Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL00913:Sema4a'

27081

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: 0.913) question?

Stock #

IGL00913

Quality Score

Status

Chromosome

Chromosomal Location

88343266-88368489 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 88357117 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 153 (T153S)

Ref Sequence

ENSEMBL: ENSMUSP00000103155 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029700] [ENSMUST00000107531] [ENSMUST00000123753] [ENSMUST00000125526] [ENSMUST00000127436] [ENSMUST00000169222] [ENSMUST00000165898] [ENSMUST00000166237] [ENSMUST00000185137] [ENSMUST00000147200] [ENSMUST00000184487] [ENSMUST00000184876] [ENSMUST00000141471]

AlphaFold

Q62178

Predicted Effect

probably damaging
Transcript: ENSMUST00000029700
AA Change: T285S

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000029700
Gene: ENSMUSG00000028064
AA Change: T285S

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: T153S

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

SMART Domains

Protein: ENSMUSP00000103155
Gene: ENSMUSG00000028064
AA Change: T153S

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: ENSMUST00000123753

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 damaging
Transcript: ENSMUST00000169222
AA Change: T285S

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000128887
Gene: ENSMUSG00000028064
AA Change: T285S

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: T285S

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000128510
Gene: ENSMUSG00000028064
AA Change: T285S

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: ENSMUST00000166237
AA Change: T285S

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000125909
Gene: ENSMUSG00000028064
AA Change: T285S

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: 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

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: ENSMUST00000141471

SMART Domains

Protein: ENSMUSP00000114330
Gene: ENSMUSG00000028064

Domain	Start	End	E-Value	Type
signal peptide	1	32	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.] 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: 34 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrf4	A	G	17: 42,977,793 (GRCm39)	S517P	possibly damaging	Het
Arl4c	T	C	1: 88,629,106 (GRCm39)	D94G	probably damaging	Het
Bag5	T	C	12: 111,677,766 (GRCm39)	E19G	probably damaging	Het
Carf	T	A	1: 60,187,114 (GRCm39)	D537E	probably benign	Het
Cd177	C	A	7: 24,455,620 (GRCm39)	D301Y	probably damaging	Het
Csmd1	C	T	8: 16,121,301 (GRCm39)	V1799I	probably benign	Het
Cyp4x1	T	A	4: 114,970,060 (GRCm39)	I356F	probably benign	Het
F5	A	T	1: 164,032,465 (GRCm39)	H1804L	probably damaging	Het
Fras1	G	T	5: 96,842,935 (GRCm39)	G1718C	probably damaging	Het
Ganc	T	C	2: 120,269,933 (GRCm39)		probably benign	Het
Hs3st5	A	G	10: 36,708,846 (GRCm39)	D127G	probably damaging	Het
Inpp5a	A	G	7: 139,096,637 (GRCm39)	D154G	probably benign	Het
Kif16b	T	A	2: 142,545,927 (GRCm39)	R1134*	probably null	Het
Lrrc66	C	T	5: 73,765,499 (GRCm39)	A515T	possibly damaging	Het
Map3k10	C	T	7: 27,362,640 (GRCm39)		probably benign	Het
Mideas	T	A	12: 84,219,632 (GRCm39)	I441L	probably benign	Het
Mrpl12	G	A	11: 120,376,202 (GRCm39)	D71N	possibly damaging	Het
Nfix	A	T	8: 85,453,106 (GRCm39)	V316E	probably damaging	Het
Nop2	A	G	6: 125,116,784 (GRCm39)	Y346C	probably damaging	Het
Nrbp1	A	G	5: 31,408,403 (GRCm39)	E513G	possibly damaging	Het
Ogfrl1	T	C	1: 23,409,171 (GRCm39)	I352V	probably benign	Het
Or7a35	A	G	10: 78,854,085 (GRCm39)	T310A	probably benign	Het
Or8b48	T	A	9: 38,492,672 (GRCm39)	V33E	probably damaging	Het
Oxr1	G	A	15: 41,683,539 (GRCm39)	V15I	possibly damaging	Het
Pik3r6	T	G	11: 68,442,147 (GRCm39)	F697C	probably damaging	Het
Ptk2	A	G	15: 73,167,238 (GRCm39)		probably benign	Het
Rnft2	G	A	5: 118,339,280 (GRCm39)	T380M	probably damaging	Het
Scel	A	G	14: 103,819,245 (GRCm39)	N346S	probably benign	Het
Serinc2	A	T	4: 130,158,201 (GRCm39)	L82Q	possibly damaging	Het
Sin3a	A	G	9: 57,005,402 (GRCm39)	T392A	probably benign	Het
Slc25a38	T	A	9: 119,949,373 (GRCm39)	Y108*	probably null	Het
Tmc8	G	A	11: 117,677,330 (GRCm39)	G317R	probably damaging	Het
Trpc3	A	G	3: 36,694,788 (GRCm39)	V722A	possibly damaging	Het
Unc93a2	A	T	17: 7,637,138 (GRCm39)	V130D	probably damaging	Het

Other mutations in Sema4a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
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
IGL02202:Sema4a	APN	3	88,357,050 (GRCm39)	missense	probably damaging	1.00
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

2013-04-17