Mutagenetix > Incidental Mutation

Incidental Mutation 'R7514:Sema3a'

582294

Institutional Source

Beutler Lab

Gene Symbol

Sema3a

Ensembl Gene

ENSMUSG00000028883

Gene Name

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

Synonyms

Semad, collapsin-1, SemD, sema III, semaphorin III

MMRRC Submission

045587-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.949) question?

Stock #

R7514 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

13175381-13652533 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 13573093 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Arginine at position 207 (H207R)

Ref Sequence

ENSEMBL: ENSMUSP00000030714 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030714] [ENSMUST00000095012] [ENSMUST00000137798]

AlphaFold

no structure available at present

PDB Structure

Structure of the Semaphorin 3A Receptor-Binding Module [X-RAY DIFFRACTION]
Mouse Semaphorin 3A, domains Sema-PSI-IG [X-RAY DIFFRACTION]
Complex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1 [X-RAY DIFFRACTION]

Predicted Effect

probably benign
Transcript: ENSMUST00000030714
AA Change: H207R

PolyPhen 2 Score 0.032 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000030714
Gene: ENSMUSG00000028883
AA Change: H207R

Domain	Start	End	E-Value	Type
Sema	57	498	4.09e-219	SMART
PSI	516	568	3.03e-12	SMART
IG	583	669	3.54e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000095012
AA Change: H207R

PolyPhen 2 Score 0.032 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000092621
Gene: ENSMUSG00000028883
AA Change: H207R

Domain	Start	End	E-Value	Type
Sema	57	498	4.09e-219	SMART
PSI	516	568	3.03e-12	SMART
IG	583	669	3.54e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000137798
AA Change: H207R

PolyPhen 2 Score 0.032 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000128153
Gene: ENSMUSG00000028883
AA Change: H207R

Domain	Start	End	E-Value	Type
Sema	57	498	4.09e-219	SMART
PSI	516	568	3.03e-12	SMART
IG	583	669	3.54e-4	SMART

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the semaphorin family and encodes a protein with an Ig-like C2-type (immunoglobulin-like) domain, a PSI domain and a Sema domain. This secreted protein can function as either a chemorepulsive agent, inhibiting axonal outgrowth, or as a chemoattractive agent, stimulating the growth of apical dendrites. In both cases, the protein is vital for normal neuronal pattern development. Increased expression of this protein is associated with schizophrenia and is seen in a variety of human tumor cell lines. Also, aberrant release of this protein is associated with the progression of Alzheimer's disease. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations exhibit patterning abnormalities of sensory and sympathetic neurons, abnormal embryonic bones and cartilaginous structures, cardiac defects, and high postnatal mortality. [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
4933427D14Rik	A	G	11: 72,086,628 (GRCm39)	L261P	probably damaging	Het
A4gnt	A	G	9: 99,502,598 (GRCm39)	I253V	probably benign	Het
AAdacl4fm3	A	T	4: 144,429,798 (GRCm39)	V397D	possibly damaging	Het
Acap2	A	T	16: 30,973,385 (GRCm39)		probably null	Het
Adora2b	G	T	11: 62,156,146 (GRCm39)	M198I	probably damaging	Het
Akap5	C	A	12: 76,375,303 (GRCm39)	T245K	probably benign	Het
Aldh1a2	T	C	9: 71,192,245 (GRCm39)	I399T	probably damaging	Het
Ank2	G	A	3: 126,819,252 (GRCm39)	S473L	probably benign	Het
Anln	A	T	9: 22,272,153 (GRCm39)	D655E	probably damaging	Het
Arhgef10	T	C	8: 15,025,956 (GRCm39)	V820A	probably benign	Het
Arid1b	A	G	17: 5,391,989 (GRCm39)	K1787E	probably benign	Het
Art4	T	C	6: 136,831,739 (GRCm39)	H134R	probably benign	Het
Borcs6	G	A	11: 68,951,410 (GRCm39)	V263M	probably damaging	Het
C8a	A	T	4: 104,703,247 (GRCm39)	M314K	possibly damaging	Het
Cbfa2t3	T	G	8: 123,361,865 (GRCm39)	M386L	probably damaging	Het
Ccdc170	T	A	10: 4,496,839 (GRCm39)	V459E	probably benign	Het
Cdh4	T	A	2: 179,532,636 (GRCm39)	N699K	possibly damaging	Het
Cdk12	T	C	11: 98,113,484 (GRCm39)	L756P	unknown	Het
Chsy1	A	G	7: 65,821,868 (GRCm39)	D701G	probably damaging	Het
Cnot9	A	G	1: 74,567,921 (GRCm39)	T270A	probably benign	Het
Crat	C	T	2: 30,294,577 (GRCm39)	R497Q	probably benign	Het
Csnk2a1-ps3	A	G	1: 156,352,324 (GRCm39)	D175G	probably benign	Het
Cyb5r1	A	G	1: 134,338,268 (GRCm39)	E228G	probably damaging	Het
D630003M21Rik	A	G	2: 158,059,273 (GRCm39)	L209P	probably damaging	Het
Dennd2c	T	A	3: 103,070,378 (GRCm39)	D791E	probably benign	Het
Dnah14	T	C	1: 181,455,632 (GRCm39)	I919T	probably damaging	Het
Dpp8	T	C	9: 64,986,036 (GRCm39)	L842S	probably damaging	Het
Ern1	A	G	11: 106,300,719 (GRCm39)		probably null	Het
Exo1	T	C	1: 175,734,232 (GRCm39)		probably null	Het
Fam161b	T	G	12: 84,404,512 (GRCm39)	E56A	possibly damaging	Het
Fbrsl1	T	C	5: 110,580,799 (GRCm39)	T153A	probably benign	Het
Fcgr3	T	G	1: 170,886,912 (GRCm39)	D4A	probably benign	Het
Gltp	C	T	5: 114,808,521 (GRCm39)	A193T	probably benign	Het
Gm3159	A	T	14: 4,399,690 (GRCm38)	S142C	probably damaging	Het
Gphn	T	C	12: 78,672,939 (GRCm39)	V485A	probably damaging	Het
Grik2	A	T	10: 49,399,904 (GRCm39)	N275K	probably damaging	Het
Gstt3	G	T	10: 75,612,625 (GRCm39)	Q102K	probably damaging	Het
Hivep3	T	A	4: 119,954,052 (GRCm39)	F789L	possibly damaging	Het
Ing5	A	G	1: 93,744,164 (GRCm39)	N157D	possibly damaging	Het
Itga3	C	T	11: 94,956,722 (GRCm39)	W177*	probably null	Het
Jag2	T	C	12: 112,892,672 (GRCm39)	T83A	probably benign	Het
Krt90	G	A	15: 101,461,605 (GRCm39)	T532I	unknown	Het
Lcn2	A	G	2: 32,277,861 (GRCm39)		probably null	Het
Lrig2	A	G	3: 104,373,076 (GRCm39)	S602P	probably damaging	Het
Lsm1	A	C	8: 26,282,237 (GRCm39)	R33S	probably damaging	Het
Mast4	A	T	13: 102,923,934 (GRCm39)	Y492*	probably null	Het
Mcm3	A	T	1: 20,876,120 (GRCm39)	L658Q	probably benign	Het
Myh4	G	A	11: 67,134,148 (GRCm39)		probably null	Het
Nck2	T	C	1: 43,608,381 (GRCm39)	V341A	probably benign	Het
Nucb1	T	C	7: 45,151,142 (GRCm39)		probably null	Het
Nup210l	G	C	3: 90,117,766 (GRCm39)		probably null	Het
Or1j1	A	G	2: 36,702,651 (GRCm39)	I151T	probably benign	Het
Or5al5	A	T	2: 85,961,972 (GRCm39)	F12I	probably damaging	Het
Or7g22	A	T	9: 19,049,161 (GRCm39)	S291C	possibly damaging	Het
Or8b48	T	A	9: 38,493,347 (GRCm39)	M258K	probably damaging	Het
Or8b54	G	A	9: 38,686,974 (GRCm39)	C141Y	probably damaging	Het
Pla2g4a	G	A	1: 149,727,113 (GRCm39)	P556S	probably damaging	Het
Plat	T	C	8: 23,265,658 (GRCm39)	C234R	probably damaging	Het
Ppfia1	T	C	7: 144,071,450 (GRCm39)	I321V	probably benign	Het
Prrc1	T	A	18: 57,496,325 (GRCm39)	V92E	probably benign	Het
Prss3	A	G	6: 41,350,848 (GRCm39)	V214A	probably damaging	Het
Ptprg	G	T	14: 12,179,342 (GRCm38)	K786N	possibly damaging	Het
Rabgap1	G	T	2: 37,427,354 (GRCm39)	G645V	probably damaging	Het
Rfx4	T	C	10: 84,716,090 (GRCm39)	S470P	probably damaging	Het
Rin3	C	T	12: 102,335,909 (GRCm39)	Q607*	probably null	Het
Serpinb12	G	A	1: 106,878,534 (GRCm39)	E181K	probably damaging	Het
Serpinb6c	G	A	13: 34,081,386 (GRCm39)	Q88*	probably null	Het
Shmt1	A	C	11: 60,692,812 (GRCm39)	C90W	probably damaging	Het
Slc16a13	C	T	11: 70,109,710 (GRCm39)	V264M	probably damaging	Het
Slc17a8	G	T	10: 89,427,969 (GRCm39)	P286Q	probably damaging	Het
Slc27a6	C	T	18: 58,745,293 (GRCm39)	Q576*	probably null	Het
Slc30a9	T	C	5: 67,505,421 (GRCm39)	S470P	possibly damaging	Het
Slc44a2	G	T	9: 21,253,768 (GRCm39)	K136N	possibly damaging	Het
Smarca5	A	T	8: 81,444,163 (GRCm39)	H534Q	probably damaging	Het
Son	T	G	16: 91,451,748 (GRCm39)	L165R	probably damaging	Het
Sox10	G	A	15: 79,040,421 (GRCm39)	P373L	probably benign	Het
Sp100	C	T	1: 85,608,860 (GRCm39)	R330*	probably null	Het
Srrm4	A	G	5: 116,584,570 (GRCm39)	L500P	probably damaging	Het
Tap1	T	C	17: 34,415,639 (GRCm39)	L689P	probably damaging	Het
Tfg	A	G	16: 56,525,972 (GRCm39)		probably null	Het
Tjp2	C	T	19: 24,088,886 (GRCm39)	V677I	probably benign	Het
Tmprss11g	T	G	5: 86,645,176 (GRCm39)	D85A	probably damaging	Het
Tnfsf9	T	C	17: 57,414,238 (GRCm39)	S222P	probably damaging	Het
Trank1	A	G	9: 111,193,824 (GRCm39)	N616S	probably damaging	Het
Tubgcp6	C	A	15: 89,004,728 (GRCm39)	W297L	probably damaging	Het
Twist1	T	C	12: 34,008,355 (GRCm39)	S127P	probably damaging	Het
Ubr4	T	C	4: 139,179,966 (GRCm39)	I247T	unknown	Het
Ubr5	G	A	15: 37,988,481 (GRCm39)	T2153M		Het
Utrn	A	G	10: 12,573,833 (GRCm39)	V1079A	probably benign	Het
Vcan	T	C	13: 89,852,237 (GRCm39)	T908A	probably damaging	Het
Vmn2r104	A	G	17: 20,249,791 (GRCm39)	F827L	probably damaging	Het
Vmn2r111	T	A	17: 22,767,380 (GRCm39)	T706S	probably benign	Het
Vmn2r114	T	C	17: 23,527,035 (GRCm39)	D499G	probably null	Het
Vmn2r92	T	C	17: 18,391,533 (GRCm39)	S512P	probably damaging	Het
Vps4b	A	T	1: 106,708,232 (GRCm39)		probably null	Het
Vwa8	A	C	14: 79,219,674 (GRCm39)		probably null	Het
Wnt10b	T	C	15: 98,672,045 (GRCm39)	Q224R	probably benign	Het
Ylpm1	C	T	12: 85,077,268 (GRCm39)	P1331L	possibly damaging	Het
Zfhx4	G	A	3: 5,307,267 (GRCm39)	M164I	possibly damaging	Het
Zfp51	A	G	17: 21,683,762 (GRCm39)	T126A	probably benign	Het
Zfp609	A	G	9: 65,613,418 (GRCm39)	V339A	probably benign	Het
Zfp687	C	T	3: 94,914,841 (GRCm39)	R1220H	probably damaging	Het
Zfyve21	C	T	12: 111,790,249 (GRCm39)	L84F	probably damaging	Het

Other mutations in Sema3a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01022:Sema3a	APN	5	13,523,433 (GRCm39)	missense	probably damaging	1.00
IGL01783:Sema3a	APN	5	13,611,767 (GRCm39)	missense	probably damaging	1.00
IGL02423:Sema3a	APN	5	13,615,776 (GRCm39)	missense	probably damaging	1.00
IGL02728:Sema3a	APN	5	13,615,881 (GRCm39)	missense	probably damaging	1.00
IGL02739:Sema3a	APN	5	13,501,128 (GRCm39)	missense	probably damaging	1.00
IGL02987:Sema3a	APN	5	13,615,863 (GRCm39)	missense	probably damaging	1.00
IGL03106:Sema3a	APN	5	13,649,456 (GRCm39)	missense	probably damaging	1.00
R0055:Sema3a	UTSW	5	13,450,004 (GRCm39)	missense	possibly damaging	0.92
R0334:Sema3a	UTSW	5	13,607,268 (GRCm39)	missense	probably damaging	0.99
R0684:Sema3a	UTSW	5	13,606,494 (GRCm39)	critical splice acceptor site	probably null
R0750:Sema3a	UTSW	5	13,607,092 (GRCm39)	critical splice donor site	probably null
R1204:Sema3a	UTSW	5	13,573,142 (GRCm39)	critical splice donor site	probably benign
R1221:Sema3a	UTSW	5	13,566,190 (GRCm39)	missense	probably benign
R1484:Sema3a	UTSW	5	13,523,407 (GRCm39)	missense	probably damaging	1.00
R1663:Sema3a	UTSW	5	13,607,092 (GRCm39)	critical splice donor site	probably null
R2079:Sema3a	UTSW	5	13,501,098 (GRCm39)	missense	possibly damaging	0.95
R4165:Sema3a	UTSW	5	13,523,364 (GRCm39)	critical splice acceptor site	probably null
R4596:Sema3a	UTSW	5	13,620,125 (GRCm39)	missense	probably damaging	1.00
R4867:Sema3a	UTSW	5	13,501,208 (GRCm39)	missense	probably benign	0.05
R4904:Sema3a	UTSW	5	13,631,066 (GRCm39)	missense	probably damaging	1.00
R5107:Sema3a	UTSW	5	13,627,572 (GRCm39)	nonsense	probably null
R5327:Sema3a	UTSW	5	13,649,357 (GRCm39)	missense	probably benign	0.25
R5343:Sema3a	UTSW	5	13,523,373 (GRCm39)	missense	probably damaging	1.00
R5430:Sema3a	UTSW	5	13,615,730 (GRCm39)	missense	probably damaging	0.97
R5604:Sema3a	UTSW	5	13,523,487 (GRCm39)	critical splice donor site	probably null
R5774:Sema3a	UTSW	5	13,573,131 (GRCm39)	missense	probably damaging	1.00
R6057:Sema3a	UTSW	5	13,615,832 (GRCm39)	missense	probably damaging	1.00
R6110:Sema3a	UTSW	5	13,630,969 (GRCm39)	missense	probably damaging	1.00
R6132:Sema3a	UTSW	5	13,573,142 (GRCm39)	critical splice donor site	probably null
R6310:Sema3a	UTSW	5	13,606,986 (GRCm39)	missense	probably damaging	1.00
R6754:Sema3a	UTSW	5	13,649,243 (GRCm39)	missense	possibly damaging	0.94
R6788:Sema3a	UTSW	5	13,647,584 (GRCm39)	missense	possibly damaging	0.95
R6878:Sema3a	UTSW	5	13,505,511 (GRCm39)	missense	possibly damaging	0.88
R7411:Sema3a	UTSW	5	13,566,230 (GRCm39)	nonsense	probably null
R7501:Sema3a	UTSW	5	13,607,008 (GRCm39)	missense	probably damaging	1.00
R7531:Sema3a	UTSW	5	13,615,805 (GRCm39)	missense	probably damaging	1.00
R7538:Sema3a	UTSW	5	13,611,787 (GRCm39)	missense	probably benign	0.42
R7970:Sema3a	UTSW	5	13,649,375 (GRCm39)	missense	possibly damaging	0.93
R8121:Sema3a	UTSW	5	13,649,215 (GRCm39)	missense	probably damaging	1.00
R8283:Sema3a	UTSW	5	13,450,030 (GRCm39)	missense	probably damaging	0.98
R8434:Sema3a	UTSW	5	13,523,487 (GRCm39)	critical splice donor site	probably null
R8918:Sema3a	UTSW	5	13,573,099 (GRCm39)	missense	probably damaging	1.00
R9500:Sema3a	UTSW	5	13,615,854 (GRCm39)	missense	possibly damaging	0.88
X0064:Sema3a	UTSW	5	13,631,066 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGCTTTTAGGACCCAAGGATG -3'
(R):5'- TTCTCACACCCACAGTCATG -3'

Sequencing Primer
(F):5'- GCTTTTAGGACCCAAGGATGAAATAC -3'
(R):5'- TGACACCACCACCATTATCTTAACAG -3'

Posted On

2019-10-17