Mutagenetix > Incidental Mutation

Incidental Mutation 'R5580:Sema5a'

438434

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

043134-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5580 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

32244959-32696487 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 32575031 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Phenylalanine at position 380 (I380F)

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: I380F

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000069024
Gene: ENSMUSG00000022231
AA Change: I380F

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: ENSMUST00000227802

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000227976

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000228015

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000228442

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.6%
20x: 96.2%

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: 102 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2410002F23Rik	A	G	7: 43,900,664 (GRCm39)	T73A	possibly damaging	Het
A1bg	A	T	15: 60,790,881 (GRCm39)	V365E	probably benign	Het
Abcg5	A	C	17: 84,967,582 (GRCm39)	V406G	probably damaging	Het
Adamts12	A	G	15: 11,152,086 (GRCm39)	Y192C	probably benign	Het
Add3	C	T	19: 53,233,642 (GRCm39)	S649L	probably damaging	Het
Adgrg6	A	T	10: 14,286,228 (GRCm39)	C1129*	probably null	Het
Arsb	T	A	13: 93,944,053 (GRCm39)	V248D	probably damaging	Het
AW554918	A	T	18: 25,472,922 (GRCm39)	N39I	probably damaging	Het
Cacna1b	A	T	2: 24,540,566 (GRCm39)	I1383N	probably damaging	Het
Caprin2	A	T	6: 148,760,232 (GRCm39)	V625D	possibly damaging	Het
Cd9	A	G	6: 125,441,420 (GRCm39)	L67P	probably damaging	Het
Cdh5	T	A	8: 104,852,126 (GRCm39)	Y80*	probably null	Het
Csf2ra	A	G	19: 61,214,655 (GRCm39)	L223P	probably damaging	Het
Cyp2c67	T	C	19: 39,604,094 (GRCm39)	K421E	probably damaging	Het
Dzank1	T	C	2: 144,348,098 (GRCm39)	R223G	probably damaging	Het
Emilin2	A	G	17: 71,582,225 (GRCm39)	V167A	probably benign	Het
Eps8l3	A	G	3: 107,788,919 (GRCm39)	T81A	probably damaging	Het
Esrra	T	C	19: 6,897,755 (GRCm39)	M1V	probably null	Het
Evpl	C	A	11: 116,125,058 (GRCm39)	A135S	probably benign	Het
Fam193a	A	G	5: 34,578,132 (GRCm39)	I209V	probably benign	Het
Fbxl19	C	A	7: 127,350,168 (GRCm39)	C253*	probably null	Het
Fer1l5	T	A	1: 36,424,539 (GRCm39)	Y305*	probably null	Het
Fzd2	A	C	11: 102,496,665 (GRCm39)	I370L	probably damaging	Het
Gnl3	T	C	14: 30,737,242 (GRCm39)	K212R	probably benign	Het
Golm1	A	G	13: 59,790,179 (GRCm39)	L207P	probably benign	Het
Gphn	T	A	12: 78,538,818 (GRCm39)	F155I	probably damaging	Het
Grhl1	G	A	12: 24,659,739 (GRCm39)	G500S	probably benign	Het
Gucd1	C	A	10: 75,346,968 (GRCm39)	G55V	possibly damaging	Het
Haus6	A	T	4: 86,517,503 (GRCm39)	I287K	possibly damaging	Het
Hmcn1	G	A	1: 150,453,290 (GRCm39)	P5342S	probably benign	Het
Hspa12a	A	G	19: 58,788,092 (GRCm39)	S577P	probably benign	Het
Ido2	T	A	8: 25,040,882 (GRCm39)	I113F	possibly damaging	Het
Ifrd2	C	T	9: 107,469,511 (GRCm39)	P396S	probably damaging	Het
Igkv4-86	T	A	6: 68,887,990 (GRCm39)		probably benign	Het
Ipo11	A	G	13: 107,037,255 (GRCm39)	V196A	probably benign	Het
Itih2	T	C	2: 10,128,287 (GRCm39)	E138G	probably damaging	Het
Kidins220	T	G	12: 25,097,896 (GRCm39)	C1179G	probably benign	Het
Kif20b	T	A	19: 34,927,128 (GRCm39)		probably null	Het
Klk1	T	A	7: 43,878,238 (GRCm39)	Y63N	probably benign	Het
L3mbtl3	T	G	10: 26,179,604 (GRCm39)	D517A	unknown	Het
Lars1	G	T	18: 42,347,916 (GRCm39)	P969H	probably damaging	Het
Lrp1	C	T	10: 127,424,389 (GRCm39)	V766I	probably benign	Het
Lrrc8c	A	G	5: 105,755,553 (GRCm39)	I443V	probably benign	Het
Lsg1	T	C	16: 30,387,985 (GRCm39)	M439V	probably null	Het
Magi2	T	A	5: 20,420,422 (GRCm39)	M286K	probably benign	Het
Med11	T	C	11: 70,342,891 (GRCm39)		probably null	Het
Med13l	A	G	5: 118,889,695 (GRCm39)	K1819E	possibly damaging	Het
Ms4a14	T	A	19: 11,280,590 (GRCm39)	Q656L	probably benign	Het
Muc5b	A	G	7: 141,415,084 (GRCm39)	T2677A	possibly damaging	Het
Myo7a	A	T	7: 97,722,367 (GRCm39)	L1186H	probably damaging	Het
Naca	C	A	10: 127,876,462 (GRCm39)		probably benign	Het
Nbeal1	T	C	1: 60,281,761 (GRCm39)	I828T	probably benign	Het
Ncor1	A	T	11: 62,280,604 (GRCm39)	C75*	probably null	Het
Nepn	A	C	10: 52,280,398 (GRCm39)	S497R	probably damaging	Het
Nf2	A	G	11: 4,753,689 (GRCm39)	F222L	probably damaging	Het
Nlrp9b	A	C	7: 19,757,089 (GRCm39)	T109P	probably damaging	Het
Nr1h4	A	T	10: 89,352,302 (GRCm39)	F22I	probably benign	Het
Ogg1	A	G	6: 113,306,337 (GRCm39)	Y178C	probably damaging	Het
Or1e22	G	T	11: 73,377,036 (GRCm39)	P205T	probably benign	Het
Or4b12	C	A	2: 90,096,694 (GRCm39)	V27L	probably benign	Het
Or5b119	T	A	19: 13,456,791 (GRCm39)	Y257F	probably damaging	Het
Or5b21	G	A	19: 12,839,168 (GRCm39)	V10M	possibly damaging	Het
Or5d14	A	T	2: 87,880,668 (GRCm39)	M100K	possibly damaging	Het
Osr1	G	A	12: 9,629,325 (GRCm39)	R66Q	probably damaging	Het
Pi4ka	A	G	16: 17,098,951 (GRCm39)	S1978P	probably damaging	Het
Pik3c2g	A	T	6: 139,603,531 (GRCm39)	Q239L	probably damaging	Het
Pin1rt1	A	G	2: 104,544,670 (GRCm39)	I154T	probably damaging	Het
Pkdcc	A	G	17: 83,527,511 (GRCm39)	T230A	probably damaging	Het
Por	A	T	5: 135,762,675 (GRCm39)	I430F	probably damaging	Het
Prb1c	T	C	6: 132,338,432 (GRCm39)	N262S	unknown	Het
Prkcsh	T	A	9: 21,922,551 (GRCm39)		probably null	Het
Pros1	A	G	16: 62,746,689 (GRCm39)		probably null	Het
Pus10	T	A	11: 23,622,556 (GRCm39)	L59I	probably benign	Het
Pxmp2	A	G	5: 110,431,542 (GRCm39)	V67A	possibly damaging	Het
Rab3gap1	C	A	1: 127,858,727 (GRCm39)	A612E	probably benign	Het
Rpap2	A	G	5: 107,768,011 (GRCm39)	E206G	probably benign	Het
Rpl31	C	T	1: 39,409,108 (GRCm39)	R41C	probably benign	Het
Ryr3	C	T	2: 112,672,293 (GRCm39)	G1393R	probably damaging	Het
Scara5	T	C	14: 65,968,528 (GRCm39)	M267T	probably benign	Het
Slc36a3	A	G	11: 55,026,279 (GRCm39)	S180P	probably benign	Het
Slc44a5	A	G	3: 153,966,922 (GRCm39)	K536R	probably benign	Het
Smg1	T	C	7: 117,748,125 (GRCm39)		probably benign	Het
Spata31d1e	A	T	13: 59,890,070 (GRCm39)	D583E	probably benign	Het
Strc	T	C	2: 121,205,493 (GRCm39)	K879R	probably damaging	Het
Swt1	T	C	1: 151,260,206 (GRCm39)	E731G	probably benign	Het
Syngap1	G	A	17: 27,181,305 (GRCm39)	A9T	probably damaging	Het
Tex15	C	T	8: 34,062,457 (GRCm39)	T903I	probably damaging	Het
Tg	A	G	15: 66,557,149 (GRCm39)	I937V	possibly damaging	Het
Tm9sf4	T	C	2: 153,024,350 (GRCm39)	Y58H	probably damaging	Het
Tsen2	A	T	6: 115,554,941 (GRCm39)	D458V	probably damaging	Het
Ttn	T	A	2: 76,748,146 (GRCm39)	D4301V	probably benign	Het
Txk	C	A	5: 72,864,932 (GRCm39)	L314F	probably damaging	Het
Ube3b	A	G	5: 114,553,384 (GRCm39)	T919A	probably benign	Het
Ubn2	A	G	6: 38,460,187 (GRCm39)	M641V	probably damaging	Het
Usp4	C	T	9: 108,243,058 (GRCm39)	T242I	probably benign	Het
Usp53	A	G	3: 122,727,883 (GRCm39)	S900P	probably benign	Het
Vmn1r225	T	C	17: 20,723,101 (GRCm39)	Y181H	probably damaging	Het
Vmn1r83	T	A	7: 12,055,800 (GRCm39)	I86L	probably benign	Het
Vmn2r65	T	C	7: 84,596,802 (GRCm39)	I84M	probably damaging	Het
Vstm2b	A	G	7: 40,552,050 (GRCm39)	H126R	probably damaging	Het
Zfp524	A	T	7: 5,021,416 (GRCm39)	I315F	probably benign	Het
Zfp975	A	T	7: 42,314,513 (GRCm39)	L20*	probably null	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
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'- GCACACTCAGTAATACATCATGGC -3'
(R):5'- AATACAGGTCCATGGCTGTGC -3'

Sequencing Primer
(F):5'- ACATCATGGCTTATTCAGTTTGTAG -3'
(R):5'- CCATGGCTGTGCTTAAAGATGAG -3'

Posted On

2016-10-26