Mutagenetix > Incidental Mutation

Incidental Mutation 'R0741:Sema6a'

70705

Institutional Source

Beutler Lab

Gene Symbol

Sema6a

Ensembl Gene

ENSMUSG00000019647

Gene Name

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

Synonyms

VIa, Semaq, Sema6A-1, sema, A730020P05Rik

MMRRC Submission

038922-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0741 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

47378321-47504267 bp(-) (GRCm39)

Type of Mutation

splice site (1849 bp from exon)

DNA Base Change (assembly)

G to A at 47423112 bp (GRCm39)

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: 99.3%
3x: 98.8%
10x: 97.5%
20x: 95.1%

Validation Efficiency

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: 35 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ano7	T	A	1: 93,329,309 (GRCm39)	I701N	probably damaging	Het
Asb7	A	T	7: 66,309,882 (GRCm39)	N111K	probably benign	Het
Atp10a	T	A	7: 58,478,337 (GRCm39)	L1460Q	possibly damaging	Het
Auh	T	C	13: 53,083,638 (GRCm39)	T14A	possibly damaging	Het
Caskin2	A	G	11: 115,695,626 (GRCm39)	V245A	probably damaging	Het
Cryba4	G	A	5: 112,394,554 (GRCm39)	R192C	probably damaging	Het
Ctsq	T	A	13: 61,184,019 (GRCm39)	D301V	probably damaging	Het
Dpyd	A	G	3: 118,468,154 (GRCm39)	E56G	possibly damaging	Het
Dtd2	T	C	12: 52,046,455 (GRCm39)	K128R	probably benign	Het
Eps8l3	A	G	3: 107,790,141 (GRCm39)	T141A	probably benign	Het
Evc	A	T	5: 37,483,739 (GRCm39)	I187N	possibly damaging	Het
Fam120a	A	G	13: 49,045,416 (GRCm39)	S807P	possibly damaging	Het
Fbxw22	G	A	9: 109,211,287 (GRCm39)	S338L	probably benign	Het
Gcnt4	G	T	13: 97,082,940 (GRCm39)	E79*	probably null	Het
Get4	G	A	5: 139,249,384 (GRCm39)		probably benign	Het
Hipk1	A	G	3: 103,654,128 (GRCm39)	V954A	probably benign	Het
Ifi206	C	T	1: 173,301,315 (GRCm39)	V788M	probably benign	Het
Iqgap1	A	G	7: 80,370,735 (GRCm39)	S1545P	probably benign	Het
Kif21b	A	G	1: 136,087,482 (GRCm39)	T933A	probably damaging	Het
Lgr6	C	T	1: 134,921,748 (GRCm39)	A199T	probably damaging	Het
Magee2	A	G	X: 103,899,472 (GRCm39)	L393P	probably damaging	Het
Mtrr	T	C	13: 68,727,658 (GRCm39)		probably null	Het
Nes	A	G	3: 87,886,274 (GRCm39)	E1467G	probably damaging	Het
Nol3	C	G	8: 106,005,756 (GRCm39)	A50G	probably damaging	Het
Nr2f2	G	A	7: 70,007,745 (GRCm39)	R113C	probably damaging	Het
Obscn	CCACACACACACAC	CCACACACACAC	11: 58,954,279 (GRCm39)		probably null	Het
Or10a3m	T	A	7: 108,312,811 (GRCm39)	C84S	probably benign	Het
Pnkd	T	A	1: 74,391,018 (GRCm39)	S337R	possibly damaging	Het
Ptprh	A	G	7: 4,557,172 (GRCm39)		probably null	Het
Ralgapa1	A	C	12: 55,723,366 (GRCm39)	V1767G	probably damaging	Het
Skap1	A	C	11: 96,383,759 (GRCm39)		probably benign	Het
Trip12	A	G	1: 84,722,902 (GRCm39)	S1250P	probably benign	Het
Txndc5	T	C	13: 38,712,236 (GRCm39)	H50R	possibly damaging	Het
Usp25	C	A	16: 76,868,596 (GRCm39)	D332E	possibly damaging	Het
Vgll1	A	T	X: 56,141,644 (GRCm39)		probably benign	Het

Other mutations in Sema6a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00336:Sema6a	APN	18	47,423,042 (GRCm39)	critical splice donor site	probably null
IGL01351:Sema6a	APN	18	47,414,369 (GRCm39)	missense	possibly damaging	0.84
IGL01594:Sema6a	APN	18	47,381,884 (GRCm39)	missense	probably damaging	1.00
IGL01953:Sema6a	APN	18	47,423,187 (GRCm39)	nonsense	probably null
IGL02077:Sema6a	APN	18	47,416,465 (GRCm39)	missense	possibly damaging	0.94
IGL02632:Sema6a	APN	18	47,423,222 (GRCm39)	missense	probably damaging	1.00
IGL02957:Sema6a	APN	18	47,382,291 (GRCm39)	missense	probably damaging	1.00
IGL03013:Sema6a	APN	18	47,381,461 (GRCm39)	missense	probably benign	0.01
IGL03279:Sema6a	APN	18	47,433,157 (GRCm39)	nonsense	probably null
saphire	UTSW	18	47,439,496 (GRCm39)	nonsense	probably null
IGL02988:Sema6a	UTSW	18	47,431,281 (GRCm39)	missense	probably damaging	1.00
R0114:Sema6a	UTSW	18	47,423,244 (GRCm39)	missense	probably damaging	1.00
R0311:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0312:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0347:Sema6a	UTSW	18	47,424,196 (GRCm39)	missense	probably damaging	1.00
R0350:Sema6a	UTSW	18	47,403,785 (GRCm39)	missense	probably benign
R0366:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0368:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0391:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0403:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0466:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0515:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0517:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0542:Sema6a	UTSW	18	47,381,643 (GRCm39)	missense	probably damaging	1.00
R0557:Sema6a	UTSW	18	47,382,567 (GRCm39)	missense	probably benign	0.01
R0569:Sema6a	UTSW	18	47,403,872 (GRCm39)	splice site	probably null
R0650:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0689:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0694:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0726:Sema6a	UTSW	18	47,425,048 (GRCm39)	missense	probably damaging	1.00
R0821:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0824:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
R0924:Sema6a	UTSW	18	47,381,559 (GRCm39)	missense	probably damaging	1.00
R1108:Sema6a	UTSW	18	47,439,498 (GRCm39)	missense	probably benign	0.02
R1255:Sema6a	UTSW	18	47,382,366 (GRCm39)	missense	probably damaging	0.98
R1422:Sema6a	UTSW	18	47,439,498 (GRCm39)	missense	probably benign	0.02
R1531:Sema6a	UTSW	18	47,382,066 (GRCm39)	missense	probably damaging	1.00
R1707:Sema6a	UTSW	18	47,416,512 (GRCm39)	missense	probably benign	0.04
R1746:Sema6a	UTSW	18	47,439,416 (GRCm39)	splice site	probably benign
R1807:Sema6a	UTSW	18	47,409,491 (GRCm39)	missense	possibly damaging	0.85
R1974:Sema6a	UTSW	18	47,403,696 (GRCm39)	missense	probably benign	0.04
R1987:Sema6a	UTSW	18	47,433,209 (GRCm39)	missense	probably damaging	1.00
R2044:Sema6a	UTSW	18	47,439,496 (GRCm39)	nonsense	probably null
R3719:Sema6a	UTSW	18	47,382,144 (GRCm39)	missense	probably damaging	1.00
R4491:Sema6a	UTSW	18	47,439,524 (GRCm39)	utr 5 prime	probably benign
R4552:Sema6a	UTSW	18	47,424,990 (GRCm39)	missense	probably damaging	1.00
R4707:Sema6a	UTSW	18	47,381,779 (GRCm39)	missense	probably benign	0.43
R4710:Sema6a	UTSW	18	47,403,750 (GRCm39)	missense	probably benign	0.00
R4713:Sema6a	UTSW	18	47,382,363 (GRCm39)	missense	possibly damaging	0.79
R4963:Sema6a	UTSW	18	47,431,318 (GRCm39)	missense	possibly damaging	0.48
R5088:Sema6a	UTSW	18	47,382,196 (GRCm39)	missense	probably damaging	1.00
R5133:Sema6a	UTSW	18	47,433,195 (GRCm39)	missense	probably damaging	1.00
R5135:Sema6a	UTSW	18	47,424,239 (GRCm39)	missense	probably damaging	1.00
R5141:Sema6a	UTSW	18	47,381,455 (GRCm39)	missense	probably damaging	1.00
R5277:Sema6a	UTSW	18	47,409,611 (GRCm39)	intron	probably benign
R5551:Sema6a	UTSW	18	47,381,595 (GRCm39)	missense	possibly damaging	0.76
R5618:Sema6a	UTSW	18	47,415,015 (GRCm39)	missense	probably damaging	0.98
R5717:Sema6a	UTSW	18	47,382,330 (GRCm39)	missense	probably benign	0.01
R5729:Sema6a	UTSW	18	47,414,410 (GRCm39)	missense	probably damaging	1.00
R5779:Sema6a	UTSW	18	47,381,893 (GRCm39)	missense	probably damaging	1.00
R5917:Sema6a	UTSW	18	47,414,405 (GRCm39)	missense	probably benign	0.05
R6054:Sema6a	UTSW	18	47,416,470 (GRCm39)	missense	possibly damaging	0.94
R6142:Sema6a	UTSW	18	47,414,266 (GRCm39)	missense	probably benign	0.00
R6209:Sema6a	UTSW	18	47,431,369 (GRCm39)	splice site	probably null
R6307:Sema6a	UTSW	18	47,382,231 (GRCm39)	missense	probably damaging	1.00
R6734:Sema6a	UTSW	18	47,412,236 (GRCm39)	missense	probably benign	0.31
R7014:Sema6a	UTSW	18	47,431,284 (GRCm39)	missense	probably damaging	1.00
R7033:Sema6a	UTSW	18	47,381,637 (GRCm39)	missense	probably damaging	0.96
R7574:Sema6a	UTSW	18	47,424,231 (GRCm39)	missense	probably damaging	1.00
R8054:Sema6a	UTSW	18	47,424,972 (GRCm39)	missense	probably damaging	1.00
R8250:Sema6a	UTSW	18	47,423,182 (GRCm39)	missense	probably damaging	0.99
R8408:Sema6a	UTSW	18	47,381,958 (GRCm39)	missense	probably benign	0.34
R8411:Sema6a	UTSW	18	47,382,022 (GRCm39)	missense	probably benign	0.00
R8900:Sema6a	UTSW	18	47,424,182 (GRCm39)	missense	probably damaging	1.00
R9140:Sema6a	UTSW	18	47,415,009 (GRCm39)	missense	probably benign
R9158:Sema6a	UTSW	18	47,431,330 (GRCm39)	missense	probably damaging	0.98
R9488:Sema6a	UTSW	18	47,437,216 (GRCm39)	missense	probably damaging	1.00
R9565:Sema6a	UTSW	18	47,382,594 (GRCm39)	missense	probably null	1.00
R9652:Sema6a	UTSW	18	47,382,252 (GRCm39)	missense	probably damaging	1.00
R9732:Sema6a	UTSW	18	47,381,925 (GRCm39)	missense	probably damaging	0.96
X0065:Sema6a	UTSW	18	47,416,386 (GRCm39)	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

2013-09-30