Mutagenetix > Incidental Mutation

Incidental Mutation 'R5686:Lrp3'

443360

Institutional Source

Beutler Lab

Gene Symbol

Lrp3

Ensembl Gene

ENSMUSG00000001802

Gene Name

low density lipoprotein receptor-related protein 3

Synonyms

MMRRC Submission

043319-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.107) question?

Stock #

R5686 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

35200027-35215498 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 35203485 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 479 (T479S)

Ref Sequence

ENSEMBL: ENSMUSP00000114026 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001854] [ENSMUST00000118444] [ENSMUST00000122409] [ENSMUST00000131048]

AlphaFold

E9Q1T6

Predicted Effect

probably benign
Transcript: ENSMUST00000001854

SMART Domains

Protein: ENSMUSP00000001854
Gene: ENSMUSG00000030495

Domain	Start	End	E-Value	Type
low complexity region	14	37	N/A	INTRINSIC
Pfam:AA_permease_2	46	474	4.8e-65	PFAM
Pfam:AA_permease	51	467	9.3e-37	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000118444
AA Change: T458S

PolyPhen 2 Score 0.831 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000113406
Gene: ENSMUSG00000001802
AA Change: T458S

Domain	Start	End	E-Value	Type
signal peptide	1	35	N/A	INTRINSIC
CUB	43	159	9.97e-20	SMART
LDLa	165	202	7.21e-11	SMART
LDLa	211	251	1.37e-11	SMART
CUB	254	365	1.98e-3	SMART
LDLa	367	414	1.85e-1	SMART
LDLa	415	453	4.44e-3	SMART
LDLa	454	490	8.74e-10	SMART
transmembrane domain	497	519	N/A	INTRINSIC
low complexity region	584	606	N/A	INTRINSIC
low complexity region	641	652	N/A	INTRINSIC
low complexity region	674	684	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000122409
AA Change: T479S

PolyPhen 2 Score 0.843 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000114026
Gene: ENSMUSG00000001802
AA Change: T479S

Domain	Start	End	E-Value	Type
signal peptide	1	35	N/A	INTRINSIC
CUB	64	180	9.97e-20	SMART
LDLa	186	223	7.21e-11	SMART
LDLa	232	272	1.37e-11	SMART
CUB	275	386	1.98e-3	SMART
LDLa	388	435	1.85e-1	SMART
LDLa	436	474	4.44e-3	SMART
LDLa	475	511	8.74e-10	SMART
transmembrane domain	518	540	N/A	INTRINSIC
low complexity region	605	627	N/A	INTRINSIC
low complexity region	662	673	N/A	INTRINSIC
low complexity region	695	705	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000131048

SMART Domains

Protein: ENSMUSP00000118331
Gene: ENSMUSG00000030495

Domain	Start	End	E-Value	Type
low complexity region	14	37	N/A	INTRINSIC
Pfam:AA_permease_2	46	346	8.6e-48	PFAM
Pfam:AA_permease	51	346	1e-28	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000146959

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153163

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155404

Meta Mutation Damage Score

0.0835

Coding Region Coverage

1x: 99.4%
3x: 98.7%
10x: 97.2%
20x: 95.1%

Validation Efficiency

97% (73/75)

Allele List at MGI

Other mutations in this stock

Total: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210408I21Rik	A	G	13: 77,303,314	E839G	possibly damaging	Het
2410141K09Rik	T	C	13: 66,431,663	R254G	probably benign	Het
4932438A13Rik	T	A	3: 36,917,660	F514Y	probably benign	Het
Adgrf3	T	A	5: 30,197,306	T575S	probably damaging	Het
Akap9	T	A	5: 3,971,926	C1158S	probably benign	Het
Arhgap39	A	G	15: 76,726,633	F926L	probably damaging	Het
BC035947	G	T	1: 78,497,930	T655K	probably benign	Het
Bcas1	T	C	2: 170,406,810	T64A	probably benign	Het
Brca2	A	G	5: 150,540,904	K1378E	probably benign	Het
Card6	A	T	15: 5,100,953	N320K	probably damaging	Het
Ccdc3	A	T	2: 5,138,060	I43F	probably damaging	Het
Cd200r1	T	C	16: 44,790,164	S212P	probably damaging	Het
Cdh8	T	C	8: 99,033,222	I632V	probably benign	Het
Col25a1	A	G	3: 130,564,154	E477G	probably damaging	Het
Cpne5	A	T	17: 29,184,017	C215S	possibly damaging	Het
Crim1	T	A	17: 78,374,083	S989T	possibly damaging	Het
Dnhd1	G	A	7: 105,703,209	R2523Q	probably damaging	Het
Dync1h1	T	A	12: 110,616,404	N340K	probably benign	Het
Eif4e2	G	A	1: 87,226,238		probably null	Het
Ephb6	G	T	6: 41,619,704	R895L	possibly damaging	Het
Esrrg	T	A	1: 188,150,198	H217Q	probably benign	Het
Fgl1	T	A	8: 41,200,557	K100*	probably null	Het
Flt4	T	C	11: 49,630,603	V450A	probably benign	Het
G6pc2	A	T	2: 69,220,784	I74L	probably benign	Het
Gabrr1	T	C	4: 33,161,684	M336T	probably damaging	Het
Gli1	T	A	10: 127,337,436	T118S	probably benign	Het
Gm5435	A	T	12: 82,496,026		noncoding transcript	Het
Got1l1	A	G	8: 27,198,059	L314P	probably damaging	Het
Hk3	T	A	13: 55,006,813	I740F	probably damaging	Het
Htr7	C	A	19: 35,969,871	A248S	probably damaging	Het
Igsf9b	A	G	9: 27,324,179	T508A	probably damaging	Het
Il16	T	A	7: 83,648,728	N431I	probably benign	Het
Lax1	G	A	1: 133,680,176	P276S	probably damaging	Het
Lrp2	A	T	2: 69,511,061	V925E	possibly damaging	Het
Metrn	G	A	17: 25,795,217	R212C	probably damaging	Het
Mlip	A	C	9: 77,347,693		probably null	Het
Mmp24	C	T	2: 155,799,777	T175I	probably damaging	Het
N6amt1	A	T	16: 87,354,335	D28V	probably damaging	Het
Olfr1289	G	A	2: 111,484,143	G238R	probably damaging	Het
Olfr215	T	C	6: 116,582,929	T6A	probably benign	Het
Olfr380	A	T	11: 73,453,851	Y120*	probably null	Het
Olfr472	A	G	7: 107,902,912	H65R	probably damaging	Het
Olfr490	G	T	7: 108,286,742	A128E	probably damaging	Het
Olfr870	T	A	9: 20,170,969	I201F	possibly damaging	Het
Pcdh17	T	A	14: 84,532,993	N970K	probably damaging	Het
Pdzrn3	T	C	6: 101,151,428	Y759C	probably damaging	Het
Pkd2l2	T	C	18: 34,425,237	L323P	probably damaging	Het
Psg21	G	T	7: 18,652,258		probably benign	Het
Rest	T	C	5: 77,281,726	V664A	probably benign	Het
Sco2	G	A	15: 89,371,972	R160*	probably null	Het
Sfswap	T	A	5: 129,514,818	S300T	probably damaging	Het
Slc5a10	A	T	11: 61,678,566	M329K	probably benign	Het
Slco1a5	G	A	6: 142,236,307	P564S	probably damaging	Het
Stk38	A	G	17: 28,982,129	F191S	probably damaging	Het
Svep1	T	A	4: 58,072,826	Y2161F	possibly damaging	Het
Tada2a	G	A	11: 84,079,602	T441M	possibly damaging	Het
Tg	T	A	15: 66,688,889	N1033K	probably benign	Het
Thoc3	A	T	13: 54,467,873	I126N	probably damaging	Het
Tnc	T	C	4: 64,007,730		probably null	Het
Tnc	A	T	4: 64,008,795	D831E	possibly damaging	Het
Uhmk1	A	T	1: 170,211,218	V100E	probably damaging	Het
Usp43	G	A	11: 67,921,916		probably benign	Het
Vmn2r90	A	T	17: 17,713,450	Y424F	probably benign	Het
Vps33a	C	T	5: 123,547,001		probably null	Het
Xirp2	A	T	2: 67,482,298	K37I	probably damaging	Het
Zfp106	A	T	2: 120,533,507		probably null	Het
Zfp748	A	T	13: 67,542,528	C204*	probably null	Het

Other mutations in Lrp3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00656:Lrp3	APN	7	35206028	splice site	probably benign
IGL01714:Lrp3	APN	7	35206071	splice site	probably null
IGL03033:Lrp3	APN	7	35202627	missense	possibly damaging	0.61
IGL03166:Lrp3	APN	7	35202480	missense	probably benign	0.00
Blackball	UTSW	7	35206052	missense	probably damaging	1.00
lowball	UTSW	7	35204168	missense	probably benign	0.00
PIT4434001:Lrp3	UTSW	7	35203995	missense	probably damaging	0.99
R0416:Lrp3	UTSW	7	35202353	missense	probably benign
R0733:Lrp3	UTSW	7	35202120	missense	possibly damaging	0.93
R0907:Lrp3	UTSW	7	35203293	missense	probably damaging	0.99
R1437:Lrp3	UTSW	7	35213170	missense	probably damaging	1.00
R1591:Lrp3	UTSW	7	35202365	missense	probably benign	0.03
R1625:Lrp3	UTSW	7	35203925	missense	probably damaging	1.00
R1703:Lrp3	UTSW	7	35213161	missense	possibly damaging	0.95
R3976:Lrp3	UTSW	7	35204105	missense	probably benign	0.06
R4196:Lrp3	UTSW	7	35203410	missense	probably damaging	1.00
R4679:Lrp3	UTSW	7	35203940	missense	probably damaging	1.00
R5836:Lrp3	UTSW	7	35203322	missense	probably damaging	1.00
R6160:Lrp3	UTSW	7	35204123	missense	possibly damaging	0.79
R6342:Lrp3	UTSW	7	35202306	missense	probably benign	0.01
R6364:Lrp3	UTSW	7	35203709	missense	probably benign	0.03
R6415:Lrp3	UTSW	7	35204168	missense	probably benign	0.00
R6502:Lrp3	UTSW	7	35203988	missense	possibly damaging	0.89
R6747:Lrp3	UTSW	7	35211437	missense	probably benign
R7205:Lrp3	UTSW	7	35202626	missense	probably damaging	0.99
R7232:Lrp3	UTSW	7	35206052	missense	probably damaging	1.00
R7522:Lrp3	UTSW	7	35204330	missense	probably damaging	0.99
R7870:Lrp3	UTSW	7	35211497	missense	probably damaging	0.99
R7963:Lrp3	UTSW	7	35202979	nonsense	probably null
R9094:Lrp3	UTSW	7	35203757	missense	probably damaging	1.00
R9242:Lrp3	UTSW	7	35202509	missense	probably benign	0.01
R9474:Lrp3	UTSW	7	35204064	missense	probably damaging	1.00
Z1177:Lrp3	UTSW	7	35203012	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- GGCAATAACAAGCAGCAGTC -3'
(R):5'- ATACCAGGTGAAGGGCTACTGC -3'

Sequencing Primer
(F):5'- TCCGCATACTAGGCTGCCAATG -3'
(R):5'- ACAACGCTGTGATGGCTG -3'

Posted On

2016-11-09