Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02365:Vldlr'

290696

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Vldlr

Ensembl Gene

ENSMUSG00000024924

Gene Name

very low density lipoprotein receptor

Synonyms

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.285) question?

Stock #

IGL02365

Quality Score

Status

Chromosome

Chromosomal Location

27193884-27231631 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 27223025 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 732 (Y732C)

Ref Sequence

ENSEMBL: ENSMUSP00000127329 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025866] [ENSMUST00000047645] [ENSMUST00000165761] [ENSMUST00000167487] [ENSMUST00000172302]

AlphaFold

P98156

Predicted Effect

probably benign
Transcript: ENSMUST00000025866

SMART Domains

Protein: ENSMUSP00000025866
Gene: ENSMUSG00000024924

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
EGF_like	32	68	7.38e1	SMART
LDLa	32	69	1.69e-16	SMART
LDLa	71	110	5.81e-15	SMART
LDLa	112	151	1.96e-12	SMART
LDLa	153	190	7.15e-15	SMART
LDLa	192	231	1.23e-13	SMART
LDLa	238	275	1.1e-15	SMART
LDLa	277	314	1.13e-12	SMART
LDLa	317	357	3.86e-11	SMART
EGF_CA	356	395	1e-5	SMART
EGF_CA	396	435	6.1e-10	SMART
Blast:LY	461	495	4e-15	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000047645
AA Change: Y691C

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000049145
Gene: ENSMUSG00000024924
AA Change: Y691C

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
EGF_like	32	68	7.38e1	SMART
LDLa	32	69	1.69e-16	SMART
LDLa	71	110	1.25e-14	SMART
LDLa	112	149	7.15e-15	SMART
LDLa	151	190	1.23e-13	SMART
LDLa	197	234	1.1e-15	SMART
LDLa	236	273	1.13e-12	SMART
LDLa	276	316	3.86e-11	SMART
EGF_CA	315	354	1e-5	SMART
EGF_CA	355	394	6.1e-10	SMART
LY	420	462	2.16e-1	SMART
LY	464	506	9.54e-12	SMART
LY	507	550	2.22e-12	SMART
LY	551	593	1.66e-11	SMART
LY	594	637	5.97e-4	SMART
EGF	664	709	2.16e-1	SMART
transmembrane domain	728	750	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000164509

Predicted Effect

probably benign
Transcript: ENSMUST00000165761

SMART Domains

Protein: ENSMUSP00000130382
Gene: ENSMUSG00000024924

Domain	Start	End	E-Value	Type
LDLa	1	26	1.58e0	SMART
EGF	28	64	4e-5	SMART
LY	88	130	2.16e-1	SMART
LY	132	174	9.54e-12	SMART
LY	175	218	2.22e-12	SMART
LY	219	258	3.25e-5	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000167487
AA Change: Y732C

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000127329
Gene: ENSMUSG00000024924
AA Change: Y732C

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
EGF_like	32	68	7.38e1	SMART
LDLa	32	69	1.69e-16	SMART
LDLa	71	110	5.81e-15	SMART
LDLa	112	151	1.96e-12	SMART
LDLa	153	190	7.15e-15	SMART
LDLa	192	231	1.23e-13	SMART
LDLa	238	275	1.1e-15	SMART
LDLa	277	314	1.13e-12	SMART
LDLa	317	357	3.86e-11	SMART
EGF_CA	356	395	1e-5	SMART
EGF_CA	396	435	6.1e-10	SMART
LY	461	503	2.16e-1	SMART
LY	505	547	9.54e-12	SMART
LY	548	591	2.22e-12	SMART
LY	592	634	1.66e-11	SMART
LY	635	678	5.97e-4	SMART
EGF	705	750	2.16e-1	SMART
transmembrane domain	797	819	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000172302
AA Change: Y732C

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000126730
Gene: ENSMUSG00000024924
AA Change: Y732C

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
EGF_like	32	68	7.38e1	SMART
LDLa	32	69	1.69e-16	SMART
LDLa	71	110	5.81e-15	SMART
LDLa	112	151	1.96e-12	SMART
LDLa	153	190	7.15e-15	SMART
LDLa	192	231	1.23e-13	SMART
LDLa	238	275	1.1e-15	SMART
LDLa	277	314	1.13e-12	SMART
LDLa	317	357	3.86e-11	SMART
EGF_CA	356	395	1e-5	SMART
EGF_CA	396	435	6.1e-10	SMART
LY	461	503	2.16e-1	SMART
LY	505	547	9.54e-12	SMART
LY	548	591	2.22e-12	SMART
LY	592	634	1.66e-11	SMART
LY	635	678	5.97e-4	SMART
EGF	705	750	2.16e-1	SMART
transmembrane domain	769	791	N/A	INTRINSIC

Coding Region Coverage

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. This gene encodes a lipoprotein receptor that is a member of the LDLR family and plays important roles in VLDL-triglyceride metabolism and the reelin signaling pathway. Mutations in this gene cause VLDLR-associated cerebellar hypoplasia. Alternative splicing generates multiple transcript variants encoding distinct isoforms for this gene. [provided by RefSeq, Aug 2009]
PHENOTYPE: Homozygous null mutants exhibit modest reductions in body weight and adiposity. In behavioral tests, mutants display deficits in contextual fear conditioning and long term potentiation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 38 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acyp2	A	T	11: 30,599,318 (GRCm39)	V21E	probably damaging	Het
Adgrl3	A	G	5: 81,660,428 (GRCm39)	D331G	probably damaging	Het
Arfgef1	A	T	1: 10,270,108 (GRCm39)	I347N	probably benign	Het
Bfsp1	T	G	2: 143,668,656 (GRCm39)	E647A	probably damaging	Het
Bhmt	A	T	13: 93,754,146 (GRCm39)	N354K	probably benign	Het
Brinp3	A	T	1: 146,776,860 (GRCm39)	T436S	probably benign	Het
Capza1b	T	C	X: 168,559,526 (GRCm39)	N272D	probably benign	Het
Cog7	C	A	7: 121,576,959 (GRCm39)	M66I	possibly damaging	Het
Csf2rb2	A	T	15: 78,171,260 (GRCm39)	M333K	possibly damaging	Het
Cyp2u1	A	G	3: 131,091,878 (GRCm39)	V214A	probably damaging	Het
Dcaf5	A	T	12: 80,445,547 (GRCm39)	H177Q	probably benign	Het
Dchs1	T	C	7: 105,404,395 (GRCm39)	T2716A	probably benign	Het
Dsc1	T	C	18: 20,241,873 (GRCm39)	Q156R	probably damaging	Het
Dspp	G	T	5: 104,323,927 (GRCm39)	G357W	probably damaging	Het
Efr3b	C	T	12: 4,033,391 (GRCm39)	V139I	probably benign	Het
Fto	T	G	8: 92,195,003 (GRCm39)	S265R	probably damaging	Het
Gphb5	A	G	12: 75,462,591 (GRCm39)		probably benign	Het
Iars1	T	C	13: 49,844,975 (GRCm39)	V162A	probably benign	Het
Klk13	A	C	7: 43,373,290 (GRCm39)	K107T	possibly damaging	Het
Kpna7	T	A	5: 144,922,543 (GRCm39)	D507V	possibly damaging	Het
Lamb1	A	T	12: 31,368,344 (GRCm39)	E1158V	probably damaging	Het
Lonp2	A	T	8: 87,442,993 (GRCm39)	D818V	possibly damaging	Het
Med15	A	G	16: 17,489,470 (GRCm39)		probably benign	Het
Or5p51	T	A	7: 107,444,119 (GRCm39)	N274Y	probably damaging	Het
Or6c69b	T	C	10: 129,627,404 (GRCm39)	D18G	possibly damaging	Het
Or8g52	A	T	9: 39,630,970 (GRCm39)	Y149F	possibly damaging	Het
Or8g52	G	A	9: 39,631,396 (GRCm39)	S291N	probably damaging	Het
Plpbp	A	G	8: 27,535,952 (GRCm39)	I82V	probably benign	Het
Ptprcap	A	G	19: 4,206,267 (GRCm39)	I117V	probably benign	Het
Rhox12	T	A	X: 37,196,758 (GRCm39)	D88V	possibly damaging	Het
Rnpc3	A	G	3: 113,402,048 (GRCm39)	S500P	probably damaging	Het
Sdhd	A	T	9: 50,510,125 (GRCm39)	Y84N	possibly damaging	Het
Sema6d	G	A	2: 124,498,788 (GRCm39)	V233I	probably benign	Het
Vegfb	A	T	19: 6,962,855 (GRCm39)	I140N	probably benign	Het
Vmn2r17	T	A	5: 109,601,175 (GRCm39)	F824L	probably damaging	Het
Xdh	A	T	17: 74,250,885 (GRCm39)	N22K	probably benign	Het
Zc3h11a	A	C	1: 133,565,151 (GRCm39)	N249K	probably benign	Het
Zwilch	T	A	9: 64,068,206 (GRCm39)	D203V	probably damaging	Het

Other mutations in Vldlr

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01346:Vldlr	APN	19	27,217,081 (GRCm39)	missense	possibly damaging	0.93
IGL01575:Vldlr	APN	19	27,224,031 (GRCm39)	missense	probably benign
IGL01626:Vldlr	APN	19	27,221,173 (GRCm39)	missense	probably damaging	1.00
IGL02213:Vldlr	APN	19	27,218,726 (GRCm39)	missense	probably benign	0.09
IGL02488:Vldlr	APN	19	27,215,675 (GRCm39)	missense	probably damaging	1.00
IGL02708:Vldlr	APN	19	27,215,485 (GRCm39)	missense	possibly damaging	0.92
IGL02947:Vldlr	APN	19	27,217,120 (GRCm39)	missense	probably benign	0.03
disturbed	UTSW	19	27,216,204 (GRCm39)	nonsense	probably null
r26	UTSW	19	27,223,054 (GRCm39)	missense	probably damaging	0.99
spotty	UTSW	19	27,216,192 (GRCm39)	missense	probably damaging	1.00
PIT4142001:Vldlr	UTSW	19	27,212,269 (GRCm39)	missense	probably benign	0.05
R0195:Vldlr	UTSW	19	27,215,786 (GRCm39)	missense	probably damaging	1.00
R0288:Vldlr	UTSW	19	27,218,051 (GRCm39)	splice site	probably benign
R0536:Vldlr	UTSW	19	27,217,364 (GRCm39)	missense	probably damaging	1.00
R0537:Vldlr	UTSW	19	27,225,318 (GRCm39)	missense	probably damaging	1.00
R0542:Vldlr	UTSW	19	27,213,655 (GRCm39)	missense	probably benign	0.01
R0594:Vldlr	UTSW	19	27,212,219 (GRCm39)	missense	probably damaging	1.00
R0624:Vldlr	UTSW	19	27,215,663 (GRCm39)	missense	possibly damaging	0.91
R0726:Vldlr	UTSW	19	27,215,786 (GRCm39)	missense	probably damaging	1.00
R1017:Vldlr	UTSW	19	27,218,733 (GRCm39)	missense	probably damaging	1.00
R1148:Vldlr	UTSW	19	27,218,691 (GRCm39)	missense	probably benign	0.01
R1148:Vldlr	UTSW	19	27,218,691 (GRCm39)	missense	probably benign	0.01
R1443:Vldlr	UTSW	19	27,217,121 (GRCm39)	missense	possibly damaging	0.91
R1493:Vldlr	UTSW	19	27,218,691 (GRCm39)	missense	probably benign	0.01
R1520:Vldlr	UTSW	19	27,224,466 (GRCm39)	missense	possibly damaging	0.96
R1520:Vldlr	UTSW	19	27,217,943 (GRCm39)	missense	probably damaging	0.99
R1657:Vldlr	UTSW	19	27,223,070 (GRCm39)	missense	probably benign	0.00
R1901:Vldlr	UTSW	19	27,218,709 (GRCm39)	missense	probably damaging	1.00
R2047:Vldlr	UTSW	19	27,212,238 (GRCm39)	missense	probably damaging	1.00
R2258:Vldlr	UTSW	19	27,215,786 (GRCm39)	missense	probably damaging	1.00
R2273:Vldlr	UTSW	19	27,225,415 (GRCm39)	missense	probably damaging	1.00
R2423:Vldlr	UTSW	19	27,213,688 (GRCm39)	missense	possibly damaging	0.49
R3196:Vldlr	UTSW	19	27,220,554 (GRCm39)	missense	probably damaging	0.98
R3752:Vldlr	UTSW	19	27,215,731 (GRCm39)	missense	probably damaging	1.00
R3801:Vldlr	UTSW	19	27,195,021 (GRCm39)	missense	probably damaging	0.99
R3835:Vldlr	UTSW	19	27,212,214 (GRCm39)	missense	probably damaging	1.00
R4027:Vldlr	UTSW	19	27,215,713 (GRCm39)	missense	probably benign
R4301:Vldlr	UTSW	19	27,215,802 (GRCm39)	missense	possibly damaging	0.80
R4470:Vldlr	UTSW	19	27,212,219 (GRCm39)	missense	probably damaging	0.96
R4541:Vldlr	UTSW	19	27,216,192 (GRCm39)	missense	probably damaging	1.00
R4765:Vldlr	UTSW	19	27,217,947 (GRCm39)	missense	probably damaging	1.00
R4771:Vldlr	UTSW	19	27,217,290 (GRCm39)	missense	probably damaging	0.97
R4795:Vldlr	UTSW	19	27,216,252 (GRCm39)	splice site	probably null
R4839:Vldlr	UTSW	19	27,215,465 (GRCm39)	missense	probably damaging	1.00
R5074:Vldlr	UTSW	19	27,215,677 (GRCm39)	missense	probably damaging	1.00
R5134:Vldlr	UTSW	19	27,216,212 (GRCm39)	nonsense	probably null
R5281:Vldlr	UTSW	19	27,221,631 (GRCm39)	missense	probably benign	0.44
R5466:Vldlr	UTSW	19	27,217,243 (GRCm39)	critical splice acceptor site	probably null
R5514:Vldlr	UTSW	19	27,221,624 (GRCm39)	missense	probably damaging	0.97
R5886:Vldlr	UTSW	19	27,221,171 (GRCm39)	missense	probably benign	0.03
R5889:Vldlr	UTSW	19	27,217,064 (GRCm39)	missense	probably damaging	1.00
R6110:Vldlr	UTSW	19	27,215,477 (GRCm39)	missense	possibly damaging	0.92
R6343:Vldlr	UTSW	19	27,223,049 (GRCm39)	missense	probably damaging	0.99
R6833:Vldlr	UTSW	19	27,217,974 (GRCm39)	missense	probably damaging	1.00
R6838:Vldlr	UTSW	19	27,225,370 (GRCm39)	missense	probably damaging	1.00
R7169:Vldlr	UTSW	19	27,221,728 (GRCm39)	missense	probably benign
R7197:Vldlr	UTSW	19	27,212,241 (GRCm39)	missense	probably benign	0.36
R7304:Vldlr	UTSW	19	27,216,004 (GRCm39)	missense	possibly damaging	0.93
R7403:Vldlr	UTSW	19	27,213,674 (GRCm39)	nonsense	probably null
R7658:Vldlr	UTSW	19	27,220,536 (GRCm39)	missense	probably benign	0.33
R7754:Vldlr	UTSW	19	27,195,015 (GRCm39)	start codon destroyed	probably benign	0.01
R8105:Vldlr	UTSW	19	27,216,204 (GRCm39)	nonsense	probably null
R8377:Vldlr	UTSW	19	27,212,258 (GRCm39)	missense	probably damaging	1.00
R8529:Vldlr	UTSW	19	27,207,656 (GRCm39)	missense	probably benign	0.03
R8777:Vldlr	UTSW	19	27,217,946 (GRCm39)	missense	probably benign	0.00
R8777-TAIL:Vldlr	UTSW	19	27,217,946 (GRCm39)	missense	probably benign	0.00
R9380:Vldlr	UTSW	19	27,216,192 (GRCm39)	missense	possibly damaging	0.63
R9400:Vldlr	UTSW	19	27,216,175 (GRCm39)	missense	probably damaging	0.99
R9483:Vldlr	UTSW	19	27,224,031 (GRCm39)	missense	probably benign	0.00
R9502:Vldlr	UTSW	19	27,218,742 (GRCm39)	missense	probably damaging	1.00
R9509:Vldlr	UTSW	19	27,221,687 (GRCm39)	missense	probably benign	0.44
R9630:Vldlr	UTSW	19	27,207,623 (GRCm39)	missense	probably damaging	1.00
R9767:Vldlr	UTSW	19	27,212,274 (GRCm39)	missense	probably damaging	1.00
R9768:Vldlr	UTSW	19	27,218,720 (GRCm39)	missense	possibly damaging	0.47

Posted On

2015-04-16