Mutagenetix > Incidental Mutation

Incidental Mutation 'R4840:Sema5a'

371773

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

042453-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4840 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

32244959-32696487 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 32550400 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 146 (S146R)

Ref Sequence

ENSEMBL: ENSMUSP00000069024 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000067458
AA Change: S146R

PolyPhen 2 Score 0.631 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000069024
Gene: ENSMUSG00000022231
AA Change: S146R

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: ENSMUST00000226876

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000227802

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000227976

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000228015

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000228442

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000228555

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.1%

Validation Efficiency

97% (114/117)

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: 103 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2810459M11Rik	C	A	1: 85,974,166 (GRCm39)	T161K	probably benign	Het
Actn3	G	A	19: 4,914,539 (GRCm39)	R530W	probably damaging	Het
Alg11	C	T	8: 22,558,026 (GRCm39)	A404V	possibly damaging	Het
Alkbh8	T	A	9: 3,369,751 (GRCm39)	V340D	probably damaging	Het
Arhgef12	T	C	9: 42,886,364 (GRCm39)	H1166R	probably benign	Het
Aspm	T	A	1: 139,398,269 (GRCm39)	D978E	possibly damaging	Het
Bod1l	C	T	5: 41,975,815 (GRCm39)	G1833D	probably damaging	Het
Brd3	A	G	2: 27,339,251 (GRCm39)	V676A	possibly damaging	Het
Brip1	G	A	11: 86,037,009 (GRCm39)	T454I	possibly damaging	Het
C3ar1	T	C	6: 122,827,723 (GRCm39)	I165V	probably benign	Het
Camta1	T	A	4: 151,228,864 (GRCm39)	Q656L	probably benign	Het
Casp14	A	T	10: 78,549,178 (GRCm39)	L256*	probably null	Het
Cdh23	G	T	10: 60,255,556 (GRCm39)	H773Q	possibly damaging	Het
Chd1	G	T	17: 15,989,016 (GRCm39)	D1590Y	probably damaging	Het
Chd1	G	A	17: 15,989,015 (GRCm39)	W1589*	probably null	Het
Cldn19	A	G	4: 119,112,951 (GRCm39)	Q61R	probably damaging	Het
Cyp2a22	A	G	7: 26,631,949 (GRCm39)	S436P	probably benign	Het
Emc10	A	C	7: 44,142,051 (GRCm39)	V124G	probably damaging	Het
Enam	A	T	5: 88,650,885 (GRCm39)	D723V	probably benign	Het
Eps8	C	A	6: 137,504,128 (GRCm39)	Q158H	probably damaging	Het
Ercc6	G	A	14: 32,263,253 (GRCm39)	D486N	probably damaging	Het
Fasn	T	C	11: 120,703,885 (GRCm39)	E1485G	possibly damaging	Het
Fat2	T	C	11: 55,169,844 (GRCm39)	K2972E	probably benign	Het
Fbxw28	T	C	9: 109,168,602 (GRCm39)	K30R	probably null	Het
Flot2	T	A	11: 77,948,339 (GRCm39)	L164Q	probably damaging	Het
Fsip2	A	T	2: 82,779,739 (GRCm39)	I162L	probably benign	Het
Fsip2	A	T	2: 82,815,815 (GRCm39)	L3849F	probably benign	Het
Gabrb1	C	G	5: 71,858,154 (GRCm39)	P60R	probably damaging	Het
Galnt14	T	C	17: 73,811,893 (GRCm39)	R443G	probably benign	Het
Gas8	C	T	8: 124,257,753 (GRCm39)	T400M	probably benign	Het
Gfap	T	C	11: 102,785,214 (GRCm39)	Y254C	probably damaging	Het
Git2	A	G	5: 114,883,543 (GRCm39)	S396P	probably damaging	Het
Glb1l3	A	T	9: 26,740,349 (GRCm39)	M327K	probably benign	Het
Gm10715	A	C	9: 3,038,062 (GRCm39)		probably benign	Het
Gm10787	G	A	10: 76,857,841 (GRCm39)		noncoding transcript	Het
Gm1123	T	A	9: 98,900,622 (GRCm39)	D78V	probably damaging	Het
Gm27013	T	C	6: 130,655,079 (GRCm39)	T128A	probably benign	Het
Gpbp1	A	G	13: 111,577,164 (GRCm39)		probably null	Het
Gphn	G	A	12: 78,569,729 (GRCm39)		probably null	Het
Gpr157	A	G	4: 150,186,823 (GRCm39)	E317G	probably benign	Het
Gsdmc4	T	A	15: 63,765,596 (GRCm39)	M318L	probably benign	Het
Gtf2f2	A	T	14: 76,248,131 (GRCm39)	W19R	probably damaging	Het
Gvin-ps3	T	C	7: 105,680,627 (GRCm39)		noncoding transcript	Het
Helb	A	G	10: 119,920,763 (GRCm39)	V1060A	probably benign	Het
Igfn1	C	T	1: 135,895,778 (GRCm39)	G1596D	probably benign	Het
Il1rl2	T	C	1: 40,366,547 (GRCm39)	I27T	possibly damaging	Het
Inpp5j	A	G	11: 3,449,676 (GRCm39)	V702A	probably damaging	Het
Kmt2d	A	C	15: 98,759,775 (GRCm39)	V1161G	unknown	Het
Krtap1-3	T	G	11: 99,481,715 (GRCm39)	Y144S	possibly damaging	Het
Layn	C	T	9: 50,968,682 (GRCm39)	V354M	probably damaging	Het
Lrba	G	A	3: 86,526,816 (GRCm39)		probably null	Het
Lrp8	T	A	4: 107,727,234 (GRCm39)	L893Q	possibly damaging	Het
Mrps9	T	A	1: 42,937,575 (GRCm39)		probably benign	Het
Mug1	T	A	6: 121,862,813 (GRCm39)	M1387K	probably damaging	Het
Myo18b	A	C	5: 113,021,895 (GRCm39)	V499G	probably benign	Het
Nbea	T	C	3: 55,618,091 (GRCm39)	E2321G	probably benign	Het
Nrsn2	C	T	2: 152,211,552 (GRCm39)	V160I	probably benign	Het
Nup210	G	A	6: 91,008,650 (GRCm39)	Q510*	probably null	Het
Ofcc1	G	A	13: 40,168,864 (GRCm39)	T841I	probably damaging	Het
Or2ag12	T	G	7: 106,277,330 (GRCm39)	D121A	probably damaging	Het
P3h3	G	T	6: 124,827,600 (GRCm39)	Q479K	possibly damaging	Het
Paqr9	T	A	9: 95,442,723 (GRCm39)	F238I	probably damaging	Het
Parp3	A	T	9: 106,350,308 (GRCm39)	L343H	probably damaging	Het
Pcdh18	A	C	3: 49,699,117 (GRCm39)	M1115R	probably damaging	Het
Pcdh8	A	G	14: 80,008,308 (GRCm39)	V85A	possibly damaging	Het
Pcdhb4	A	G	18: 37,441,452 (GRCm39)	N254S	possibly damaging	Het
Pld1	T	C	3: 28,130,700 (GRCm39)	V500A	probably benign	Het
Pramel29	T	C	4: 143,935,144 (GRCm39)	K199R	probably damaging	Het
Prkg2	A	T	5: 99,129,002 (GRCm39)	D311E	probably benign	Het
Prss42	T	C	9: 110,628,369 (GRCm39)	L171P	probably damaging	Het
Pth2	T	A	7: 44,830,767 (GRCm39)	L17H	probably damaging	Het
Reln	A	T	5: 22,223,844 (GRCm39)		probably null	Het
Rmi2	G	T	16: 10,657,701 (GRCm39)	V104L	probably damaging	Het
Rpusd4	T	A	9: 35,179,831 (GRCm39)	V108D	probably damaging	Het
Rufy4	C	A	1: 74,168,198 (GRCm39)	T82K	possibly damaging	Het
Scimp	G	A	11: 70,682,294 (GRCm39)	Q141*	probably null	Het
Sel1l2	T	C	2: 140,105,390 (GRCm39)	T267A	probably benign	Het
Sh2d3c	T	C	2: 32,611,172 (GRCm39)	M1T	probably null	Het
Slc30a6	T	C	17: 74,712,716 (GRCm39)	L71P	probably damaging	Het
Srrm3	A	G	5: 135,883,449 (GRCm39)	Y224C	possibly damaging	Het
Tacr3	A	T	3: 134,560,615 (GRCm39)	T185S	possibly damaging	Het
Tas2r140	T	A	6: 133,032,528 (GRCm39)	T77S	probably benign	Het
Thsd7b	T	C	1: 129,523,581 (GRCm39)	V128A	probably benign	Het
Tnfrsf10b	T	G	14: 70,013,608 (GRCm39)	H179Q	probably damaging	Het
Tonsl	A	G	15: 76,517,409 (GRCm39)	V770A	probably benign	Het
Trim42	G	A	9: 97,244,982 (GRCm39)	P606L	probably benign	Het
Trim45	A	T	3: 100,832,804 (GRCm39)	T346S	possibly damaging	Het
Ttc28	C	A	5: 111,433,947 (GRCm39)	S2296Y	probably damaging	Het
Ttc41	C	T	10: 86,566,989 (GRCm39)	R552C	probably benign	Het
Tube1	A	G	10: 39,020,842 (GRCm39)	N243D	probably benign	Het
Tvp23b	G	T	11: 62,770,424 (GRCm39)		probably null	Het
Ubxn11	T	A	4: 133,836,919 (GRCm39)	I49N	probably damaging	Het
Usp17le	T	A	7: 104,418,977 (GRCm39)	E55V	probably benign	Het
Vmn2r114	A	T	17: 23,510,353 (GRCm39)	V709D	probably damaging	Het
Vmn2r129	G	C	4: 156,685,733 (GRCm39)		noncoding transcript	Het
Vmn2r23	C	T	6: 123,690,033 (GRCm39)	T303M	probably damaging	Het
Vmn2r60	C	T	7: 41,785,285 (GRCm39)	P166S	probably damaging	Het
Vmn2r83	A	G	10: 79,313,682 (GRCm39)	I97V	possibly damaging	Het
Wbp2nl	A	T	15: 82,198,537 (GRCm39)	K358M	possibly damaging	Het
Xpo1	T	A	11: 23,228,183 (GRCm39)	I150N	probably damaging	Het
Zfp113	G	A	5: 138,143,687 (GRCm39)	L188F	probably damaging	Het
Zfp189	T	G	4: 49,529,984 (GRCm39)	S362R	probably damaging	Het
Zfp593os	A	G	4: 133,972,587 (GRCm39)		probably benign	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
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
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'- AGGAAGGATTCTCTGGCCAAG -3'
(R):5'- CATTGAGCCATTTGGAGTTGTACTG -3'

Sequencing Primer
(F):5'- CTCTGGCCAAGATTATAGAGAACTG -3'
(R):5'- TACTGTGCAGTTCGAAGAGG -3'

Posted On

2016-03-01