Mutagenetix > Incidental Mutation

Incidental Mutation 'R8539:Sema5a'

659344

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

068505-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8539 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

32244959-32696487 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 32618989 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tryptophan to Arginine at position 506 (W506R)

Ref Sequence

ENSEMBL: ENSMUSP00000069024 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000067458
AA Change: W506R

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000069024
Gene: ENSMUSG00000022231
AA Change: W506R

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

100% (38/38)

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: 38 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Akr1c6	G	A	13: 4,484,474 (GRCm39)		probably null	Het
Amz1	T	C	5: 140,734,412 (GRCm39)	L215S	probably benign	Het
Aplnr	A	G	2: 84,967,251 (GRCm39)	D92G	probably benign	Het
Arpc5	A	G	1: 152,642,552 (GRCm39)	D26G	probably damaging	Het
Cntrob	G	A	11: 69,211,652 (GRCm39)	R191C	possibly damaging	Het
Ephb4	A	G	5: 137,356,117 (GRCm39)	D242G	probably damaging	Het
Eppk1	C	T	15: 75,994,319 (GRCm39)	R854Q	probably benign	Het
Galnt13	A	T	2: 54,823,584 (GRCm39)		probably null	Het
Hcrt	T	A	11: 100,652,051 (GRCm39)		probably benign	Het
Hnf1a	A	G	5: 115,108,576 (GRCm39)		probably null	Het
Hykk	A	G	9: 54,844,444 (GRCm39)	S170G	probably benign	Het
Igf1r	C	A	7: 67,653,596 (GRCm39)	Q45K	probably benign	Het
Klhl8	C	T	5: 104,015,392 (GRCm39)	V511I	probably damaging	Het
Loxl3	A	T	6: 83,026,507 (GRCm39)	M488L	probably benign	Het
Myo7a	G	A	7: 97,721,668 (GRCm39)	P1221S	probably damaging	Het
Myom2	A	T	8: 15,164,254 (GRCm39)	I1050F	probably benign	Het
Ncapd3	T	G	9: 26,959,520 (GRCm39)	C319G	probably benign	Het
Ndufaf5	C	A	2: 140,025,894 (GRCm39)	T151K	possibly damaging	Het
Notch3	A	T	17: 32,375,329 (GRCm39)	D364E	possibly damaging	Het
Nudt21	G	A	8: 94,763,601 (GRCm39)		probably benign	Het
Or2p2	T	C	13: 21,257,343 (GRCm39)	I43V	probably benign	Het
Pkd1l3	T	A	8: 110,362,919 (GRCm39)	V1060E	probably damaging	Het
Plxnd1	G	C	6: 115,939,768 (GRCm39)	P1404A	possibly damaging	Het
Ret	A	G	6: 118,152,770 (GRCm39)	V523A	possibly damaging	Het
Ror1	T	C	4: 100,299,084 (GRCm39)	I819T	possibly damaging	Het
Scn10a	T	A	9: 119,467,840 (GRCm39)	K767*	probably null	Het
Sorbs1	G	C	19: 40,365,244 (GRCm39)	R180G	probably benign	Het
Sult1b1	C	A	5: 87,681,838 (GRCm39)	V67F	possibly damaging	Het
Suz12	T	A	11: 79,889,904 (GRCm39)	D13E	probably damaging	Het
Tap1	C	T	17: 34,408,409 (GRCm39)	A216V	probably benign	Het
Tlr3	A	G	8: 45,851,553 (GRCm39)	L448P	probably damaging	Het
Tnik	G	A	3: 28,596,152 (GRCm39)	V182M	probably damaging	Het
Ttn	A	G	2: 76,736,778 (GRCm39)	F4329L	probably benign	Het
Usp21	C	T	1: 171,111,246 (GRCm39)	E396K	probably damaging	Het
Vmn1r122	A	T	7: 20,867,281 (GRCm39)	I258N	possibly damaging	Het
Vmn2r106	C	A	17: 20,499,271 (GRCm39)	R213S	probably benign	Het
Vmn2r111	A	T	17: 22,790,274 (GRCm39)	M244K	probably benign	Het
Zeb1	T	A	18: 5,748,784 (GRCm39)	V117D	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
R5204:Sema5a	UTSW	15	32,686,793 (GRCm39)	missense	probably benign	0.00
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
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'- TCCCAGTTCCAGTGTTATCACAG -3'
(R):5'- TGGGTTTGCAACAATGGATCTAC -3'

Sequencing Primer
(F):5'- AGGCAGGAGATTTTCAGTCCTTCAC -3'
(R):5'- CTTTGAAAGGTAAGCTATGCAGGTC -3'

Posted On

2021-01-18