Mutagenetix > Incidental Mutation

Incidental Mutation 'R1823:Sema6d'

206548

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

039851-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1823 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

124089969-124667770 bp(+) (GRCm38)

Type of Mutation

splice site

DNA Base Change (assembly)

A to G at 124659556 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000099531 (fasta)

Gene Model

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

AlphaFold

Q76KF0

Predicted Effect

probably null
Transcript: ENSMUST00000051419

SMART Domains

Protein: ENSMUSP00000061123
Gene: ENSMUSG00000027200

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 null
Transcript: ENSMUST00000076335

SMART Domains

Protein: ENSMUSP00000075674
Gene: ENSMUSG00000027200

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 null
Transcript: ENSMUST00000077847

SMART Domains

Protein: ENSMUSP00000077014
Gene: ENSMUSG00000027200

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 null
Transcript: ENSMUST00000077847

SMART Domains

Protein: ENSMUSP00000077014
Gene: ENSMUSG00000027200

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 null
Transcript: ENSMUST00000078621

SMART Domains

Protein: ENSMUSP00000077691
Gene: ENSMUSG00000027200

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 null
Transcript: ENSMUST00000078621

SMART Domains

Protein: ENSMUSP00000077691
Gene: ENSMUSG00000027200

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 null
Transcript: ENSMUST00000103238

SMART Domains

Protein: ENSMUSP00000099528
Gene: ENSMUSG00000027200

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 null
Transcript: ENSMUST00000103239

SMART Domains

Protein: ENSMUSP00000099529
Gene: ENSMUSG00000027200

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 null
Transcript: ENSMUST00000103239

SMART Domains

Protein: ENSMUSP00000099529
Gene: ENSMUSG00000027200

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 null
Transcript: ENSMUST00000103240

SMART Domains

Protein: ENSMUSP00000099530
Gene: ENSMUSG00000027200

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 null
Transcript: ENSMUST00000103241

SMART Domains

Protein: ENSMUSP00000099531
Gene: ENSMUSG00000027200

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 null
Transcript: ENSMUST00000103241

SMART Domains

Protein: ENSMUSP00000099531
Gene: ENSMUSG00000027200

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: 97.4%
3x: 96.8%
10x: 95.1%
20x: 91.6%

Validation Efficiency

98% (87/89)

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810041L15Rik	T	C	15: 84,406,468	T213A	probably benign	Het
Adcy1	G	A	11: 7,161,312	V868I	probably benign	Het
Ahnak	G	T	19: 9,004,905	M1184I	probably damaging	Het
Akap11	T	C	14: 78,511,488	E1153G	probably damaging	Het
Amy1	T	C	3: 113,562,727	N260S	probably null	Het
Ankrd6	A	G	4: 32,824,427	L129P	probably damaging	Het
Aox2	A	T	1: 58,312,359	T702S	probably benign	Het
Apobec1	G	T	6: 122,578,886	T204K	possibly damaging	Het
Arhgef19	A	G	4: 141,249,146	R433G	probably benign	Het
Atf6b	T	A	17: 34,648,644	H110Q	possibly damaging	Het
Btnl4	C	T	17: 34,475,852		probably null	Het
Camsap2	T	C	1: 136,273,783	T662A	possibly damaging	Het
Cbs	G	A	17: 31,624,271	H229Y	probably damaging	Het
Cct8	G	A	16: 87,490,554	R111*	probably null	Het
Cdc42bpb	C	T	12: 111,327,559	A250T	probably damaging	Het
Chrd	A	G	16: 20,741,347		probably benign	Het
Ckap2l	A	G	2: 129,275,579	F559L	probably damaging	Het
D630003M21Rik	T	C	2: 158,217,557	Y141C	probably damaging	Het
Dbf4	T	C	5: 8,397,539	N557S	probably benign	Het
Dct	T	G	14: 118,036,523	N324T	probably benign	Het
Dip2a	A	T	10: 76,278,502	L999*	probably null	Het
Dock10	T	A	1: 80,543,097		probably null	Het
Dync2li1	A	T	17: 84,649,797	D330V	probably damaging	Het
Eif4g3	T	A	4: 138,180,491	D1267E	probably benign	Het
Enc1	A	G	13: 97,245,978	E332G	possibly damaging	Het
Fat2	C	T	11: 55,256,780	V3879I	probably benign	Het
Fh1	A	T	1: 175,616,548	I117K	probably damaging	Het
Fkbp15	A	G	4: 62,337,091	L227P	probably damaging	Het
Fpr1	T	A	17: 17,877,053	M225L	probably benign	Het
Fras1	A	T	5: 96,770,688	I3528F	probably damaging	Het
Grm7	A	G	6: 111,207,769	T354A	probably benign	Het
Ift27	T	A	15: 78,173,778	I9F	possibly damaging	Het
Igf1r	A	G	7: 68,194,981	D834G	possibly damaging	Het
Igsf9b	T	A	9: 27,331,732	L738Q	probably damaging	Het
Itgam	A	T	7: 128,064,732	T44S	probably benign	Het
Ivd	T	A	2: 118,862,034	I5N	probably benign	Het
Jcad	T	C	18: 4,675,780	S1181P	probably damaging	Het
Kctd18	A	G	1: 57,956,365	V251A	probably benign	Het
Mycbp2	A	G	14: 103,252,509	V953A	possibly damaging	Het
Myo18a	T	C	11: 77,825,097		probably benign	Het
Myo3a	A	T	2: 22,340,280	Y509F	probably damaging	Het
Myocd	C	A	11: 65,178,670	M909I	probably benign	Het
Ndufv3	G	A	17: 31,531,245	R467Q	probably damaging	Het
Nkpd1	G	A	7: 19,523,252	V319M	probably damaging	Het
Olfr1216	A	G	2: 89,013,378	S229P	probably benign	Het
Olfr1342	T	A	4: 118,690,192	N87Y	probably damaging	Het
Olfr1453	C	A	19: 13,027,817	V171L	probably benign	Het
Olfr31	T	A	14: 14,328,774	L221Q	probably damaging	Het
Olfr366	T	C	2: 37,220,332	V281A	probably damaging	Het
Olfr406	C	T	11: 74,270,217	A276V	probably damaging	Het
Olfr450	G	T	6: 42,818,268	A266S	possibly damaging	Het
Parp4	T	C	14: 56,589,872		probably benign	Het
Pcdhb9	A	G	18: 37,402,818	T622A	probably benign	Het
Pdpk1	A	T	17: 24,098,176		probably benign	Het
Pkhd1	C	A	1: 20,347,457	G2490V	probably damaging	Het
Plekhg1	G	T	10: 3,903,658		probably null	Het
Plekhh2	A	G	17: 84,575,189	Y708C	probably damaging	Het
Pnp	T	C	14: 50,950,329	F107L	probably damaging	Het
Postn	T	A	3: 54,385,287		probably null	Het
Prcp	A	T	7: 92,928,675	D349V	probably damaging	Het
Prl3a1	A	T	13: 27,270,194	I52F	probably damaging	Het
Pym1	G	A	10: 128,766,044		probably benign	Het
Rad9a	A	T	19: 4,197,242	I248N	probably damaging	Het
Ror2	T	G	13: 53,110,305	E917A	probably benign	Het
Rsf1	G	A	7: 97,579,910		probably benign	Het
Slc4a2	C	T	5: 24,427,620	A12V	probably damaging	Het
Slco6b1	T	G	1: 96,961,176		noncoding transcript	Het
Slf2	A	T	19: 44,935,248	H167L	possibly damaging	Het
Snx9	G	T	17: 5,920,671	G429V	probably damaging	Het
Sod3	G	T	5: 52,368,162	V68L	probably benign	Het
Spta1	T	A	1: 174,246,549	D2351E	probably benign	Het
Srpk3	G	A	X: 73,777,955	R425Q	possibly damaging	Het
Tatdn1	C	T	15: 58,916,156	G171E	probably damaging	Het
Tbc1d22a	T	C	15: 86,235,569	V22A	possibly damaging	Het
Tmem27	A	G	X: 164,118,234	D184G	possibly damaging	Het
Tnfsf9	A	G	17: 57,105,738	T103A	probably benign	Het
Tpm3-rs7	T	C	14: 113,315,163	L163P	possibly damaging	Het
Trim52	T	A	14: 106,106,967	C20S	probably damaging	Het
Ucp1	C	T	8: 83,294,032	T157I	probably damaging	Het
Uspl1	T	A	5: 149,214,414	L794Q	probably benign	Het
Vmn1r5	T	A	6: 56,985,595	V85E	probably damaging	Het
Vmn1r58	A	G	7: 5,410,406	I275T	possibly damaging	Het
Vmn2r79	A	G	7: 87,037,872	I820M	probably damaging	Het
Wscd1	C	A	11: 71,760,218	P124T	probably benign	Het
Zfp780b	A	T	7: 27,963,100	C677S	possibly damaging	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
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

Posted On

2014-06-23