Mutagenetix > Incidental Mutations

Incidental Mutation 'R0650:Sema6a'

62240

Institutional Source

Beutler Lab

Gene Symbol

Sema6a

Ensembl Gene

ENSMUSG00000019647

Gene Name

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

Synonyms

sema, Sema6A-1, Semaq, A730020P05Rik, VIa

MMRRC Submission

038835-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0650 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

47235598-47368870 bp(-) (GRCm38)

Type of Mutation

splice site (1849 bp from exon)

DNA Base Change (assembly)

G to A at 47290045 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000118655 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000019791] [ENSMUST00000076043] [ENSMUST00000115449] [ENSMUST00000126684] [ENSMUST00000135790] [ENSMUST00000156422]

AlphaFold

O35464

Predicted Effect

probably damaging
Transcript: ENSMUST00000019791
AA Change: A298V

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
AA Change: A298V

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
Sema	56	487	1.06e-185	SMART
PSI	514	569	9.57e-1	SMART
transmembrane domain	648	670	N/A	INTRINSIC
low complexity region	932	951	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000076043
AA Change: A298V

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
AA Change: A298V

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
Sema	56	487	1.06e-185	SMART
PSI	514	569	9.57e-1	SMART
transmembrane domain	593	615	N/A	INTRINSIC
low complexity region	877	896	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000115449
AA Change: A298V

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

SMART Domains

Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
AA Change: A298V

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
Sema	56	461	1.24e-168	SMART
PSI	488	543	9.57e-1	SMART
transmembrane domain	622	644	N/A	INTRINSIC
low complexity region	906	925	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000126684

SMART Domains

Protein: ENSMUSP00000118655
Gene: ENSMUSG00000019647

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
Pfam:Sema	56	216	2.5e-51	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000135790
AA Change: A298V

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: A298V

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
Sema	56	487	1.06e-185	SMART
PSI	514	569	9.57e-1	SMART
transmembrane domain	665	687	N/A	INTRINSIC
low complexity region	949	968	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141224

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151382

Predicted Effect

probably damaging
Transcript: ENSMUST00000156422
AA Change: A298V

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
AA Change: A298V

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
Sema	56	487	1.06e-185	SMART
PSI	514	569	9.57e-1	SMART
transmembrane domain	648	670	N/A	INTRINSIC
low complexity region	932	951	N/A	INTRINSIC

Meta Mutation Damage Score

0.7184

Coding Region Coverage

1x: 99.5%
3x: 99.0%
10x: 97.8%
20x: 96.0%

Validation Efficiency

99% (77/78)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The transmembrane semaphorin SEMA6A is expressed in developing neural tissue and is required for proper development of the thalamocortical projection (Leighton et al., 2001 [PubMed 11242070]).[supplied by OMIM, Feb 2011]
PHENOTYPE: Mice homozygous for a gene trapped allele exhibit defects in lamina-specific neurite stratification of specific retinal neuron subtypes and disruption of the dendritic plexus organization of On but not Off starburst amacrine cells. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700020N15Rik	A	G	X: 69,945,785	S96G	unknown	Het
4930447C04Rik	T	C	12: 72,910,056	D120G	probably damaging	Het
4930548H24Rik	T	C	5: 31,485,968		probably benign	Het
Adgrg5	T	A	8: 94,934,157		probably null	Het
Afg3l2	G	T	18: 67,415,557	H534Q	possibly damaging	Het
Ankar	G	A	1: 72,656,221		probably benign	Het
Arid2	T	A	15: 96,402,049	F1814L	possibly damaging	Het
Asb15	C	T	6: 24,566,164	A372V	probably damaging	Het
Atg16l1	A	T	1: 87,781,699	D403V	possibly damaging	Het
BC024978	A	T	7: 27,202,647	H233L	probably damaging	Het
Bnc2	T	C	4: 84,293,196	D407G	probably benign	Het
Cdan1	A	G	2: 120,726,045	V633A	probably benign	Het
Cfap46	T	C	7: 139,605,655	Y2482C	unknown	Het
Chd8	T	C	14: 52,202,304	E964G	probably benign	Het
Cyp2s1	A	G	7: 25,809,258	V253A	probably damaging	Het
Depdc1b	A	G	13: 108,323,909	N18D	probably damaging	Het
Fis1	T	A	5: 136,962,194	V4E	probably damaging	Het
Gba2	T	A	4: 43,570,424		probably null	Het
Gm2381	C	T	7: 42,820,080	G207R	probably damaging	Het
Gpr89	T	A	3: 96,897,324		probably benign	Het
Gtf2i	A	G	5: 134,261,837		probably benign	Het
Herc2	T	G	7: 56,113,210	S896A	probably damaging	Het
Huwe1	T	C	X: 151,876,313	S921P	probably damaging	Het
Iqgap1	T	A	7: 80,736,395	K936I	probably damaging	Het
Kcna4	T	A	2: 107,295,582	Y220*	probably null	Het
Krt18	A	G	15: 102,029,485	D139G	possibly damaging	Het
Krt83	T	C	15: 101,487,040	N392D	probably damaging	Het
L3mbtl4	G	A	17: 68,774,291	C558Y	probably damaging	Het
Lamc2	T	A	1: 153,143,876	I440F	possibly damaging	Het
Lrrc28	T	C	7: 67,618,085	N98S	probably damaging	Het
Lrrk1	G	A	7: 66,292,336	A718V	probably damaging	Het
Mrgprx2	T	C	7: 48,482,918	I51V	probably damaging	Het
Myt1	A	T	2: 181,782,615	R25*	probably null	Het
Npdc1	C	T	2: 25,408,009	T199I	probably benign	Het
Nup98	T	A	7: 102,152,453	Y755F	probably damaging	Het
Olfr494	T	A	7: 108,367,789	C100S	probably damaging	Het
Olfr502	G	T	7: 108,523,082	N289K	probably damaging	Het
Olfr638	A	G	7: 104,003,239		probably null	Het
Olfr936	T	A	9: 39,046,700	M240L	probably benign	Het
Osgin1	A	T	8: 119,445,472	Y335F	probably damaging	Het
Pde10a	A	T	17: 8,942,965	I493F	probably damaging	Het
Pdgfrb	A	G	18: 61,079,708	I895V	probably benign	Het
Peg10	T	TCCCCANNANNNN	6: 4,756,475		probably benign	Het
Pidd1	A	T	7: 141,440,813	L457*	probably null	Het
Pik3c2a	A	G	7: 116,346,247		probably benign	Het
Pkd1l3	C	G	8: 109,623,649	D375E	possibly damaging	Het
Plcg1	C	T	2: 160,753,363		probably benign	Het
Prr13	A	C	15: 102,462,215	*138C	probably null	Het
Prrc2b	T	C	2: 32,229,255		probably benign	Het
Psph	T	C	5: 129,791,570		probably benign	Het
Ripor1	A	G	8: 105,618,114		probably benign	Het
Scg3	A	G	9: 75,669,335	S253P	probably damaging	Het
Sgk1	A	G	10: 21,882,657	N7D	probably damaging	Het
Skor2	T	C	18: 76,876,560	F940L	probably benign	Het
Slbp	T	C	5: 33,645,489		probably benign	Het
Snrnp40	C	G	4: 130,378,043		probably null	Het
Susd5	A	T	9: 114,082,535	H171L	possibly damaging	Het
Sybu	T	C	15: 44,673,268	E354G	probably benign	Het
Synpo	T	C	18: 60,602,340	N845D	possibly damaging	Het
Tdrd6	A	T	17: 43,628,159	I666N	probably damaging	Het
Tm9sf4	T	C	2: 153,187,365	I111T	probably benign	Het
Tnc	T	C	4: 64,008,734	T852A	probably benign	Het
Tnfrsf10b	T	A	14: 69,776,176	I185K	probably damaging	Het
Tnks1bp1	A	G	2: 85,062,630	E305G	possibly damaging	Het
Tnrc6b	T	C	15: 80,784,758	V22A	probably benign	Het
Ttn	A	T	2: 76,768,612	F19319Y	probably damaging	Het
Ubr5	T	C	15: 38,030,807		probably benign	Het
Ugt2b5	T	A	5: 87,139,768	Q191L	probably benign	Het
Urod	T	C	4: 116,991,276	T300A	probably benign	Het
Vmn1r213	A	G	13: 23,011,394		probably benign	Het
Znfx1	G	A	2: 167,047,654	Q723*	probably null	Het

Other mutations in Sema6a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00336:Sema6a	APN	18	47289975	critical splice donor site	probably null
IGL01351:Sema6a	APN	18	47281302	missense	possibly damaging	0.84
IGL01594:Sema6a	APN	18	47248817	missense	probably damaging	1.00
IGL01953:Sema6a	APN	18	47290120	nonsense	probably null
IGL02077:Sema6a	APN	18	47283398	missense	possibly damaging	0.94
IGL02632:Sema6a	APN	18	47290155	missense	probably damaging	1.00
IGL02957:Sema6a	APN	18	47249224	missense	probably damaging	1.00
IGL03013:Sema6a	APN	18	47248394	missense	probably benign	0.01
IGL03279:Sema6a	APN	18	47300090	nonsense	probably null
saphire	UTSW	18	47306429	nonsense	probably null
IGL02988:Sema6a	UTSW	18	47298214	missense	probably damaging	1.00
R0114:Sema6a	UTSW	18	47290177	missense	probably damaging	1.00
R0311:Sema6a	UTSW	18	47290045	splice site	probably null
R0312:Sema6a	UTSW	18	47290045	splice site	probably null
R0347:Sema6a	UTSW	18	47291129	missense	probably damaging	1.00
R0350:Sema6a	UTSW	18	47270718	missense	probably benign
R0366:Sema6a	UTSW	18	47290045	splice site	probably null
R0368:Sema6a	UTSW	18	47290045	splice site	probably null
R0391:Sema6a	UTSW	18	47290045	splice site	probably null
R0403:Sema6a	UTSW	18	47290045	splice site	probably null
R0466:Sema6a	UTSW	18	47290045	splice site	probably null
R0515:Sema6a	UTSW	18	47290045	splice site	probably null
R0517:Sema6a	UTSW	18	47290045	splice site	probably null
R0542:Sema6a	UTSW	18	47248576	missense	probably damaging	1.00
R0557:Sema6a	UTSW	18	47249500	missense	probably benign	0.01
R0569:Sema6a	UTSW	18	47270805	splice site	probably null
R0689:Sema6a	UTSW	18	47290045	splice site	probably null
R0694:Sema6a	UTSW	18	47290045	splice site	probably null
R0726:Sema6a	UTSW	18	47291981	missense	probably damaging	1.00
R0741:Sema6a	UTSW	18	47290045	splice site	probably null
R0821:Sema6a	UTSW	18	47290045	splice site	probably null
R0824:Sema6a	UTSW	18	47290045	splice site	probably null
R0924:Sema6a	UTSW	18	47248492	missense	probably damaging	1.00
R1108:Sema6a	UTSW	18	47306431	missense	probably benign	0.02
R1255:Sema6a	UTSW	18	47249299	missense	probably damaging	0.98
R1422:Sema6a	UTSW	18	47306431	missense	probably benign	0.02
R1531:Sema6a	UTSW	18	47248999	missense	probably damaging	1.00
R1707:Sema6a	UTSW	18	47283445	missense	probably benign	0.04
R1746:Sema6a	UTSW	18	47306349	splice site	probably benign
R1807:Sema6a	UTSW	18	47276424	missense	possibly damaging	0.85
R1974:Sema6a	UTSW	18	47270629	missense	probably benign	0.04
R1987:Sema6a	UTSW	18	47300142	missense	probably damaging	1.00
R2044:Sema6a	UTSW	18	47306429	nonsense	probably null
R3719:Sema6a	UTSW	18	47249077	missense	probably damaging	1.00
R4491:Sema6a	UTSW	18	47306457	utr 5 prime	probably benign
R4552:Sema6a	UTSW	18	47291923	missense	probably damaging	1.00
R4707:Sema6a	UTSW	18	47248712	missense	probably benign	0.43
R4710:Sema6a	UTSW	18	47270683	missense	probably benign	0.00
R4713:Sema6a	UTSW	18	47249296	missense	possibly damaging	0.79
R4963:Sema6a	UTSW	18	47298251	missense	possibly damaging	0.48
R5088:Sema6a	UTSW	18	47249129	missense	probably damaging	1.00
R5133:Sema6a	UTSW	18	47300128	missense	probably damaging	1.00
R5135:Sema6a	UTSW	18	47291172	missense	probably damaging	1.00
R5141:Sema6a	UTSW	18	47248388	missense	probably damaging	1.00
R5277:Sema6a	UTSW	18	47276544	intron	probably benign
R5551:Sema6a	UTSW	18	47248528	missense	possibly damaging	0.76
R5618:Sema6a	UTSW	18	47281948	missense	probably damaging	0.98
R5717:Sema6a	UTSW	18	47249263	missense	probably benign	0.01
R5729:Sema6a	UTSW	18	47281343	missense	probably damaging	1.00
R5779:Sema6a	UTSW	18	47248826	missense	probably damaging	1.00
R5917:Sema6a	UTSW	18	47281338	missense	probably benign	0.05
R6054:Sema6a	UTSW	18	47283403	missense	possibly damaging	0.94
R6142:Sema6a	UTSW	18	47281199	missense	probably benign	0.00
R6209:Sema6a	UTSW	18	47298302	splice site	probably null
R6307:Sema6a	UTSW	18	47249164	missense	probably damaging	1.00
R6734:Sema6a	UTSW	18	47279169	missense	probably benign	0.31
R7014:Sema6a	UTSW	18	47298217	missense	probably damaging	1.00
R7033:Sema6a	UTSW	18	47248570	missense	probably damaging	0.96
R7574:Sema6a	UTSW	18	47291164	missense	probably damaging	1.00
R8054:Sema6a	UTSW	18	47291905	missense	probably damaging	1.00
R8250:Sema6a	UTSW	18	47290115	missense	probably damaging	0.99
R8408:Sema6a	UTSW	18	47248891	missense	probably benign	0.34
R8411:Sema6a	UTSW	18	47248955	missense	probably benign	0.00
R8900:Sema6a	UTSW	18	47291115	missense	probably damaging	1.00
R9140:Sema6a	UTSW	18	47281942	missense	probably benign
R9158:Sema6a	UTSW	18	47298263	missense	probably damaging	0.98
X0065:Sema6a	UTSW	18	47283319	missense	possibly damaging	0.78

Predicted Primers

PCR Primer
(F):5'- ACTGACTACCTGGTCCAGGCAAAG -3'
(R):5'- GATTGCGTCATTAAGCAGAGGCAAC -3'

Sequencing Primer
(F):5'- GTCCAGGCAAAGGAATGTTTTAATC -3'
(R):5'- CAGAGGCAACTTCTTCTAAGGTC -3'

Posted On

2013-07-30