Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01598:Sema6d'

91740

Institutional Source

Australian Phenomics Network (link to record)

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

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

IGL01598

Quality Score

Status

Chromosome

Chromosomal Location

124089969-124667770 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 124665098 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Proline to Glutamine at position 961 (P961Q)

Ref Sequence

ENSEMBL: ENSMUSP00000077691 (fasta)

Gene Model

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

AlphaFold

Q76KF0

Predicted Effect

possibly damaging
Transcript: ENSMUST00000051419
AA Change: P942Q

PolyPhen 2 Score 0.560 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000061123
Gene: ENSMUSG00000027200
AA Change: P942Q

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 benign
Transcript: ENSMUST00000076335
AA Change: P929Q

PolyPhen 2 Score 0.147 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000075674
Gene: ENSMUSG00000027200
AA Change: P929Q

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 benign
Transcript: ENSMUST00000077847
AA Change: P985Q

PolyPhen 2 Score 0.265 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000077014
Gene: ENSMUSG00000027200
AA Change: P985Q

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: P961Q

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

SMART Domains

Protein: ENSMUSP00000077691
Gene: ENSMUSG00000027200
AA Change: P961Q

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 benign
Transcript: ENSMUST00000103238
AA Change: P985Q

PolyPhen 2 Score 0.265 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000099528
Gene: ENSMUSG00000027200
AA Change: P985Q

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 benign
Transcript: ENSMUST00000103239
AA Change: P1004Q

PolyPhen 2 Score 0.418 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000099529
Gene: ENSMUSG00000027200
AA Change: P1004Q

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 benign
Transcript: ENSMUST00000103240
AA Change: P1000Q

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000099530
Gene: ENSMUSG00000027200
AA Change: P1000Q

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 benign
Transcript: ENSMUST00000103241
AA Change: P929Q

PolyPhen 2 Score 0.147 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000099531
Gene: ENSMUSG00000027200
AA Change: P929Q

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

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: 31 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2410124H12Rik	T	A	16: 92,478,929		noncoding transcript	Het
Apc2	T	A	10: 80,313,048	L1283Q	probably damaging	Het
Apol6	G	A	15: 77,050,716	A62T	probably damaging	Het
AU018091	A	T	7: 3,162,270	I204N	possibly damaging	Het
B4galnt4	G	T	7: 141,070,515	R765L	probably benign	Het
Brca1	T	C	11: 101,524,330	T993A	probably benign	Het
Cadps	C	T	14: 12,522,202		probably null	Het
Ccdc177	A	G	12: 80,758,745	S252P	unknown	Het
Cdc73	A	G	1: 143,699,279	S59P	probably damaging	Het
Cep63	G	T	9: 102,590,458	Q570K	possibly damaging	Het
Ces1c	A	T	8: 93,118,413	I120K	probably benign	Het
Cpeb1	T	C	7: 81,361,801	M131V	probably benign	Het
Dync1h1	G	A	12: 110,658,128	V3701I	probably damaging	Het
Fxr1	T	C	3: 34,064,232	S535P	possibly damaging	Het
Gldc	A	T	19: 30,133,756	V540D	probably damaging	Het
Iqcf6	A	G	9: 106,627,508	T124A	probably benign	Het
Itih4	A	G	14: 30,887,817	I35V	possibly damaging	Het
Kmt2c	T	C	5: 25,273,666	*1525W	probably null	Het
Kmt2c	A	T	5: 25,354,771	V963E	probably damaging	Het
Lmnb2	T	C	10: 80,907,165	S202G	probably benign	Het
Med23	T	G	10: 24,903,798	S924R	probably benign	Het
Olfr1454	T	C	19: 13,064,149	V246A	probably damaging	Het
Pcif1	T	C	2: 164,886,611	F263L	possibly damaging	Het
Pon2	A	T	6: 5,272,331	L163H	probably damaging	Het
Scn1a	C	T	2: 66,302,485	V165M	possibly damaging	Het
Snx27	A	G	3: 94,561,843	Y64H	probably damaging	Het
Srsf11	C	T	3: 158,012,035		probably benign	Het
Taok1	A	G	11: 77,571,684	V193A	probably damaging	Het
Vps13d	T	C	4: 145,016,901	T4137A	probably benign	Het
Zbtb26	T	C	2: 37,436,271	Y251C	probably damaging	Het
Zcchc11	A	G	4: 108,550,820		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
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
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

Posted On

2013-12-09