Mutagenetix > Incidental Mutation

Incidental Mutation 'R9768:Vldlr'

733386

Institutional Source

Beutler Lab

Gene Symbol

Vldlr

Ensembl Gene

ENSMUSG00000024924

Gene Name

very low density lipoprotein receptor

Synonyms

MMRRC Submission

Accession Numbers

Essential gene?

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

Stock #

R9768 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

27193884-27231631 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 27218720 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 524 (Y524H)

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: Y483H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000049145
Gene: ENSMUSG00000024924
AA Change: Y483H

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

probably damaging
Transcript: ENSMUST00000165761
AA Change: Y151H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000130382
Gene: ENSMUSG00000024924
AA Change: Y151H

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

possibly damaging
Transcript: ENSMUST00000167487
AA Change: Y524H

PolyPhen 2 Score 0.465 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000127329
Gene: ENSMUSG00000024924
AA Change: Y524H

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: Y524H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000126730
Gene: ENSMUSG00000024924
AA Change: Y524H

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

1x: 99.9%
3x: 99.8%
10x: 99.3%
20x: 98.2%

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: 31 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930524B15Rik	C	A	11: 31,915,770 (GRCm39)	F37L	probably benign	Het
Akna	T	C	4: 63,292,636 (GRCm39)	E1091G	probably benign	Het
Asxl3	A	G	18: 22,650,101 (GRCm39)	T697A	probably benign	Het
Cdk5r1	A	G	11: 80,368,414 (GRCm39)	Y27C	probably damaging	Het
Cdkl2	T	A	5: 92,165,244 (GRCm39)	I511L	probably benign	Het
Clp1	A	C	2: 84,556,477 (GRCm39)	M1R	probably null	Het
Csrnp1	A	C	9: 119,801,819 (GRCm39)	D413E	probably damaging	Het
Gbp2	T	C	3: 142,341,055 (GRCm39)	S479P	probably benign	Het
Il23r	A	G	6: 67,408,603 (GRCm39)	S413P	probably damaging	Het
Klb	G	T	5: 65,537,373 (GRCm39)	R901L	probably damaging	Het
Krt1	AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC	AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC	15: 101,758,813 (GRCm39)		probably benign	Het
Lta4h	G	A	10: 93,308,818 (GRCm39)	V373I	probably benign	Het
Map3k1	G	T	13: 111,904,630 (GRCm39)	Q385K	probably benign	Het
Mapk8ip2	A	T	15: 89,343,160 (GRCm39)	D634V	probably damaging	Het
Myocd	T	C	11: 65,078,217 (GRCm39)	E526G	probably damaging	Het
Nipal4	C	T	11: 46,041,473 (GRCm39)	V241M	probably damaging	Het
Nup188	T	A	2: 30,227,045 (GRCm39)	V1206E	probably damaging	Het
Pak6	A	G	2: 118,520,396 (GRCm39)	Y129C	probably damaging	Het
Pigp	T	A	16: 94,166,332 (GRCm39)	K125N	probably damaging	Het
Pmm1	G	A	15: 81,840,460 (GRCm39)	T95M	possibly damaging	Het
Prrt3	A	T	6: 113,474,032 (GRCm39)	N335K	probably damaging	Het
Rsrc2	T	C	5: 123,868,561 (GRCm39)	N361S	probably benign	Het
Slc45a1	T	C	4: 150,722,982 (GRCm39)	T301A	probably benign	Het
Spata19	A	C	9: 27,311,744 (GRCm39)	D121A	probably damaging	Het
Speg	T	A	1: 75,395,617 (GRCm39)	L1796*	probably null	Het
Stx2	A	G	5: 129,063,422 (GRCm39)	S288P	unknown	Het
Tlk1	C	T	2: 70,600,400 (GRCm39)	S93N	probably damaging	Het
Tmc8	A	G	11: 117,676,029 (GRCm39)	D256G	probably damaging	Het
Vmn1r168	T	C	7: 23,240,509 (GRCm39)	F122S	probably benign	Het
Vmn2r67	T	C	7: 84,802,037 (GRCm39)	N88S	probably benign	Het
Zhx1	A	G	15: 57,918,207 (GRCm39)	V13A	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
IGL02365:Vldlr	APN	19	27,223,025 (GRCm39)	missense	probably damaging	1.00
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

Predicted Primers

PCR Primer
(F):5'- GAATAATTTCTGTGCTGAGCGATG -3'
(R):5'- AAGCTCTCAACCTCTGTGGC -3'

Sequencing Primer
(F):5'- CCTAGAGTCTTTTCAGAGTAAAGTCC -3'
(R):5'- TCTGTGGCTTGCACCCAAAAAG -3'

Posted On

2022-11-14