Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02202:Sema4a'

284372

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Sema4a

Ensembl Gene

ENSMUSG00000028064

Gene Name

sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A

Synonyms

SemB, SemB, Semab

Accession Numbers

Essential gene?

Probably essential (E-score: 0.902) question?

Stock #

IGL02202

Quality Score

Status

Chromosome

Chromosomal Location

88343266-88368489 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 88357050 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Glutamic Acid at position 307 (A307E)

Ref Sequence

ENSEMBL: ENSMUSP00000128887 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029700] [ENSMUST00000107531] [ENSMUST00000125526] [ENSMUST00000127436] [ENSMUST00000141471] [ENSMUST00000166237] [ENSMUST00000169222] [ENSMUST00000165898] [ENSMUST00000185137] [ENSMUST00000184487] [ENSMUST00000184876] [ENSMUST00000147200]

AlphaFold

Q62178

Predicted Effect

probably damaging
Transcript: ENSMUST00000029700
AA Change: A307E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000029700
Gene: ENSMUSG00000028064
AA Change: A307E

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
Sema	64	478	1.96e-166	SMART
PSI	496	547	9.33e-13	SMART
transmembrane domain	680	702	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000107531
AA Change: A175E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000103155
Gene: ENSMUSG00000028064
AA Change: A175E

Domain	Start	End	E-Value	Type
Sema	2	346	2.06e-101	SMART
PSI	364	415	9.33e-13	SMART
transmembrane domain	548	570	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000125526

SMART Domains

Protein: ENSMUSP00000119028
Gene: ENSMUSG00000028064

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
Pfam:Sema	64	113	8.2e-9	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000127436

SMART Domains

Protein: ENSMUSP00000118706
Gene: ENSMUSG00000028064

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
Pfam:Sema	64	234	5.5e-53	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135539

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135732

Predicted Effect

probably benign
Transcript: ENSMUST00000141471

SMART Domains

Protein: ENSMUSP00000114330
Gene: ENSMUSG00000028064

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000166237
AA Change: A307E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000125909
Gene: ENSMUSG00000028064
AA Change: A307E

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
Sema	64	478	1.96e-166	SMART
PSI	496	547	9.33e-13	SMART
transmembrane domain	680	702	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000169222
AA Change: A307E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000128887
Gene: ENSMUSG00000028064
AA Change: A307E

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
Sema	64	478	1.96e-166	SMART
PSI	496	547	9.33e-13	SMART
transmembrane domain	680	702	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000165898
AA Change: A307E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000128510
Gene: ENSMUSG00000028064
AA Change: A307E

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
Sema	64	478	1.96e-166	SMART
PSI	496	547	9.33e-13	SMART
transmembrane domain	680	702	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184972

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149145

Predicted Effect

probably benign
Transcript: ENSMUST00000185137

Predicted Effect

probably benign
Transcript: ENSMUST00000184487

SMART Domains

Protein: ENSMUSP00000139126
Gene: ENSMUSG00000028064

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
Pfam:Sema	64	168	1.5e-30	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000184876

SMART Domains

Protein: ENSMUSP00000139159
Gene: ENSMUSG00000028064

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
Pfam:Sema	64	179	7.7e-31	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000147200

SMART Domains

Protein: ENSMUSP00000123061
Gene: ENSMUSG00000028064

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
Pfam:Sema	64	203	3.5e-45	PFAM

Coding Region Coverage

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the semaphorin family of soluble and transmembrane proteins. Semaphorins are involved in numerous functions, including axon guidance, morphogenesis, carcinogenesis, and immunomodulation. The encoded protein is a single-pass type I membrane protein containing an immunoglobulin-like C2-type domain, a PSI domain and a sema domain. It inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons. It is an activator of T-cell-mediated immunity and suppresses vascular endothelial growth factor (VEGF)-mediated endothelial cell migration and proliferation in vitro and angiogenesis in vivo. Mutations in this gene are associated with retinal degenerative diseases including retinitis pigmentosa type 35 (RP35) and cone-rod dystrophy type 10 (CORD10). Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]
PHENOTYPE: Homozygotes for a knock-out allele show no obvious brain defects but exhibit impaired T cell priming and defective Th1 responses. Homozygotes for a gene trap allele show severe retinal degeneration with reduced retinal vessels, depigmentation and dysfunction of both rod and cone photoreceptors. [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
Abca13	C	T	11: 9,238,529 (GRCm39)	T709I	possibly damaging	Het
Acte1	T	A	7: 143,447,910 (GRCm39)	M251K	possibly damaging	Het
Arhgef1	T	A	7: 24,612,854 (GRCm39)	Y185*	probably null	Het
Atxn7l1	T	C	12: 33,392,077 (GRCm39)	S218P	probably benign	Het
Cd200r2	T	A	16: 44,729,723 (GRCm39)	L126Q	probably damaging	Het
Cdc6	T	A	11: 98,811,641 (GRCm39)		probably null	Het
Cenph	T	C	13: 100,898,381 (GRCm39)	N174S	probably benign	Het
Cep192	A	G	18: 67,936,207 (GRCm39)	R49G	possibly damaging	Het
Edrf1	A	G	7: 133,258,699 (GRCm39)	T692A	probably benign	Het
Frem2	A	T	3: 53,562,220 (GRCm39)	H762Q	probably benign	Het
Gli2	T	C	1: 118,764,596 (GRCm39)	D1185G	probably damaging	Het
Hsd3b2	T	A	3: 98,619,183 (GRCm39)	Y254F	possibly damaging	Het
Itgal	C	A	7: 126,929,351 (GRCm39)	Y1089*	probably null	Het
Klf11	T	G	12: 24,703,631 (GRCm39)	V22G	probably benign	Het
Morc3	T	C	16: 93,667,749 (GRCm39)	V636A	probably benign	Het
Nin	T	A	12: 70,102,210 (GRCm39)	D330V	probably damaging	Het
Nlrp4a	G	T	7: 26,148,703 (GRCm39)	K103N	possibly damaging	Het
Ntsr2	T	A	12: 16,703,661 (GRCm39)	V54E	probably damaging	Het
Or7g27	C	A	9: 19,250,545 (GRCm39)	A263E	probably benign	Het
Pdha2	T	C	3: 140,916,412 (GRCm39)	I365M	probably benign	Het
Prr19	T	C	7: 25,003,462 (GRCm39)	S359P	probably damaging	Het
Ryr2	T	C	13: 11,745,274 (GRCm39)	K2040E	probably damaging	Het
Ryr2	C	A	13: 11,762,544 (GRCm39)		probably benign	Het
Setd5	T	A	6: 113,127,976 (GRCm39)	S1310T	probably benign	Het
Tph1	A	T	7: 46,303,185 (GRCm39)	D264E	probably benign	Het
Zc3h6	T	C	2: 128,858,501 (GRCm39)	L844P	probably damaging	Het

Other mutations in Sema4a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00913:Sema4a	APN	3	88,357,117 (GRCm39)	missense	probably damaging	1.00
IGL01722:Sema4a	APN	3	88,345,491 (GRCm39)	missense	probably benign	0.14
IGL01769:Sema4a	APN	3	88,357,063 (GRCm39)	missense	possibly damaging	0.86
IGL02076:Sema4a	APN	3	88,357,829 (GRCm39)	missense	probably damaging	0.99
R0145:Sema4a	UTSW	3	88,358,729 (GRCm39)	missense	probably damaging	1.00
R0386:Sema4a	UTSW	3	88,344,107 (GRCm39)	missense	possibly damaging	0.75
R0837:Sema4a	UTSW	3	88,360,405 (GRCm39)	missense	possibly damaging	0.46
R0863:Sema4a	UTSW	3	88,355,456 (GRCm39)	unclassified	probably benign
R1567:Sema4a	UTSW	3	88,359,353 (GRCm39)	missense	probably damaging	1.00
R1675:Sema4a	UTSW	3	88,362,073 (GRCm39)	missense	possibly damaging	0.66
R1739:Sema4a	UTSW	3	88,344,145 (GRCm39)	missense	possibly damaging	0.94
R1801:Sema4a	UTSW	3	88,344,056 (GRCm39)	missense	probably benign	0.04
R1961:Sema4a	UTSW	3	88,345,483 (GRCm39)	splice site	probably benign
R2029:Sema4a	UTSW	3	88,358,668 (GRCm39)	missense	probably damaging	1.00
R4934:Sema4a	UTSW	3	88,345,568 (GRCm39)	missense	probably damaging	1.00
R5006:Sema4a	UTSW	3	88,344,091 (GRCm39)	missense	probably benign
R5309:Sema4a	UTSW	3	88,344,343 (GRCm39)	missense	probably damaging	1.00
R5312:Sema4a	UTSW	3	88,344,343 (GRCm39)	missense	probably damaging	1.00
R5338:Sema4a	UTSW	3	88,358,804 (GRCm39)	missense	probably benign	0.01
R5481:Sema4a	UTSW	3	88,360,347 (GRCm39)	nonsense	probably null
R5510:Sema4a	UTSW	3	88,357,293 (GRCm39)	critical splice donor site	probably null
R6046:Sema4a	UTSW	3	88,348,008 (GRCm39)	missense	probably damaging	1.00
R7242:Sema4a	UTSW	3	88,357,416 (GRCm39)	missense	probably damaging	1.00
R8403:Sema4a	UTSW	3	88,359,341 (GRCm39)	missense	probably damaging	0.98
R8798:Sema4a	UTSW	3	88,344,004 (GRCm39)	missense	possibly damaging	0.76
R9328:Sema4a	UTSW	3	88,345,613 (GRCm39)	nonsense	probably null
R9638:Sema4a	UTSW	3	88,357,066 (GRCm39)	missense	probably damaging	1.00
R9728:Sema4a	UTSW	3	88,348,187 (GRCm39)	critical splice acceptor site	probably null
Z1176:Sema4a	UTSW	3	88,344,500 (GRCm39)	missense	probably damaging	0.97

Posted On

2015-04-16