Mutagenetix > Incidental Mutation

Incidental Mutation 'R0390:Sema6d'

31572

Institutional Source

Beutler Lab

Gene Symbol

Sema6d

Ensembl Gene

ENSMUSG00000027200

Gene Name

sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D

Synonyms

Sema6D-6, 1110067B02Rik, Sema6D-1, Sema6D-2, Sema6D-4, Sema6D-5

MMRRC Submission

038596-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0390 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

124089969-124667770 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 124658490 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 393 (I393N)

Ref Sequence

ENSEMBL: ENSMUSP00000099531 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000051419] [ENSMUST00000076335] [ENSMUST00000077847] [ENSMUST00000078621] [ENSMUST00000103238] [ENSMUST00000103239] [ENSMUST00000103240] [ENSMUST00000103241]

AlphaFold

Q76KF0

Predicted Effect

probably damaging
Transcript: ENSMUST00000051419
AA Change: I393N

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

SMART Domains

Protein: ENSMUSP00000061123
Gene: ENSMUSG00000027200
AA Change: I393N

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Sema	57	487	7.29e-184	SMART
PSI	514	582	4.57e-1	SMART
transmembrane domain	602	624	N/A	INTRINSIC
low complexity region	743	764	N/A	INTRINSIC
internal_repeat_1	797	898	7.43e-5	PROSPERO
internal_repeat_1	892	1004	7.43e-5	PROSPERO

Predicted Effect

probably damaging
Transcript: ENSMUST00000076335
AA Change: I393N

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

SMART Domains

Protein: ENSMUSP00000075674
Gene: ENSMUSG00000027200
AA Change: I393N

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Sema	57	487	7.29e-184	SMART
PSI	514	569	1.12e-1	SMART
transmembrane domain	589	611	N/A	INTRINSIC
low complexity region	730	751	N/A	INTRINSIC
internal_repeat_1	784	885	7.28e-5	PROSPERO
internal_repeat_1	879	991	7.28e-5	PROSPERO

Predicted Effect

probably damaging
Transcript: ENSMUST00000077847
AA Change: I393N

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

SMART Domains

Protein: ENSMUSP00000077014
Gene: ENSMUSG00000027200
AA Change: I393N

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Sema	57	487	7.29e-184	SMART
PSI	514	569	1.12e-1	SMART
low complexity region	573	584	N/A	INTRINSIC
transmembrane domain	645	667	N/A	INTRINSIC
low complexity region	786	807	N/A	INTRINSIC
internal_repeat_1	840	941	5.95e-5	PROSPERO
internal_repeat_1	935	1047	5.95e-5	PROSPERO

Predicted Effect

probably damaging
Transcript: ENSMUST00000078621
AA Change: I393N

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

SMART Domains

Protein: ENSMUSP00000077691
Gene: ENSMUSG00000027200
AA Change: I393N

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Sema	57	487	7.29e-184	SMART
PSI	514	582	4.57e-1	SMART
transmembrane domain	621	643	N/A	INTRINSIC
low complexity region	762	783	N/A	INTRINSIC
internal_repeat_1	816	917	8.83e-5	PROSPERO
internal_repeat_1	911	1023	8.83e-5	PROSPERO

Predicted Effect

probably damaging
Transcript: ENSMUST00000103238
AA Change: I393N

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

SMART Domains

Protein: ENSMUSP00000099528
Gene: ENSMUSG00000027200
AA Change: I393N

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Sema	57	487	7.29e-184	SMART
PSI	514	569	1.12e-1	SMART
low complexity region	573	584	N/A	INTRINSIC
transmembrane domain	645	667	N/A	INTRINSIC
low complexity region	786	807	N/A	INTRINSIC
internal_repeat_1	840	941	5.95e-5	PROSPERO
internal_repeat_1	935	1047	5.95e-5	PROSPERO

Predicted Effect

probably damaging
Transcript: ENSMUST00000103239
AA Change: I393N

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

SMART Domains

Protein: ENSMUSP00000099529
Gene: ENSMUSG00000027200
AA Change: I393N

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Sema	57	487	7.29e-184	SMART
PSI	514	569	1.12e-1	SMART
low complexity region	587	603	N/A	INTRINSIC
transmembrane domain	664	686	N/A	INTRINSIC
low complexity region	805	826	N/A	INTRINSIC
internal_repeat_1	859	960	5.78e-5	PROSPERO
internal_repeat_1	954	1066	5.78e-5	PROSPERO

Predicted Effect

probably damaging
Transcript: ENSMUST00000103240
AA Change: I393N

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

SMART Domains

Protein: ENSMUSP00000099530
Gene: ENSMUSG00000027200
AA Change: I393N

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Sema	57	487	7.29e-184	SMART
PSI	514	569	1.12e-1	SMART
low complexity region	587	603	N/A	INTRINSIC
transmembrane domain	660	682	N/A	INTRINSIC
low complexity region	801	822	N/A	INTRINSIC
internal_repeat_1	855	956	5.63e-5	PROSPERO
internal_repeat_1	950	1062	5.63e-5	PROSPERO

Predicted Effect

probably damaging
Transcript: ENSMUST00000103241
AA Change: I393N

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

SMART Domains

Protein: ENSMUSP00000099531
Gene: ENSMUSG00000027200
AA Change: I393N

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
Sema	57	487	7.29e-184	SMART
PSI	514	569	1.12e-1	SMART
transmembrane domain	589	611	N/A	INTRINSIC
low complexity region	730	751	N/A	INTRINSIC
internal_repeat_1	784	885	7.28e-5	PROSPERO
internal_repeat_1	879	991	7.28e-5	PROSPERO

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132088

Meta Mutation Damage Score

0.9305

Coding Region Coverage

1x: 99.1%
3x: 98.1%
10x: 95.9%
20x: 92.0%

Validation Efficiency

98% (110/112)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Semaphorins are a large family, including both secreted and membrane associated proteins, many of which have been implicated as inhibitors or chemorepellents in axon pathfinding, fasciculation and branching, and target selection. All semaphorins possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Additional sequence motifs C-terminal to the semaphorin domain allow classification into distinct subfamilies. Results demonstrate that transmembrane semaphorins, like the secreted ones, can act as repulsive axon guidance cues. This gene encodes a class 6 vertebrate transmembrane semaphorin that demonstrates alternative splicing. Several transcript variants have been identified and expression of the distinct encoded isoforms is thought to be regulated in a tissue- and development-dependent manner. [provided by RefSeq, Nov 2010]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit normal dendritic cell trafficking and antigen-specific T cell priming. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 110 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A730017C20Rik	T	A	18: 59,075,688	V136E	probably damaging	Het
Adam18	C	T	8: 24,674,054	G38R	probably benign	Het
Ap2m1	T	C	16: 20,541,099	M183T	probably damaging	Het
Apob	A	T	12: 7,988,678	I364F	probably damaging	Het
Arl6	A	T	16: 59,622,421		probably benign	Het
Cand2	A	G	6: 115,774,653	M15V	possibly damaging	Het
Cbl	A	G	9: 44,201,005	F131S	probably damaging	Het
Ccdc151	T	A	9: 21,991,708	H442L	probably benign	Het
Ccdc74a	A	G	16: 17,650,476	S321G	probably benign	Het
Cdc14b	T	C	13: 64,210,192		probably benign	Het
Cep152	T	C	2: 125,576,869		probably benign	Het
Cep290	A	G	10: 100,508,758	E479G	probably benign	Het
Chrm2	T	G	6: 36,524,111	I301R	probably benign	Het
Clec2e	A	G	6: 129,093,468	W197R	probably damaging	Het
Cnot10	G	T	9: 114,629,150	S96*	probably null	Het
Col19a1	A	G	1: 24,289,655		probably benign	Het
Csmd2	T	C	4: 128,133,673		probably benign	Het
Cthrc1	A	T	15: 39,086,764	*172L	probably null	Het
Cul9	A	T	17: 46,528,589	I821N	probably benign	Het
Daam1	G	C	12: 71,975,304		probably benign	Het
Dhx58	A	T	11: 100,699,264	I398N	probably damaging	Het
Dip2b	T	A	15: 100,193,913	H844Q	probably damaging	Het
Dmac2	A	G	7: 25,621,029	D50G	probably damaging	Het
Dmxl1	C	A	18: 49,879,362	Q1529K	probably benign	Het
Dtna	C	T	18: 23,597,501	P315L	probably damaging	Het
Ep300	T	C	15: 81,640,116	S1382P	unknown	Het
Fat2	A	T	11: 55,310,777	N490K	probably damaging	Het
Flg2	T	A	3: 93,200,355		probably benign	Het
Gm13084	T	A	4: 143,811,699	D234V	probably benign	Het
Gpatch1	T	C	7: 35,281,381		probably benign	Het
Grin2a	C	A	16: 9,579,585	K879N	possibly damaging	Het
Hacd3	A	C	9: 65,001,022	I164S	possibly damaging	Het
Hinfp	A	C	9: 44,298,948	C197G	probably damaging	Het
Hsd17b12	T	C	2: 94,114,990		probably benign	Het
Hsd3b1	A	T	3: 98,853,039	L212Q	probably damaging	Het
Ifrd1	C	T	12: 40,214,094		probably null	Het
Igf2bp2	A	G	16: 22,081,801	F129L	possibly damaging	Het
Kirrel3	T	A	9: 35,020,163	I409N	probably damaging	Het
Klhdc10	T	C	6: 30,447,412	I204T	probably damaging	Het
Kpna6	A	T	4: 129,657,804	S65R	possibly damaging	Het
Lama3	A	T	18: 12,407,563	D308V	probably benign	Het
Larp4b	T	A	13: 9,158,107		probably null	Het
Lgr6	C	T	1: 134,994,010	A199T	probably damaging	Het
Lyzl1	A	T	18: 4,169,175	T11S	probably benign	Het
Man1c1	A	G	4: 134,578,315	L366P	probably damaging	Het
Mef2a	A	G	7: 67,251,724	M100T	probably damaging	Het
Mettl13	G	A	1: 162,538,889	H474Y	possibly damaging	Het
Mmp3	A	G	9: 7,451,320	D352G	probably benign	Het
Mns1	T	C	9: 72,452,804	I412T	probably damaging	Het
Mon2	T	C	10: 123,007,021	D1501G	probably null	Het
Mylk	G	T	16: 34,875,620	G242W	probably damaging	Het
Nav1	T	C	1: 135,449,966	D1715G	possibly damaging	Het
Nckap1l	T	C	15: 103,453,883	S2P	probably damaging	Het
Nek3	A	T	8: 22,128,729		probably benign	Het
Nfrkb	A	G	9: 31,388,897		probably benign	Het
Nlrp4d	T	C	7: 10,388,778	D53G	probably benign	Het
Nol8	T	C	13: 49,662,152	S561P	probably damaging	Het
Nuf2	A	C	1: 169,525,297		probably benign	Het
Ofcc1	T	A	13: 40,015,313	D866V	possibly damaging	Het
Olfr195	A	G	16: 59,149,299	I150V	probably benign	Het
Optn	A	G	2: 5,046,195	L125P	probably benign	Het
Otoa	T	A	7: 121,131,341	F588Y	probably benign	Het
Pappa	T	A	4: 65,351,613		probably null	Het
Pde5a	T	G	3: 122,835,583	C635W	probably damaging	Het
Pdgfb	A	T	15: 80,003,419		probably null	Het
Pih1d2	T	A	9: 50,621,046	C135S	probably damaging	Het
Plcg1	G	T	2: 160,752,366	C361F	probably damaging	Het
Ppp4r4	T	C	12: 103,601,360		probably benign	Het
Prdm10	G	A	9: 31,349,268		probably null	Het
Prex2	T	A	1: 11,089,706		probably null	Het
Prss56	T	G	1: 87,184,730		probably null	Het
Prtg	A	G	9: 72,844,958	K209E	probably benign	Het
Ptprc	G	A	1: 138,122,575	T36I	possibly damaging	Het
Rasgrp4	A	G	7: 29,145,860	Y302C	probably damaging	Het
Rb1cc1	T	A	1: 6,248,634	M759K	probably damaging	Het
Rbm15b	T	A	9: 106,885,998	M324L	probably benign	Het
Rcbtb2	T	C	14: 73,178,547	V500A	probably damaging	Het
Rgs6	A	G	12: 83,133,677	K434R	probably damaging	Het
Rims1	C	T	1: 22,596,526	A125T	possibly damaging	Het
Robo3	A	G	9: 37,422,177	V746A	probably benign	Het
Rtl1	C	T	12: 109,591,386	E1340K	unknown	Het
Sacs	G	A	14: 61,205,640	D1712N	possibly damaging	Het
Samd4b	G	A	7: 28,403,977	P19S	probably benign	Het
Samhd1	T	C	2: 157,114,231	Y347C	probably damaging	Het
Sigmar1	C	T	4: 41,741,243	A4T	probably benign	Het
Skint9	C	A	4: 112,389,179	L245F	probably benign	Het
Slc35f5	T	C	1: 125,585,095	L372P	probably damaging	Het
Smc1b	A	T	15: 85,066,277	I1182N	probably damaging	Het
Smyd3	A	G	1: 178,957,573		probably benign	Het
Sptlc1	T	C	13: 53,337,612	D417G	probably benign	Het
Sv2c	T	C	13: 96,088,708	N31S	probably benign	Het
Tjp1	T	C	7: 65,314,990	D811G	probably damaging	Het
Top2b	A	G	14: 16,418,442	T1221A	probably benign	Het
Tph2	T	C	10: 115,174,109	D182G	probably damaging	Het
Traf6	C	T	2: 101,688,588	Q141*	probably null	Het
Ttn	T	C	2: 76,756,931	D21574G	probably damaging	Het
Uba2	T	A	7: 34,151,021	N367I	probably benign	Het
Ube2b	T	C	11: 51,988,602		probably benign	Het
Ubr5	G	T	15: 38,030,672	L426I	probably benign	Het
Ugt2a2	T	A	5: 87,464,148	H301L	probably benign	Het
Upf2	T	A	2: 6,018,894		probably benign	Het
Utrn	T	C	10: 12,710,060	D991G	probably benign	Het
Vmn2r25	T	C	6: 123,823,181	D734G	probably damaging	Het
Vmn2r68	T	A	7: 85,233,249		probably benign	Het
Vmn2r68	C	G	7: 85,233,258		probably null	Het
Vwf	T	A	6: 125,626,361	Y891*	probably null	Het
Wwox	C	T	8: 114,706,278	T228I	probably benign	Het
Zer1	C	T	2: 30,108,213		probably benign	Het
Zfp180	C	T	7: 24,104,707	H184Y	possibly damaging	Het
Zfp68	A	T	5: 138,607,225	Y279N	probably benign	Het

Other mutations in Sema6d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00155:Sema6d	APN	2	124659865	missense	possibly damaging	0.91
IGL00508:Sema6d	APN	2	124656924	splice site	probably benign
IGL00710:Sema6d	APN	2	124662288	missense	probably benign	0.00
IGL00811:Sema6d	APN	2	124658469	missense	probably damaging	1.00
IGL01457:Sema6d	APN	2	124653642	missense	unknown
IGL01524:Sema6d	APN	2	124664075	missense	possibly damaging	0.86
IGL01598:Sema6d	APN	2	124665098	missense	probably damaging	1.00
IGL01915:Sema6d	APN	2	124658571	splice site	probably benign
IGL02365:Sema6d	APN	2	124656868	missense	probably benign	0.14
IGL02698:Sema6d	APN	2	124653723	missense	possibly damaging	0.95
IGL02865:Sema6d	APN	2	124664073	missense	probably damaging	1.00
IGL03018:Sema6d	APN	2	124659600	missense	possibly damaging	0.95
IGL03333:Sema6d	APN	2	124664370	missense	possibly damaging	0.83
R0269:Sema6d	UTSW	2	124660745	missense	possibly damaging	0.63
R0541:Sema6d	UTSW	2	124665277	missense	probably benign	0.25
R0615:Sema6d	UTSW	2	124654135	splice site	probably benign
R0617:Sema6d	UTSW	2	124660745	missense	possibly damaging	0.63
R0694:Sema6d	UTSW	2	124664041	missense	probably damaging	1.00
R0854:Sema6d	UTSW	2	124665302	missense	probably damaging	0.97
R1630:Sema6d	UTSW	2	124664345	missense	possibly damaging	0.89
R1682:Sema6d	UTSW	2	124665149	missense	probably benign	0.21
R1823:Sema6d	UTSW	2	124659556	splice site	probably null
R1932:Sema6d	UTSW	2	124659886	critical splice donor site	probably null
R2249:Sema6d	UTSW	2	124659588	missense	possibly damaging	0.54
R2256:Sema6d	UTSW	2	124664150	missense	probably damaging	1.00
R2331:Sema6d	UTSW	2	124658063	missense	probably damaging	1.00
R2910:Sema6d	UTSW	2	124665037	missense	probably damaging	1.00
R3683:Sema6d	UTSW	2	124654226	missense	possibly damaging	0.88
R3937:Sema6d	UTSW	2	124656850	missense	probably benign	0.00
R4135:Sema6d	UTSW	2	124664120	missense	probably damaging	0.96
R4446:Sema6d	UTSW	2	124664059	missense	probably damaging	0.98
R4583:Sema6d	UTSW	2	124664162	missense	probably damaging	1.00
R4599:Sema6d	UTSW	2	124654231	missense	probably damaging	1.00
R4822:Sema6d	UTSW	2	124662294	missense	possibly damaging	0.79
R4884:Sema6d	UTSW	2	124656818	splice site	probably null
R5288:Sema6d	UTSW	2	124664246	missense	probably damaging	1.00
R5443:Sema6d	UTSW	2	124656836	missense	probably damaging	1.00
R5504:Sema6d	UTSW	2	124658021	missense	probably damaging	1.00
R5534:Sema6d	UTSW	2	124659815	missense	possibly damaging	0.75
R5615:Sema6d	UTSW	2	124656901	missense	probably damaging	0.97
R5747:Sema6d	UTSW	2	124664947	missense	probably damaging	0.99
R5866:Sema6d	UTSW	2	124664342	missense	probably benign	0.26
R5980:Sema6d	UTSW	2	124664708	missense	probably damaging	1.00
R6670:Sema6d	UTSW	2	124654842	small deletion	probably benign
R6803:Sema6d	UTSW	2	124664050	missense	probably damaging	0.96
R7023:Sema6d	UTSW	2	124664911	missense	probably damaging	1.00
R7068:Sema6d	UTSW	2	124657821	missense	probably benign
R7426:Sema6d	UTSW	2	124654158	missense	probably damaging	1.00
R7556:Sema6d	UTSW	2	124654189	missense	probably damaging	1.00
R7569:Sema6d	UTSW	2	124657972	missense	possibly damaging	0.92
R8427:Sema6d	UTSW	2	124665277	missense	probably benign	0.25
R8690:Sema6d	UTSW	2	124665017	missense	probably benign	0.07
R8711:Sema6d	UTSW	2	124660312	missense	possibly damaging	0.54
R8757:Sema6d	UTSW	2	124655214	missense	probably damaging	1.00
R8759:Sema6d	UTSW	2	124655214	missense	probably damaging	1.00
R8868:Sema6d	UTSW	2	124654194	missense	probably damaging	1.00
R9511:Sema6d	UTSW	2	124658023	missense	probably damaging	1.00
R9586:Sema6d	UTSW	2	124654176	missense	probably damaging	1.00
R9731:Sema6d	UTSW	2	124664197	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CCCTCCGAGGCCAATACATGTTATC -3'
(R):5'- TGCTGAACGGTCCACTTCGATG -3'

Sequencing Primer
(F):5'- CTGGGAAATGACATTACTGCTC -3'
(R):5'- GGCTGTCAACCTGTACCTAGTG -3'

Posted On

2013-04-24