damaging	Het
Olfr239	T	C	17: 33,199,777	F239S	probably damaging	Het
Olfr457	A	T	6: 42,471,287	V297E	possibly damaging	Het
Olfr589	G	A	7: 103,155,735	P4L	probably benign	Het
Olfr727	T	C	14: 50,127,012	V145A	possibly damaging	Het
Olfr822	T	C	10: 130,074,593	L61P	probably damaging	Het
Pcdhb14	T	A	18: 37,450,170	N776K	probably benign	Het
Pip5k1c	G	A	10: 81,310,889		probably null	Het
Plk4	G	A	3: 40,802,077		probably null	Het
Prmt8	A	G	6: 127,711,163	Y231H	possibly damaging	Het
Prpf4b	T	C	13: 34,883,599		probably benign	Het
Ptpn21	G	A	12: 98,679,407	R1091C	probably damaging	Het
Pwwp2b	C	T	7: 139,255,578	P312S	possibly damaging	Het
Rad21	A	T	15: 51,966,706	I503K	probably benign	Het
Rai14	A	G	15: 10,574,506	S789P	probably damaging	Het
Rbm26	C	T	14: 105,144,252	D486N	probably damaging	Het
Rnf20	A	G	4: 49,642,016		probably benign	Het
Ros1	A	G	10: 52,124,075	V1118A	possibly damaging	Het
Serpina6	A	G	12: 103,651,712	W281R	probably damaging	Het
Slc8a3	A	G	12: 81,199,558	V900A	probably damaging	Het
Spats2l	G	T	1: 57,879,556	V30L	probably damaging	Het
Spg21	A	G	9: 65,475,949	D139G	probably damaging	Het
Sun3	T	C	11: 9,038,314	T3A	probably damaging	Het
Tcrg-V1	T	A	13: 19,340,231	S42T	probably benign	Het
Tep1	A	G	14: 50,828,999	Y2335H	probably benign	Het
Timm21	C	A	18: 84,949,414	V112L	possibly damaging	Het
Tlk1	A	T	2: 70,742,065	N386K	probably benign	Het
Trappc10	G	T	10: 78,217,160	F260L	possibly damaging	Het
Trmt112	T	C	19: 6,910,753	V91A	probably benign	Het
Ucp2	A	T	7: 100,498,372	N186I	possibly damaging	Het
Vmn1r119	A	G	7: 21,012,320	S46P	probably benign	Het
Vmn2r101	A	T	17: 19,611,387		probably null	Het
Vmn2r105	T	A	17: 20,208,414	H800L	probably damaging	Het
Vmn2r69	T	C	7: 85,411,159	M406V	possibly damaging	Het
Vmn2r84	A	G	10: 130,386,548	L601P	probably damaging	Het
Vps16	A	G	2: 130,439,452	S235G	probably benign	Het
Wap	T	C	11: 6,637,339		probably benign	Het
Wdr11	A	G	7: 129,624,711	I744M	probably benign	Het
Xiap	T	C	X: 42,094,465	F23L	probably benign	Het
Xkr7	A	G	2: 153,054,380	T385A	probably benign	Het
Zfp524	A	T	7: 5,018,417	I315F	probably benign	Het
Zfp62	T	A	11: 49,215,729	S216T	probably damaging	Het
Znfx1	T	C	2: 167,039,826	Y217C	probably damaging	Het

Other mutations in Sema3d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00559:Sema3d	APN	5	12,563,222 (GRCm38)	missense	probably benign	0.01
IGL00582:Sema3d	APN	5	12,585,195 (GRCm38)	missense	probably damaging	1.00
IGL00661:Sema3d	APN	5	12,505,839 (GRCm38)	missense	probably damaging	1.00
IGL00780:Sema3d	APN	5	12,524,326 (GRCm38)	missense	probably damaging	1.00
IGL01531:Sema3d	APN	5	12,541,080 (GRCm38)	missense	probably benign
IGL01957:Sema3d	APN	5	12,563,315 (GRCm38)	missense	probably damaging	1.00
IGL02100:Sema3d	APN	5	12,584,991 (GRCm38)	missense	probably benign	0.29
IGL02676:Sema3d	APN	5	12,570,978 (GRCm38)	missense	probably benign	0.38
IGL02749:Sema3d	APN	5	12,563,145 (GRCm38)	splice site	probably benign
IGL02827:Sema3d	APN	5	12,585,118 (GRCm38)	missense	probably benign	0.04
IGL03325:Sema3d	APN	5	12,463,222 (GRCm38)	missense	probably damaging	0.99
R0050:Sema3d	UTSW	5	12,584,953 (GRCm38)	missense	probably benign	0.00
R0085:Sema3d	UTSW	5	12,570,986 (GRCm38)	missense	probably benign	0.00
R0095:Sema3d	UTSW	5	12,563,347 (GRCm38)	missense	probably damaging	1.00
R0157:Sema3d	UTSW	5	12,508,137 (GRCm38)	missense	possibly damaging	0.95
R0328:Sema3d	UTSW	5	12,448,075 (GRCm38)	missense	possibly damaging	0.48
R0924:Sema3d	UTSW	5	12,463,216 (GRCm38)	missense	possibly damaging	0.69
R0930:Sema3d	UTSW	5	12,463,216 (GRCm38)	missense	possibly damaging	0.69
R1609:Sema3d	UTSW	5	12,541,056 (GRCm38)	missense	probably damaging	1.00
R1657:Sema3d	UTSW	5	12,584,974 (GRCm38)	missense	possibly damaging	0.82
R1669:Sema3d	UTSW	5	12,508,084 (GRCm38)	splice site	probably benign
R1795:Sema3d	UTSW	5	12,584,887 (GRCm38)	missense	probably benign	0.02
R1861:Sema3d	UTSW	5	12,497,603 (GRCm38)	missense	probably benign	0.00
R1889:Sema3d	UTSW	5	12,485,021 (GRCm38)	splice site	probably null
R1895:Sema3d	UTSW	5	12,573,843 (GRCm38)	missense	probably damaging	1.00
R1946:Sema3d	UTSW	5	12,573,843 (GRCm38)	missense	probably damaging	1.00
R1975:Sema3d	UTSW	5	12,584,998 (GRCm38)	missense	probably benign
R1975:Sema3d	UTSW	5	12,563,318 (GRCm38)	missense	probably damaging	1.00
R2117:Sema3d	UTSW	5	12,563,273 (GRCm38)	missense	probably benign
R2148:Sema3d	UTSW	5	12,484,959 (GRCm38)	missense	probably damaging	0.99
R2276:Sema3d	UTSW	5	12,542,582 (GRCm38)	missense	possibly damaging	0.63
R3761:Sema3d	UTSW	5	12,571,037 (GRCm38)	missense	probably damaging	1.00
R4063:Sema3d	UTSW	5	12,585,124 (GRCm38)	missense	probably benign	0.25
R4428:Sema3d	UTSW	5	12,448,120 (GRCm38)	missense	probably benign	0.32
R4903:Sema3d	UTSW	5	12,563,158 (GRCm38)	missense	probably benign	0.00
R4999:Sema3d	UTSW	5	12,508,087 (GRCm38)	splice site	probably null
R5000:Sema3d	UTSW	5	12,448,038 (GRCm38)	missense	probably benign	0.01
R5186:Sema3d	UTSW	5	12,584,908 (GRCm38)	missense	probably benign
R5584:Sema3d	UTSW	5	12,570,987 (GRCm38)	missense	possibly damaging	0.73
R5584:Sema3d	UTSW	5	12,566,008 (GRCm38)	missense	possibly damaging	0.49
R6270:Sema3d	UTSW	5	12,448,107 (GRCm38)	missense	probably benign
R6368:Sema3d	UTSW	5	12,571,013 (GRCm38)	missense	probably damaging	1.00
R6426:Sema3d	UTSW	5	12,563,264 (GRCm38)	missense	probably damaging	1.00
R6750:Sema3d	UTSW	5	12,585,100 (GRCm38)	nonsense	probably null
R7403:Sema3d	UTSW	5	12,497,584 (GRCm38)	missense	probably damaging	0.97
R7450:Sema3d	UTSW	5	12,584,934 (GRCm38)	nonsense	probably null
R7470:Sema3d	UTSW	5	12,508,185 (GRCm38)	missense	probably damaging	1.00
R7548:Sema3d	UTSW	5	12,577,816 (GRCm38)	missense	unknown
R7593:Sema3d	UTSW	5	12,508,145 (GRCm38)	missense	probably benign	0.02
R7683:Sema3d	UTSW	5	12,573,856 (GRCm38)	nonsense	probably null
R8155:Sema3d	UTSW	5	12,448,181 (GRCm38)	critical splice donor site	probably null
R8442:Sema3d	UTSW	5	12,542,641 (GRCm38)	missense	probably damaging	0.99
R8725:Sema3d	UTSW	5	12,505,855 (GRCm38)	missense	probably damaging	1.00
R8754:Sema3d	UTSW	5	12,553,224 (GRCm38)	critical splice donor site	probably null
R9293:Sema3d	UTSW	5	12,553,214 (GRCm38)	missense	probably damaging	1.00
R9771:Sema3d	UTSW	5	12,563,240 (GRCm38)	missense	probably damaging	0.99
Z1176:Sema3d	UTSW	5	12,585,059 (GRCm38)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- AACCATCTTCAACTATGGCTGACAATG -3'
(R):5'- CTGAAGTTCGGGCTGCTAAG -3'

Sequencing Primer
(F):5'- GGCTGACAATGTTATAGTTGATGAC -3'
(R):5'- AAGTTCGGGCTGCTAAGGATTTG -3'

Posted On

2016-06-06