Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02077:Sema6a'

186007

Institutional Source

Australian Phenomics Network (link to record)

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

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

IGL02077

Quality Score

Status

Chromosome

Chromosomal Location

47378321-47504267 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 47416465 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 387 (D387E)

Ref Sequence

ENSEMBL: ENSMUSP00000111109 (fasta)

Gene Model

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

AlphaFold

O35464

Predicted Effect

probably benign
Transcript: ENSMUST00000019791
AA Change: D387E

PolyPhen 2 Score 0.352 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000019791
Gene: ENSMUSG00000019647
AA Change: D387E

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 benign
Transcript: ENSMUST00000076043
AA Change: D387E

PolyPhen 2 Score 0.352 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000075420
Gene: ENSMUSG00000019647
AA Change: D387E

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

possibly damaging
Transcript: ENSMUST00000115449
AA Change: D387E

PolyPhen 2 Score 0.945 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000111109
Gene: ENSMUSG00000019647
AA Change: D387E

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 benign
Transcript: ENSMUST00000123228

SMART Domains

Protein: ENSMUSP00000120249
Gene: ENSMUSG00000019647

Domain	Start	End	E-Value	Type
Blast:PSI	2	45	4e-26	BLAST
PDB:3OKY\|B	2	47	2e-26	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000135790
AA Change: D387E

PolyPhen 2 Score 0.114 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000120011
Gene: ENSMUSG00000019647
AA Change: D387E

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 benign
Transcript: ENSMUST00000156422
AA Change: D387E

PolyPhen 2 Score 0.352 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000121442
Gene: ENSMUSG00000019647
AA Change: D387E

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

Coding Region Coverage

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: 26 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Arhgap11a	G	T	2: 113,667,816 (GRCm39)	T395K	possibly damaging	Het
Dop1b	T	C	16: 93,577,648 (GRCm39)	S58P	probably damaging	Het
F5	T	A	1: 164,026,435 (GRCm39)	V1669E	probably damaging	Het
Fndc7	T	A	3: 108,790,784 (GRCm39)	T81S	probably benign	Het
Hnf4a	G	T	2: 163,404,527 (GRCm39)		probably null	Het
Il27	C	T	7: 126,194,051 (GRCm39)		probably null	Het
Lhcgr	G	A	17: 89,057,558 (GRCm39)	T311I	probably benign	Het
Mafb	A	G	2: 160,207,687 (GRCm39)	S304P	probably benign	Het
Mfrp	C	T	9: 44,016,517 (GRCm39)	T404M	probably damaging	Het
Ntpcr	T	A	8: 126,464,107 (GRCm39)	Y77*	probably null	Het
Otof	A	G	5: 30,556,579 (GRCm39)	S301P	probably damaging	Het
Prpf6	G	A	2: 181,282,457 (GRCm39)	G533R	probably damaging	Het
Prpf8	T	A	11: 75,386,635 (GRCm39)	H1041Q	probably damaging	Het
Pyurf	T	C	6: 57,666,820 (GRCm39)	I81V	probably benign	Het
Rsl1d1	A	G	16: 11,012,320 (GRCm39)		probably benign	Het
Serpinb3a	T	G	1: 106,974,111 (GRCm39)	T267P	probably damaging	Het
Tgm7	A	T	2: 120,934,316 (GRCm39)	M192K	probably damaging	Het
Thbs1	G	T	2: 117,943,591 (GRCm39)	V70L	probably benign	Het
Thsd7b	T	A	1: 129,744,419 (GRCm39)	I769N	probably damaging	Het
Tlr9	A	G	9: 106,102,704 (GRCm39)	Y665C	possibly damaging	Het
Ttn	T	C	2: 76,600,506 (GRCm39)	D18928G	probably damaging	Het
Uggt1	A	G	1: 36,215,875 (GRCm39)	S131P	probably damaging	Het
Unc80	A	G	1: 66,564,875 (GRCm39)	N854S	possibly damaging	Het
Vps13b	A	G	15: 35,910,759 (GRCm39)	T3508A	possibly damaging	Het
Wdr43	G	A	17: 71,947,286 (GRCm39)	A381T	probably benign	Het
Zfyve26	A	T	12: 79,323,169 (GRCm39)	M859K	possibly damaging	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
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
R0741:Sema6a	UTSW	18	47,423,112 (GRCm39)	splice site	probably null
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

Posted On

2014-05-07