Mutagenetix > Incidental Mutation

Incidental Mutation 'R6816:Sema3c'

537325

Institutional Source

Beutler Lab

Gene Symbol

Sema3c

Ensembl Gene

ENSMUSG00000028780

Gene Name

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

Synonyms

1110036B02Rik, Semae

MMRRC Submission

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R6816 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

17574281-17730268 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 17670465 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Alanine at position 40 (D40A)

Ref Sequence

ENSEMBL: ENSMUSP00000126614 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030568] [ENSMUST00000169603] [ENSMUST00000170181]

AlphaFold

Q62181

Predicted Effect

probably benign
Transcript: ENSMUST00000030568
AA Change: I155L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000030568
Gene: ENSMUSG00000028780
AA Change: I155L

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
Sema	54	495	1.16e-200	SMART
PSI	513	565	2.87e-13	SMART
IG	577	662	7.08e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000169603
AA Change: I153L

PolyPhen 2 Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000132330
Gene: ENSMUSG00000028780
AA Change: I153L

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
Pfam:Sema	54	226	9.6e-65	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000170181
AA Change: D40A

PolyPhen 2 Score 0.361 (Sensitivity: 0.90; Specificity: 0.89)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

Validation Efficiency

96% (49/51)

MGI Phenotype

PHENOTYPE: Mice homozygous for an ENU mutation exhibit perinatal lethality, hypopigmentation and abnormal heart development. Mice homozygous for a knock-out allele exhibit prenatal lethality associated with heart defects. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 49 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrg5	A	G	8: 94,941,683	T458A	probably damaging	Het
Ankrd36	T	G	11: 5,643,765	F457V	possibly damaging	Het
Cep152	T	C	2: 125,595,027	E531G	probably damaging	Het
Dpf1	A	C	7: 29,311,662	D162A	possibly damaging	Het
E2f8	A	T	7: 48,875,583	Y214N	possibly damaging	Het
Fer1l5	A	T	1: 36,406,510	Y786F	possibly damaging	Het
Fhod1	G	T	8: 105,330,544	Q933K	probably benign	Het
Gdap2	T	C	3: 100,191,705		probably null	Het
Gm6205	A	T	5: 94,683,914	Q260L	possibly damaging	Het
Gm996	C	CTCTA	2: 25,579,721		probably null	Het
Grin2d	A	G	7: 45,833,682		probably benign	Het
Hgs	T	A	11: 120,471,571	V112D	probably damaging	Het
Hist1h2bp	C	T	13: 21,787,777	S88L	probably benign	Het
Igf2r	A	T	17: 12,714,082	V851E	probably damaging	Het
Igfn1	T	A	1: 135,959,728	T2533S	probably benign	Het
Iqch	C	T	9: 63,480,759	V750I	probably benign	Het
Itih2	A	G	2: 10,105,706	Y525H	probably damaging	Het
Kcnu1	C	T	8: 25,937,734	Q360*	probably null	Het
Klk1b26	A	G	7: 44,016,868	N245S	probably benign	Het
Kmt2c	T	C	5: 25,405,532		probably null	Het
Lhpp	T	C	7: 132,634,033	S116P	probably benign	Het
Madcam1	A	G	10: 79,665,440	D113G	probably damaging	Het
Magi3	A	T	3: 104,089,911		probably null	Het
Map3k9	A	G	12: 81,722,254	S1007P	possibly damaging	Het
Mkrn2	C	T	6: 115,611,728	P144L	probably damaging	Het
Mon1a	T	C	9: 107,900,410	S171P	probably damaging	Het
Nrarp	T	C	2: 25,181,307	L66P	probably damaging	Het
P2ry1	T	A	3: 61,003,832	F131I	probably benign	Het
Pdzk1	A	G	3: 96,854,570	Q166R	probably benign	Het
Pigt	G	T	2: 164,501,132	V249F	probably damaging	Het
Ppp1r16b	G	T	2: 158,761,675	V407L	probably benign	Het
Rab6a	G	T	7: 100,629,873	E73D	probably damaging	Het
Ralb	C	A	1: 119,477,982	G33*	probably null	Het
Sema3b	T	A	9: 107,600,350	M491L	probably benign	Het
Slc22a1	T	C	17: 12,652,483	N464D	possibly damaging	Het
Spire2	T	A	8: 123,359,413	S295T	probably benign	Het
Stat3	T	G	11: 100,911,267	Q32P	probably damaging	Het
Sulf2	T	C	2: 166,082,754	T471A	probably benign	Het
Sult2b1	A	G	7: 45,733,678	W227R	probably damaging	Het
Syt2	T	A	1: 134,745,800	I294N	probably damaging	Het
Taar8b	A	T	10: 24,092,181	F38L	probably benign	Het
Tbl2	T	A	5: 135,159,215		probably null	Het
Tex48	G	A	4: 63,611,955	S9L	probably damaging	Het
Tmprss2	A	T	16: 97,568,467	M369K	possibly damaging	Het
Trip12	A	T	1: 84,793,714	S280T	probably damaging	Het
Tspoap1	T	C	11: 87,765,665	V263A	probably benign	Het
Vmn2r74	T	A	7: 85,961,413	R24*	probably null	Het
Wdr35	G	A	12: 9,027,724		probably null	Het
Zfp202	A	G	9: 40,211,813	R624G	probably damaging	Het

Other mutations in Sema3c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00559:Sema3c	APN	5	17694860	missense	probably damaging	1.00
IGL01528:Sema3c	APN	5	17714415	missense	probably benign
IGL01618:Sema3c	APN	5	17672506	missense	probably damaging	1.00
IGL01730:Sema3c	APN	5	17711436	missense	probably benign	0.01
IGL01762:Sema3c	APN	5	17694851	missense	possibly damaging	0.81
IGL02049:Sema3c	APN	5	17721925	splice site	probably benign
IGL02249:Sema3c	APN	5	17662963	missense	probably damaging	1.00
IGL02657:Sema3c	APN	5	17576868	start codon destroyed	possibly damaging	0.71
IGL02657:Sema3c	APN	5	17662974	missense	probably damaging	1.00
IGL03213:Sema3c	APN	5	17694639	splice site	probably benign
PIT4651001:Sema3c	UTSW	5	17694733	missense	probably benign	0.37
R0031:Sema3c	UTSW	5	17694728	missense	probably damaging	1.00
R0558:Sema3c	UTSW	5	17714415	missense	probably benign	0.00
R0964:Sema3c	UTSW	5	17721909	missense	probably damaging	1.00
R1164:Sema3c	UTSW	5	17678314	missense	probably benign	0.40
R1351:Sema3c	UTSW	5	17678336	missense	possibly damaging	0.60
R1368:Sema3c	UTSW	5	17678332	missense	possibly damaging	0.96
R1480:Sema3c	UTSW	5	17682031	missense	possibly damaging	0.57
R1880:Sema3c	UTSW	5	17727466	nonsense	probably null
R1916:Sema3c	UTSW	5	17727401	missense	probably benign	0.06
R3934:Sema3c	UTSW	5	17681940	missense	probably damaging	0.97
R4284:Sema3c	UTSW	5	17678347	missense	probably benign	0.01
R4449:Sema3c	UTSW	5	17576846	start gained	probably benign
R4545:Sema3c	UTSW	5	17694772	missense	probably benign	0.01
R4546:Sema3c	UTSW	5	17694772	missense	probably benign	0.01
R4660:Sema3c	UTSW	5	17672513	missense	probably damaging	1.00
R4890:Sema3c	UTSW	5	17675159	missense	probably benign	0.00
R4937:Sema3c	UTSW	5	17694686	missense	probably benign	0.01
R5065:Sema3c	UTSW	5	17727617	missense	possibly damaging	0.89
R5145:Sema3c	UTSW	5	17727617	missense	possibly damaging	0.89
R5452:Sema3c	UTSW	5	17717070	critical splice donor site	probably null
R5586:Sema3c	UTSW	5	17711424	missense	probably damaging	0.99
R5811:Sema3c	UTSW	5	17675190	splice site	probably null
R5886:Sema3c	UTSW	5	17681986	missense	possibly damaging	0.90
R6120:Sema3c	UTSW	5	17727632	missense	probably benign	0.00
R6191:Sema3c	UTSW	5	17653806	missense	probably damaging	1.00
R6318:Sema3c	UTSW	5	17672432	missense	probably damaging	0.96
R6416:Sema3c	UTSW	5	17576961	missense	probably damaging	0.99
R6441:Sema3c	UTSW	5	17724132	missense	possibly damaging	0.96
R7146:Sema3c	UTSW	5	17694703	missense	probably benign	0.22
R7526:Sema3c	UTSW	5	17727596	missense	possibly damaging	0.46
R7832:Sema3c	UTSW	5	17694847	missense	probably damaging	0.99
R8034:Sema3c	UTSW	5	17727482	missense	probably damaging	1.00
R8053:Sema3c	UTSW	5	17655022	missense	probably benign	0.00
R8076:Sema3c	UTSW	5	17727364	missense	probably benign	0.00
R8264:Sema3c	UTSW	5	17676539	intron	probably benign
R8359:Sema3c	UTSW	5	17653728	missense	possibly damaging	0.56
R8437:Sema3c	UTSW	5	17662938	missense	probably damaging	0.99
R9174:Sema3c	UTSW	5	17663041	critical splice donor site	probably null
R9295:Sema3c	UTSW	5	17727497	missense	probably benign	0.09
R9477:Sema3c	UTSW	5	17716983	missense
R9599:Sema3c	UTSW	5	17714454	critical splice donor site	probably null
R9702:Sema3c	UTSW	5	17653830	missense	probably damaging	1.00
Z1176:Sema3c	UTSW	5	17727519	missense	probably benign	0.04
Z1177:Sema3c	UTSW	5	17717031	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCTTCATAGAGGGCAATTAAGTC -3'
(R):5'- TACAGCACATTGAGAGATCCAC -3'

Sequencing Primer
(F):5'- AGGGCAATTAAGTCTTAATATAGCAC -3'
(R):5'- AACACACACTGATTCATGATCTTCTC -3'

Posted On

2018-10-18