Mutagenetix > Incidental Mutation

Incidental Mutation 'R4599:Sema6d'

345412

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

041815-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4599 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

124089969-124667770 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 124654231 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 65 (I65N)

Ref Sequence

ENSEMBL: ENSMUSP00000099530 (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: I65N

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

SMART Domains

Protein: ENSMUSP00000061123
Gene: ENSMUSG00000027200
AA Change: I65N

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: I65N

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

SMART Domains

Protein: ENSMUSP00000075674
Gene: ENSMUSG00000027200
AA Change: I65N

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: I65N

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

SMART Domains

Protein: ENSMUSP00000077014
Gene: ENSMUSG00000027200
AA Change: I65N

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: I65N

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

SMART Domains

Protein: ENSMUSP00000077691
Gene: ENSMUSG00000027200
AA Change: I65N

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: I65N

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

SMART Domains

Protein: ENSMUSP00000099528
Gene: ENSMUSG00000027200
AA Change: I65N

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: I65N

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

SMART Domains

Protein: ENSMUSP00000099529
Gene: ENSMUSG00000027200
AA Change: I65N

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: I65N

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

SMART Domains

Protein: ENSMUSP00000099530
Gene: ENSMUSG00000027200
AA Change: I65N

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: I65N

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

SMART Domains

Protein: ENSMUSP00000099531
Gene: ENSMUSG00000027200
AA Change: I65N

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: 98.7%
10x: 97.4%
20x: 95.4%

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca14	T	C	7: 120,255,403	V930A	probably benign	Het
Ankrd13b	T	C	11: 77,471,668	R677G	probably benign	Het
Apc	T	A	18: 34,317,987	Y2611*	probably null	Het
Apold1	A	G	6: 134,984,069	Y162C	probably damaging	Het
Atp6v0a4	T	C	6: 38,078,802	I325V	probably benign	Het
Cab39	A	G	1: 85,848,329	Y249C	probably damaging	Het
Cd22	T	A	7: 30,875,900	H239L	probably damaging	Het
Chrna7	A	G	7: 63,103,790	M327T	probably damaging	Het
Clock	T	C	5: 76,235,810	M499V	probably benign	Het
Clspn	A	G	4: 126,581,460	E1002G	probably benign	Het
Clta	C	T	4: 44,012,819	P10S	probably damaging	Het
Col5a3	A	G	9: 20,774,559		probably null	Het
Coq6	T	C	12: 84,362,139	V30A	probably benign	Het
Csmd2	G	T	4: 127,988,128	R20L	probably benign	Het
D430041D05Rik	A	T	2: 104,208,183	V1547D	probably damaging	Het
Dapk1	C	T	13: 60,718,047	P153S	probably benign	Het
Dock2	T	A	11: 34,239,536	Y1545F	probably damaging	Het
Dpp6	G	T	5: 27,634,548	G354C	probably damaging	Het
Dyrk1b	T	C	7: 28,182,431	L105P	probably damaging	Het
Epor	A	G	9: 21,961,859	S86P	probably benign	Het
Fam166b	T	C	4: 43,427,574	H250R	possibly damaging	Het
Gale	C	A	4: 135,967,837	S341*	probably null	Het
Galnt4	T	A	10: 99,109,493	V360E	probably damaging	Het
Gart	A	T	16: 91,622,945	C24*	probably null	Het
Gcnt2	G	T	13: 40,887,490	V42L	probably benign	Het
Herc6	A	G	6: 57,659,713	I805V	probably benign	Het
Ints12	T	A	3: 133,098,453	I67N	probably benign	Het
Irx1	C	A	13: 71,960,113	R150L	probably damaging	Het
Kif26b	A	G	1: 178,530,459	Y45C	unknown	Het
Krt35	T	C	11: 100,094,008	T275A	probably damaging	Het
Laptm5	G	T	4: 130,916,005		probably benign	Het
Lin7a	T	C	10: 107,412,166	S111P	unknown	Het
Med27	A	G	2: 29,524,458	D159G	probably damaging	Het
Msh2	A	G	17: 87,708,578	K546R	probably damaging	Het
Myo1a	A	T	10: 127,720,151		probably null	Het
Myo1c	T	C	11: 75,668,193	F604L	probably damaging	Het
Myrip	A	G	9: 120,464,784	K782E	probably damaging	Het
Ndc80	T	C	17: 71,521,068	D88G	probably damaging	Het
Nrxn2	A	G	19: 6,455,252	D375G	probably damaging	Het
Olfr1380	T	C	11: 49,564,718	S266P	probably damaging	Het
Olfr676	A	G	7: 105,036,073	I292V	probably benign	Het
Padi3	T	C	4: 140,798,111	H187R	probably damaging	Het
Pcdhgb1	A	T	18: 37,681,557	N367I	probably damaging	Het
Pdrg1	T	C	2: 153,012,390	I77V	probably benign	Het
Pfas	T	C	11: 68,991,069	E930G	probably benign	Het
Pik3cb	C	T	9: 99,061,764	R662Q	probably benign	Het
Pla2g4e	T	G	2: 120,186,382	H226P	possibly damaging	Het
Plxnd1	A	T	6: 115,994,276	V177E	probably damaging	Het
Prmt7	A	G	8: 106,250,329	S558G	possibly damaging	Het
Pspc1	A	C	14: 56,777,789		probably null	Het
Rilp	T	C	11: 75,512,760	S343P	probably benign	Het
Ror1	A	G	4: 100,407,910	M194V	probably damaging	Het
Rsu1	T	C	2: 13,170,004	Y225C	probably damaging	Het
Rundc1	A	G	11: 101,433,926	N486S	probably damaging	Het
Slc5a11	A	G	7: 123,258,378	E230G	probably benign	Het
Spint1	T	C	2: 119,246,460	S342P	probably damaging	Het
Stard3nl	A	G	13: 19,367,753	S214P	probably damaging	Het
Tcp10a	A	C	17: 7,336,924	T271P	probably damaging	Het
Tie1	A	G	4: 118,472,634	Y1091H	probably benign	Het
Tlr12	T	C	4: 128,617,332	Y375C	probably benign	Het
Tmem107	T	A	11: 69,071,448	M77K	probably damaging	Het
Tns2	C	T	15: 102,108,934	R281C	probably damaging	Het
Tns3	T	C	11: 8,531,747	K202E	probably damaging	Het
Tspoap1	C	T	11: 87,779,521	P1634L	probably damaging	Het
Ttc7b	G	A	12: 100,500,117	R79C	probably damaging	Het
Ush2a	A	G	1: 188,911,647	N4402S	probably benign	Het
Vmn2r13	A	T	5: 109,156,456	I703N	probably damaging	Het
Xrcc4	A	G	13: 90,062,007		probably null	Het
Zp3	A	T	5: 135,984,235	K168*	probably null	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
R4583:Sema6d	UTSW	2	124664162	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'- CCTTCCTACAAGTGCTATATACAGC -3'
(R):5'- CTGGATGTGACACTGAACGC -3'

Sequencing Primer
(F):5'- CAGCTAATCAATGCTGGCTATTG -3'
(R):5'- CTGGATGTGACACTGAACGCTTTAAC -3'

Posted On

2015-09-25