Mutagenetix > Incidental Mutation

Incidental Mutation 'R4583:Sema6d'

343786

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

041804-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4583 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

124089969-124667770 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 124664162 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 630 (R630L)

Ref Sequence

ENSEMBL: ENSMUSP00000061123 (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: R630L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000061123
Gene: ENSMUSG00000027200
AA Change: R630L

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: R617L

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000075674
Gene: ENSMUSG00000027200
AA Change: R617L

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: R673L

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

SMART Domains

Protein: ENSMUSP00000077014
Gene: ENSMUSG00000027200
AA Change: R673L

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: R649L

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000077691
Gene: ENSMUSG00000027200
AA Change: R649L

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: R673L

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

SMART Domains

Protein: ENSMUSP00000099528
Gene: ENSMUSG00000027200
AA Change: R673L

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: R692L

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000099529
Gene: ENSMUSG00000027200
AA Change: R692L

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: R688L

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000099530
Gene: ENSMUSG00000027200
AA Change: R688L

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: R617L

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000099531
Gene: ENSMUSG00000027200
AA Change: R617L

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

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.2%
20x: 95.1%

Validation Efficiency

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: 119 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310022A10Rik	T	C	7: 27,574,592	L86P	unknown	Het
Aimp1	C	T	3: 132,677,047	E23K	probably damaging	Het
Ap2b1	A	T	11: 83,397,779	N884I	probably benign	Het
Apoe	G	T	7: 19,697,498	Q65K	possibly damaging	Het
Arhgef1	T	A	7: 24,912,571	D93E	probably benign	Het
Arhgef12	G	T	9: 42,977,662	T1085K	probably damaging	Het
Arid5a	T	C	1: 36,317,664		probably null	Het
Atp9a	A	T	2: 168,689,360		probably null	Het
Baz1a	T	C	12: 54,922,540	I635V	probably damaging	Het
Bbs10	A	G	10: 111,301,134	K703E	probably benign	Het
Cckar	T	A	5: 53,699,782	M429L	probably benign	Het
Ccl3	A	T	11: 83,648,338	L65Q	probably benign	Het
Ccr3	A	G	9: 124,029,440	T271A	probably benign	Het
Cd8b1	T	A	6: 71,326,097	I52N	probably damaging	Het
Cdh15	G	A	8: 122,865,028	E551K	probably damaging	Het
Cdh17	A	G	4: 11,810,466	K719R	probably benign	Het
Cfap43	T	C	19: 47,837,216	R38G	probably null	Het
Chd6	T	C	2: 161,014,194	E715G	probably damaging	Het
Cldn34b2	T	A	X: 155,125,629	R68*	probably null	Het
Col19a1	T	G	1: 24,561,329	D44A	unknown	Het
Colgalt2	C	T	1: 152,506,876	S493F	probably damaging	Het
Cr1l	T	C	1: 195,129,831	I99M	probably damaging	Het
Crybg1	T	C	10: 43,997,620	E1164G	probably damaging	Het
Cym	G	T	3: 107,211,402	D367E	probably damaging	Het
Dennd2a	G	T	6: 39,522,842	T263K	probably damaging	Het
Dhx9	T	A	1: 153,460,303	M869L	probably damaging	Het
Dnm2	A	G	9: 21,504,446	H692R	probably damaging	Het
Ern1	A	T	11: 106,407,205	S697T	probably damaging	Het
F12	G	A	13: 55,421,130	T273I	probably benign	Het
Fam151b	A	T	13: 92,468,109	L124Q	probably damaging	Het
Fancg	A	G	4: 43,002,991	V622A	probably benign	Het
Fbxo2	T	A	4: 148,164,899	N159K	possibly damaging	Het
Fgd2	C	A	17: 29,367,078	T212K	possibly damaging	Het
Fhl3	T	A	4: 124,707,549	D178E	probably benign	Het
Filip1	G	T	9: 79,815,809	A1176D	possibly damaging	Het
Fndc1	T	C	17: 7,739,249	Y1722C	probably damaging	Het
Frem3	T	C	8: 80,613,514	V812A	probably benign	Het
Fsip2	A	G	2: 82,978,673	I1779V	probably benign	Het
Gli2	C	T	1: 118,842,068	V585I	probably benign	Het
Gm15056	C	G	8: 20,900,681	S80T	probably benign	Het
Gm4951	T	C	18: 60,246,080	I229T	possibly damaging	Het
Gm5145	A	G	17: 20,570,453	E31G	probably benign	Het
Gmfg	A	G	7: 28,445,944	Y71C	probably damaging	Het
Grk1	A	G	8: 13,409,322	E291G	probably damaging	Het
Gtpbp1	A	G	15: 79,715,951	E393G	possibly damaging	Het
Gtpbp2	A	G	17: 46,161,145	D2G	probably damaging	Het
Hc	A	T	2: 35,028,177	V698E	probably benign	Het
Helz	G	A	11: 107,646,069	R249H	probably damaging	Het
Hmcn2	A	G	2: 31,413,265	I2973V	possibly damaging	Het
Hnrnpa3	A	G	2: 75,663,606	R286G	probably benign	Het
Hus1b	A	T	13: 30,947,518	W53R	probably damaging	Het
Hydin	C	T	8: 110,595,225	T4503I	probably benign	Het
Ighmbp2	G	C	19: 3,265,324	P699A	probably benign	Het
Igkv1-122	A	T	6: 68,017,458	Y110F	probably benign	Het
Igkv8-28	T	C	6: 70,143,620	Y113C	probably damaging	Het
Il16	A	G	7: 83,682,899	S158P	probably damaging	Het
Kalrn	T	A	16: 34,235,267	H876L	probably damaging	Het
Kdm5d	T	A	Y: 914,134	L357H	probably damaging	Het
Krt78	T	C	15: 101,946,620	T919A	possibly damaging	Het
L3mbtl2	T	C	15: 81,684,906	C594R	probably damaging	Het
Lcorl	A	T	5: 45,733,589	L474*	probably null	Het
Lgals3	A	T	14: 47,381,687		probably null	Het
Lnx1	C	T	5: 74,610,796	V350I	probably benign	Het
Lpcat3	T	G	6: 124,703,323	W429G	possibly damaging	Het
Lrp1	T	C	10: 127,541,372	T4149A	probably benign	Het
Memo1	G	A	17: 74,258,461	Q36*	probably null	Het
Micalcl	A	G	7: 112,412,947	N668S	probably benign	Het
Ms4a10	A	T	19: 10,968,189	I76N	possibly damaging	Het
Mthfr	T	G	4: 148,051,872	L362V	possibly damaging	Het
Myh3	T	A	11: 67,096,453	Y1376*	probably null	Het
Mymk	C	A	2: 27,062,280	V192F	probably benign	Het
Myo1c	A	G	11: 75,671,862	D966G	possibly damaging	Het
Ncam2	A	G	16: 81,517,557	N474D	probably damaging	Het
Nmnat1	T	C	4: 149,469,151	N168S	possibly damaging	Het
Nmur1	C	T	1: 86,386,645	V323M	possibly damaging	Het
Npr2	C	A	4: 43,633,522		probably null	Het
Nsd3	T	A	8: 25,710,676	M1265K	probably benign	Het
Olfr1206	G	T	2: 88,865,494	M296I	probably benign	Het
Olfr1212	T	A	2: 88,959,212	F249I	probably damaging	Het
Olfr1462	T	A	19: 13,190,698	F10L	probably damaging	Het
Olfr152	T	C	2: 87,783,221	V227A	possibly damaging	Het
Olfr155	A	G	4: 43,855,262	T318A	probably benign	Het
Olfr345	A	C	2: 36,640,614	T192P	probably damaging	Het
Olfr394	T	C	11: 73,887,803	T190A	probably damaging	Het
Olfr812	T	C	10: 129,842,475	D189G	probably damaging	Het
Otub1	G	A	19: 7,204,436	A25V	possibly damaging	Het
Paqr3	T	A	5: 97,108,210	R102*	probably null	Het
Patl2	A	G	2: 122,126,745	S103P	probably benign	Het
Pcdhb15	A	T	18: 37,475,575	H620L	possibly damaging	Het
Pdgfc	A	T	3: 81,141,528	D81V	possibly damaging	Het
Pdia2	T	C	17: 26,196,502	D447G	probably damaging	Het
Pold1	C	A	7: 44,538,913	A514S	probably damaging	Het
Pomgnt1	C	T	4: 116,158,494	T552I	probably benign	Het
Ppl	T	C	16: 5,104,536	E294G	probably benign	Het
Pramef8	A	G	4: 143,416,754	Y30C	probably damaging	Het
Prkcb	A	G	7: 122,457,224	S100G	probably benign	Het
Psg16	T	G	7: 17,095,172	I227S	probably benign	Het
Rbbp6	AAAGAAGAAGAAGAAGAAG	AAAGAAGAAGAAGAAG	7: 123,001,952		probably benign	Het
Reck	T	C	4: 43,931,062		probably null	Het
Rrbp1	C	T	2: 143,988,751	G499S	probably benign	Het
Slc29a1	A	G	17: 45,589,956	V94A	possibly damaging	Het
Slc35a1	T	A	4: 34,664,146	Q324L	probably benign	Het
Slc35c1	A	T	2: 92,458,921	L80Q	probably damaging	Het
Slc7a10	G	T	7: 35,197,952		probably null	Het
Srrm2	C	T	17: 23,819,619		probably benign	Het
Stk38	T	G	17: 28,982,156	D182A	probably damaging	Het
Tas2r104	C	T	6: 131,685,435	G104S	probably benign	Het
Tmem121b	T	C	6: 120,492,094	E554G	probably damaging	Het
Tor1aip2	A	G	1: 156,065,142	H398R	probably benign	Het
Tram2	C	T	1: 21,013,449	V83I	probably benign	Het
Ube3a	C	T	7: 59,286,063	T565I	probably damaging	Het
Ubr4	T	C	4: 139,380,853	V56A	possibly damaging	Het
Vmn1r128	T	C	7: 21,349,719	V116A	possibly damaging	Het
Vmn1r170	C	T	7: 23,606,662	T163I	probably benign	Het
Vmn2r75	T	A	7: 86,164,082	D504V	possibly damaging	Het
Vps36	G	A	8: 22,218,420	M363I	probably benign	Het
Wdsub1	A	G	2: 59,878,317	S71P	probably damaging	Het
Zdhhc12	A	G	2: 30,091,484	F189L	probably benign	Het
Zfp521	T	C	18: 13,844,330	M1009V	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
R0390:Sema6d	UTSW	2	124658490	missense	probably damaging	1.00
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
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'- CTAGGCATATGGAGTTTGAAGGTAG -3'
(R):5'- AGTTCCTTCCGACTGGTCAG -3'

Sequencing Primer
(F):5'- AAAAAGCATTTTGTTCAAAGCCTTCC -3'
(R):5'- ACTGGTCAGCAGGTTGC -3'

Posted On

2015-09-24