Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL00559:Sema3d'

6498

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Sema3d

Ensembl Gene

ENSMUSG00000040254

Gene Name

sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D

Synonyms

4631426B19Rik

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.207) question?

Stock #

IGL00559

Quality Score

Status

Chromosome

Chromosomal Location

12433352-12638915 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 12613189 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Lysine at position 422 (R422K)

Ref Sequence

ENSEMBL: ENSMUSP00000142453 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030868] [ENSMUST00000197927]

AlphaFold

Q8BH34

Predicted Effect

probably benign
Transcript: ENSMUST00000030868
AA Change: R422K

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000030868
Gene: ENSMUSG00000040254
AA Change: R422K

Domain	Start	End	E-Value	Type
transmembrane domain	16	35	N/A	INTRINSIC
Sema	70	515	2.97e-207	SMART
PSI	533	585	2.03e-13	SMART
IG	598	682	1.39e-2	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196618

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196982

Predicted Effect

probably benign
Transcript: ENSMUST00000197927
AA Change: R422K

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000142453
Gene: ENSMUSG00000040254
AA Change: R422K

Domain	Start	End	E-Value	Type
signal peptide	1	37	N/A	INTRINSIC
Sema	70	515	1e-209	SMART
PSI	533	585	8.5e-16	SMART
Blast:Sema	590	622	1e-9	BLAST

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 III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit pulmonary vein connection to the right atrium and atrial septal defect. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 16 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Cers4	G	A	8: 4,571,216 (GRCm39)	D262N	probably benign	Het
Cyp2d26	G	A	15: 82,675,244 (GRCm39)	A370V	probably benign	Het
Dnah7c	T	C	1: 46,846,449 (GRCm39)	M4000T	possibly damaging	Het
Enkd1	C	T	8: 106,430,974 (GRCm39)		probably benign	Het
H60b	A	G	10: 22,161,692 (GRCm39)	H60R	probably benign	Het
Hmgb4	T	C	4: 128,154,082 (GRCm39)	N162S	probably benign	Het
Htt	T	C	5: 35,006,448 (GRCm39)		probably benign	Het
Kbtbd6	A	G	14: 79,690,688 (GRCm39)	D461G	probably damaging	Het
Nell2	A	G	15: 95,425,166 (GRCm39)	L62P	possibly damaging	Het
Pi4k2b	T	A	5: 52,908,790 (GRCm39)	F205L	probably damaging	Het
Polr1b	G	T	2: 128,955,651 (GRCm39)	V521F	probably damaging	Het
Prn	G	A	2: 131,795,335 (GRCm39)	V152I	probably benign	Het
Ryr1	T	C	7: 28,711,667 (GRCm39)		probably benign	Het
Sema3c	G	T	5: 17,899,858 (GRCm39)	G450V	probably damaging	Het
Snw1	T	C	12: 87,515,501 (GRCm39)	D16G	probably damaging	Het
Tas2r121	T	C	6: 132,677,484 (GRCm39)	I163V	probably benign	Het

Other mutations in Sema3d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00582:Sema3d	APN	5	12,635,162 (GRCm39)	missense	probably damaging	1.00
IGL00661:Sema3d	APN	5	12,555,806 (GRCm39)	missense	probably damaging	1.00
IGL00780:Sema3d	APN	5	12,574,293 (GRCm39)	missense	probably damaging	1.00
IGL01531:Sema3d	APN	5	12,591,047 (GRCm39)	missense	probably benign
IGL01957:Sema3d	APN	5	12,613,282 (GRCm39)	missense	probably damaging	1.00
IGL02100:Sema3d	APN	5	12,634,958 (GRCm39)	missense	probably benign	0.29
IGL02676:Sema3d	APN	5	12,620,945 (GRCm39)	missense	probably benign	0.38
IGL02749:Sema3d	APN	5	12,613,112 (GRCm39)	splice site	probably benign
IGL02827:Sema3d	APN	5	12,635,085 (GRCm39)	missense	probably benign	0.04
IGL03325:Sema3d	APN	5	12,513,189 (GRCm39)	missense	probably damaging	0.99
R0050:Sema3d	UTSW	5	12,634,920 (GRCm39)	missense	probably benign	0.00
R0085:Sema3d	UTSW	5	12,620,953 (GRCm39)	missense	probably benign	0.00
R0095:Sema3d	UTSW	5	12,613,314 (GRCm39)	missense	probably damaging	1.00
R0157:Sema3d	UTSW	5	12,558,104 (GRCm39)	missense	possibly damaging	0.95
R0328:Sema3d	UTSW	5	12,498,042 (GRCm39)	missense	possibly damaging	0.48
R0924:Sema3d	UTSW	5	12,513,183 (GRCm39)	missense	possibly damaging	0.69
R0930:Sema3d	UTSW	5	12,513,183 (GRCm39)	missense	possibly damaging	0.69
R1609:Sema3d	UTSW	5	12,591,023 (GRCm39)	missense	probably damaging	1.00
R1657:Sema3d	UTSW	5	12,634,941 (GRCm39)	missense	possibly damaging	0.82
R1669:Sema3d	UTSW	5	12,558,051 (GRCm39)	splice site	probably benign
R1795:Sema3d	UTSW	5	12,634,854 (GRCm39)	missense	probably benign	0.02
R1861:Sema3d	UTSW	5	12,547,570 (GRCm39)	missense	probably benign	0.00
R1889:Sema3d	UTSW	5	12,534,988 (GRCm39)	splice site	probably null
R1895:Sema3d	UTSW	5	12,623,810 (GRCm39)	missense	probably damaging	1.00
R1946:Sema3d	UTSW	5	12,623,810 (GRCm39)	missense	probably damaging	1.00
R1975:Sema3d	UTSW	5	12,634,965 (GRCm39)	missense	probably benign
R1975:Sema3d	UTSW	5	12,613,285 (GRCm39)	missense	probably damaging	1.00
R2117:Sema3d	UTSW	5	12,613,240 (GRCm39)	missense	probably benign
R2148:Sema3d	UTSW	5	12,534,926 (GRCm39)	missense	probably damaging	0.99
R2276:Sema3d	UTSW	5	12,592,549 (GRCm39)	missense	possibly damaging	0.63
R3761:Sema3d	UTSW	5	12,621,004 (GRCm39)	missense	probably damaging	1.00
R4063:Sema3d	UTSW	5	12,635,091 (GRCm39)	missense	probably benign	0.25
R4428:Sema3d	UTSW	5	12,498,087 (GRCm39)	missense	probably benign	0.32
R4903:Sema3d	UTSW	5	12,613,125 (GRCm39)	missense	probably benign	0.00
R4999:Sema3d	UTSW	5	12,558,054 (GRCm39)	splice site	probably null
R5000:Sema3d	UTSW	5	12,498,005 (GRCm39)	missense	probably benign	0.01
R5022:Sema3d	UTSW	5	12,634,923 (GRCm39)	missense	probably damaging	1.00
R5186:Sema3d	UTSW	5	12,634,875 (GRCm39)	missense	probably benign
R5584:Sema3d	UTSW	5	12,620,954 (GRCm39)	missense	possibly damaging	0.73
R5584:Sema3d	UTSW	5	12,615,975 (GRCm39)	missense	possibly damaging	0.49
R6270:Sema3d	UTSW	5	12,498,074 (GRCm39)	missense	probably benign
R6368:Sema3d	UTSW	5	12,620,980 (GRCm39)	missense	probably damaging	1.00
R6426:Sema3d	UTSW	5	12,613,231 (GRCm39)	missense	probably damaging	1.00
R6750:Sema3d	UTSW	5	12,635,067 (GRCm39)	nonsense	probably null
R7403:Sema3d	UTSW	5	12,547,551 (GRCm39)	missense	probably damaging	0.97
R7450:Sema3d	UTSW	5	12,634,901 (GRCm39)	nonsense	probably null
R7470:Sema3d	UTSW	5	12,558,152 (GRCm39)	missense	probably damaging	1.00
R7548:Sema3d	UTSW	5	12,627,783 (GRCm39)	missense	unknown
R7593:Sema3d	UTSW	5	12,558,112 (GRCm39)	missense	probably benign	0.02
R7683:Sema3d	UTSW	5	12,623,823 (GRCm39)	nonsense	probably null
R8155:Sema3d	UTSW	5	12,498,148 (GRCm39)	critical splice donor site	probably null
R8442:Sema3d	UTSW	5	12,592,608 (GRCm39)	missense	probably damaging	0.99
R8725:Sema3d	UTSW	5	12,555,822 (GRCm39)	missense	probably damaging	1.00
R8754:Sema3d	UTSW	5	12,603,191 (GRCm39)	critical splice donor site	probably null
R9293:Sema3d	UTSW	5	12,603,181 (GRCm39)	missense	probably damaging	1.00
R9771:Sema3d	UTSW	5	12,613,207 (GRCm39)	missense	probably damaging	0.99
Z1176:Sema3d	UTSW	5	12,635,026 (GRCm39)	nonsense	probably null

Posted On

2012-04-20