Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01769:Sema4a'

153814

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 #

IGL01769

Quality Score

Status

Chromosome

Chromosomal Location

88343266-88368489 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 88357063 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Phenylalanine at position 303 (I303F)

Ref Sequence

ENSEMBL: ENSMUSP00000128887 (fasta)

Gene Model

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

AlphaFold

Q62178

Predicted Effect

possibly damaging
Transcript: ENSMUST00000029700
AA Change: I303F

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000029700
Gene: ENSMUSG00000028064
AA Change: I303F

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

possibly damaging
Transcript: ENSMUST00000107531
AA Change: I171F

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000103155
Gene: ENSMUSG00000028064
AA Change: I171F

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

possibly damaging
Transcript: ENSMUST00000169222
AA Change: I303F

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000128887
Gene: ENSMUSG00000028064
AA Change: I303F

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

possibly damaging
Transcript: ENSMUST00000166237
AA Change: I303F

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000125909
Gene: ENSMUSG00000028064
AA Change: I303F

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

possibly damaging
Transcript: ENSMUST00000165898
AA Change: I303F

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000128510
Gene: ENSMUSG00000028064
AA Change: I303F

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

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: 36 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310057M21Rik	T	A	7: 130,959,215 (GRCm39)	M162L	probably benign	Het
Aldh1a1	A	T	19: 20,620,283 (GRCm39)	T487S	probably benign	Het
Bahcc1	T	C	11: 120,171,030 (GRCm39)		probably benign	Het
Cldn10	G	A	14: 119,111,129 (GRCm39)		probably benign	Het
Cntn3	G	A	6: 102,185,145 (GRCm39)	T657I	probably damaging	Het
Crb1	A	T	1: 139,264,806 (GRCm39)	I204K	probably damaging	Het
Crim1	C	A	17: 78,620,664 (GRCm39)	T368K	probably benign	Het
Csad	C	A	15: 102,088,516 (GRCm39)	V237L	probably benign	Het
Cyp39a1	T	G	17: 44,060,806 (GRCm39)	H451Q	possibly damaging	Het
Dclk2	T	C	3: 86,723,667 (GRCm39)	E376G	possibly damaging	Het
Dnah10	A	T	5: 124,842,008 (GRCm39)	Y1331F	possibly damaging	Het
Dnajc11	A	T	4: 152,063,759 (GRCm39)	I452L	probably damaging	Het
Dpf2	T	C	19: 5,962,810 (GRCm39)		probably benign	Het
Elovl2	A	C	13: 41,340,420 (GRCm39)	V225G	probably damaging	Het
Fancd2	T	A	6: 113,522,072 (GRCm39)	H222Q	possibly damaging	Het
Fhdc1	G	A	3: 84,352,042 (GRCm39)	A1061V	possibly damaging	Het
Flt4	C	T	11: 49,525,998 (GRCm39)		probably benign	Het
Foxp2	T	C	6: 15,409,834 (GRCm39)	V478A	possibly damaging	Het
H2-Q1	G	A	17: 35,542,505 (GRCm39)	V317M	probably benign	Het
Hrob	T	C	11: 102,146,422 (GRCm39)	C233R	probably benign	Het
Igkv3-5	G	A	6: 70,640,336 (GRCm39)		probably benign	Het
Isg20	G	A	7: 78,564,129 (GRCm39)	C12Y	probably damaging	Het
Itgb4	G	A	11: 115,879,752 (GRCm39)	V635I	probably damaging	Het
Nat8f5	G	A	6: 85,794,859 (GRCm39)	R34C	probably benign	Het
Or8d2	T	C	9: 38,759,629 (GRCm39)	V73A	probably benign	Het
Pramel7	A	G	2: 87,319,932 (GRCm39)	S454P	probably benign	Het
Rarb	T	A	14: 16,443,760 (GRCm38)	E176V	probably damaging	Het
Slc25a24	G	A	3: 109,056,816 (GRCm39)	E110K	probably damaging	Het
Slc7a13	A	T	4: 19,839,527 (GRCm39)	I377L	probably benign	Het
Smim19	T	C	8: 22,953,393 (GRCm39)		probably null	Het
Tiam2	A	G	17: 3,477,565 (GRCm39)	Y596C	probably damaging	Het
Tlr1	A	T	5: 65,083,290 (GRCm39)	L429*	probably null	Het
Ubxn8	G	A	8: 34,119,406 (GRCm39)		probably benign	Het
Vmn2r108	C	A	17: 20,691,280 (GRCm39)	M414I	probably benign	Het
Vmn2r99	A	G	17: 19,600,377 (GRCm39)	N467S	probably damaging	Het
Zfp456	T	A	13: 67,515,272 (GRCm39)	T145S	probably benign	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
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

2014-02-04