Mutagenetix > Incidental Mutation

Incidental Mutation 'R5204:Sema5a'

398372

Institutional Source

Beutler Lab

Gene Symbol

Sema5a

Ensembl Gene

ENSMUSG00000022231

Gene Name

sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A

Synonyms

M-Sema D, semF, Semaf, 9130201M22Rik

MMRRC Submission

042779-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5204 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

32244959-32696487 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 32686793 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Isoleucine at position 968 (M968I)

Ref Sequence

ENSEMBL: ENSMUSP00000069024 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000067458]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000067458
AA Change: M968I

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

SMART Domains

Protein: ENSMUSP00000069024
Gene: ENSMUSG00000022231
AA Change: M968I

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
Sema	58	468	2.18e-173	SMART
PSI	486	533	1.78e-9	SMART
TSP1	543	597	2.23e-1	SMART
TSP1	598	651	2.05e-15	SMART
TSP1	656	702	6.94e-13	SMART
low complexity region	707	715	N/A	INTRINSIC
low complexity region	755	771	N/A	INTRINSIC
TSP1	787	839	4.17e-16	SMART
TSP1	844	896	9.08e-17	SMART
TSP1	899	946	3.19e-3	SMART
low complexity region	949	960	N/A	INTRINSIC
transmembrane domain	971	993	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000227429

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 95.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the semaphorin gene family that encodes membrane proteins containing a semaphorin domain and several thrombospondin type-1 repeats. Members of this family are involved in axonal guidance during neural development. This gene has been implicated as an autism susceptibility gene.[provided by RefSeq, Jan 2010]
PHENOTYPE: Mice homozygous for one null mutation die during organogenesis and display defects in branching of cranial vessels. Mice homozygous for another null mutation appear normal. [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
Aarsd1	A	T	11: 101,297,752 (GRCm39)	L532Q	probably damaging	Het
Abt1	G	A	13: 23,606,838 (GRCm39)	R88C	probably damaging	Het
Aopep	G	A	13: 63,180,904 (GRCm39)	V289I	probably benign	Het
Arhgef7	T	A	8: 11,850,775 (GRCm39)	L129*	probably null	Het
Arid1b	T	C	17: 5,393,316 (GRCm39)	V2282A	probably damaging	Het
Bivm	G	C	1: 44,177,738 (GRCm39)	G346A	probably damaging	Het
Cav1	T	C	6: 17,339,254 (GRCm39)	L102P	probably damaging	Het
Ccdc57	A	G	11: 120,776,888 (GRCm39)	V504A	possibly damaging	Het
Cd7	A	T	11: 120,928,860 (GRCm39)		probably null	Het
Cdh3	T	C	8: 107,270,871 (GRCm39)	V508A	probably benign	Het
Chrd	A	T	16: 20,554,822 (GRCm39)	I413F	probably benign	Het
Clec4b1	T	A	6: 123,048,494 (GRCm39)	*210R	probably null	Het
Clock	A	T	5: 76,391,017 (GRCm39)		probably null	Het
Col4a2	T	A	8: 11,448,651 (GRCm39)		probably null	Het
Gpx7	T	C	4: 108,260,512 (GRCm39)	T95A	probably benign	Het
Hivep3	T	A	4: 119,961,053 (GRCm39)		probably null	Het
Hrc	A	G	7: 44,985,128 (GRCm39)	Y93C	possibly damaging	Het
Igkv4-80	A	C	6: 68,993,649 (GRCm39)	S81A	probably benign	Het
Klhl5	G	T	5: 65,288,781 (GRCm39)	L14F	possibly damaging	Het
Mcm6	A	G	1: 128,261,375 (GRCm39)	L743P	probably benign	Het
Nrxn1	A	T	17: 90,469,792 (GRCm39)	F57Y	probably damaging	Het
Or51af1	C	T	7: 103,141,747 (GRCm39)	V113M	probably damaging	Het
Otx1	C	A	11: 21,947,037 (GRCm39)	A91S	probably damaging	Het
Pcdh20	G	T	14: 88,706,351 (GRCm39)	D316E	probably damaging	Het
Pcdhb12	T	A	18: 37,569,142 (GRCm39)	V96E	probably damaging	Het
Pi4ka	A	T	16: 17,176,909 (GRCm39)	L346M	possibly damaging	Het
Pkhd1l1	A	C	15: 44,410,437 (GRCm39)	N2648T	possibly damaging	Het
Rufy1	C	T	11: 50,297,261 (GRCm39)	R397Q	probably damaging	Het
Slc33a1	A	G	3: 63,871,167 (GRCm39)	Y149H	probably damaging	Het
Tln2	T	A	9: 67,261,764 (GRCm39)	R658S	probably benign	Het
Tmem30c	T	C	16: 57,090,385 (GRCm39)	N274S	possibly damaging	Het
Tor3a	A	G	1: 156,483,270 (GRCm39)	L384P	probably damaging	Het
Trpm3	T	A	19: 22,425,705 (GRCm39)	L20*	probably null	Het
Ttn	T	A	2: 76,560,556 (GRCm39)	I20955F	probably damaging	Het
Usp15	A	T	10: 122,949,545 (GRCm39)	S908R	probably benign	Het
Zfp866	A	G	8: 70,218,690 (GRCm39)	L310P	probably damaging	Het

Other mutations in Sema5a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00672:Sema5a	APN	15	32,619,026 (GRCm39)	missense	probably benign	0.06
IGL01148:Sema5a	APN	15	32,681,641 (GRCm39)	missense	probably benign	0.00
IGL01285:Sema5a	APN	15	32,575,143 (GRCm39)	missense	possibly damaging	0.66
IGL01647:Sema5a	APN	15	32,417,587 (GRCm39)	missense	possibly damaging	0.82
IGL01845:Sema5a	APN	15	32,474,514 (GRCm39)	splice site	probably benign
IGL01970:Sema5a	APN	15	32,686,792 (GRCm39)	missense	probably benign	0.02
IGL01986:Sema5a	APN	15	32,682,506 (GRCm39)	splice site	probably benign
IGL02053:Sema5a	APN	15	32,550,413 (GRCm39)	missense	probably benign	0.00
IGL02234:Sema5a	APN	15	32,679,318 (GRCm39)	missense	probably damaging	1.00
IGL02325:Sema5a	APN	15	32,686,977 (GRCm39)	missense	possibly damaging	0.63
IGL02370:Sema5a	APN	15	32,682,445 (GRCm39)	splice site	probably benign
IGL02427:Sema5a	APN	15	32,673,690 (GRCm39)	splice site	probably benign
IGL02621:Sema5a	APN	15	32,538,802 (GRCm39)	splice site	probably benign
IGL02656:Sema5a	APN	15	32,631,431 (GRCm39)	missense	possibly damaging	0.95
IGL03091:Sema5a	APN	15	32,538,880 (GRCm39)	splice site	probably benign
IGL03107:Sema5a	APN	15	32,669,554 (GRCm39)	missense	probably damaging	0.98
IGL03114:Sema5a	APN	15	32,673,573 (GRCm39)	missense	probably damaging	0.99
IGL03222:Sema5a	APN	15	32,628,304 (GRCm39)	missense	probably benign	0.32
PIT4305001:Sema5a	UTSW	15	32,628,345 (GRCm39)	missense	probably benign
R0190:Sema5a	UTSW	15	32,562,920 (GRCm39)	missense	possibly damaging	0.93
R0409:Sema5a	UTSW	15	32,681,755 (GRCm39)	missense	probably damaging	1.00
R0413:Sema5a	UTSW	15	32,669,590 (GRCm39)	missense	probably damaging	1.00
R0504:Sema5a	UTSW	15	32,574,949 (GRCm39)	splice site	probably benign
R1235:Sema5a	UTSW	15	32,609,372 (GRCm39)	missense	probably benign	0.04
R1484:Sema5a	UTSW	15	32,460,431 (GRCm39)	missense	probably damaging	1.00
R1550:Sema5a	UTSW	15	32,618,995 (GRCm39)	missense	probably benign	0.00
R1557:Sema5a	UTSW	15	32,460,418 (GRCm39)	missense	probably benign	0.04
R1670:Sema5a	UTSW	15	32,548,945 (GRCm39)	missense	probably damaging	1.00
R1688:Sema5a	UTSW	15	32,669,570 (GRCm39)	missense	probably benign	0.01
R1760:Sema5a	UTSW	15	32,641,252 (GRCm39)	missense	probably damaging	0.99
R1960:Sema5a	UTSW	15	32,562,877 (GRCm39)	missense	possibly damaging	0.66
R1967:Sema5a	UTSW	15	32,681,765 (GRCm39)	missense	probably damaging	0.99
R2062:Sema5a	UTSW	15	32,609,363 (GRCm39)	splice site	probably benign
R2082:Sema5a	UTSW	15	32,619,002 (GRCm39)	missense	probably benign	0.04
R2218:Sema5a	UTSW	15	32,631,455 (GRCm39)	missense	probably damaging	0.99
R2267:Sema5a	UTSW	15	32,575,065 (GRCm39)	missense	probably benign	0.03
R2299:Sema5a	UTSW	15	32,562,922 (GRCm39)	missense	possibly damaging	0.95
R2438:Sema5a	UTSW	15	32,550,399 (GRCm39)	missense	possibly damaging	0.63
R2698:Sema5a	UTSW	15	32,673,546 (GRCm39)	missense	probably damaging	1.00
R3950:Sema5a	UTSW	15	32,689,484 (GRCm39)	missense	probably damaging	1.00
R4197:Sema5a	UTSW	15	32,619,064 (GRCm39)	missense	probably benign
R4496:Sema5a	UTSW	15	32,641,133 (GRCm39)	missense	probably damaging	1.00
R4840:Sema5a	UTSW	15	32,550,400 (GRCm39)	missense	possibly damaging	0.63
R4842:Sema5a	UTSW	15	32,609,563 (GRCm39)	missense	probably benign
R4867:Sema5a	UTSW	15	32,550,436 (GRCm39)	missense	possibly damaging	0.60
R4934:Sema5a	UTSW	15	32,679,310 (GRCm39)	missense	probably damaging	1.00
R4977:Sema5a	UTSW	15	32,679,332 (GRCm39)	missense	probably damaging	1.00
R5580:Sema5a	UTSW	15	32,575,031 (GRCm39)	missense	probably benign	0.00
R5937:Sema5a	UTSW	15	32,574,987 (GRCm39)	missense	probably damaging	1.00
R6220:Sema5a	UTSW	15	32,686,875 (GRCm39)	missense	probably damaging	0.99
R6897:Sema5a	UTSW	15	32,550,421 (GRCm39)	missense	probably benign	0.05
R7037:Sema5a	UTSW	15	32,686,993 (GRCm39)	missense	probably damaging	1.00
R7072:Sema5a	UTSW	15	32,575,105 (GRCm39)	missense	possibly damaging	0.94
R7273:Sema5a	UTSW	15	32,417,608 (GRCm39)	missense	probably benign
R7572:Sema5a	UTSW	15	32,673,574 (GRCm39)	missense	probably damaging	1.00
R7621:Sema5a	UTSW	15	32,609,378 (GRCm39)	missense	possibly damaging	0.65
R7642:Sema5a	UTSW	15	32,682,471 (GRCm39)	missense	probably damaging	0.97
R7870:Sema5a	UTSW	15	32,609,485 (GRCm39)	missense	probably benign	0.23
R7880:Sema5a	UTSW	15	32,686,954 (GRCm39)	missense	probably damaging	1.00
R8025:Sema5a	UTSW	15	32,548,928 (GRCm39)	missense	probably benign	0.37
R8034:Sema5a	UTSW	15	32,574,987 (GRCm39)	missense	probably damaging	1.00
R8241:Sema5a	UTSW	15	32,575,064 (GRCm39)	missense	probably benign
R8539:Sema5a	UTSW	15	32,618,989 (GRCm39)	missense	probably damaging	0.98
R8728:Sema5a	UTSW	15	32,562,703 (GRCm39)	missense	probably damaging	0.98
R8807:Sema5a	UTSW	15	32,562,868 (GRCm39)	missense	possibly damaging	0.83
R8825:Sema5a	UTSW	15	32,689,498 (GRCm39)	missense	probably benign	0.02
R9109:Sema5a	UTSW	15	32,619,040 (GRCm39)	missense	probably benign	0.02
R9235:Sema5a	UTSW	15	32,619,034 (GRCm39)	missense	probably benign	0.01
R9298:Sema5a	UTSW	15	32,619,040 (GRCm39)	missense	probably benign	0.02
R9354:Sema5a	UTSW	15	32,562,902 (GRCm39)	nonsense	probably null
R9515:Sema5a	UTSW	15	32,679,373 (GRCm39)	missense	probably damaging	1.00
R9663:Sema5a	UTSW	15	32,673,546 (GRCm39)	nonsense	probably null
X0020:Sema5a	UTSW	15	32,417,646 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- AACCAGACTGCTCACTGTG -3'
(R):5'- CTTACCTTGATGGCCTCCACAG -3'

Sequencing Primer
(F):5'- ACTGCTCACTGTGGACAAG -3'
(R):5'- GGCCTCCACAGAATCATATTTG -3'

Posted On

2016-07-06