Mutagenetix > Incidental Mutation

Incidental Mutation 'R6049:Pdzk1'

483431

Institutional Source

Beutler Lab

Gene Symbol

Pdzk1

Ensembl Gene

ENSMUSG00000038298

Gene Name

PDZ domain containing 1

Synonyms

Nherf3, 4921513F16Rik, mPDZK1, 1700023D20Rik, 2610507N21Rik, D3Ertd537e

MMRRC Submission

044217-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.149) question?

Stock #

R6049 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

96736772-96778242 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 96758979 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 128 (E128G)

Ref Sequence

ENSEMBL: ENSMUSP00000115584 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000058865] [ENSMUST00000107069] [ENSMUST00000107070] [ENSMUST00000128789] [ENSMUST00000135031] [ENSMUST00000138014] [ENSMUST00000153256]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000058865
AA Change: E128G

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

SMART Domains

Protein: ENSMUSP00000058936
Gene: ENSMUSG00000038298
AA Change: E128G

Domain	Start	End	E-Value	Type
PDZ	18	90	2.41e-17	SMART
PDZ	143	215	1e-14	SMART
PDZ	251	323	2.81e-18	SMART
PDZ	386	458	4.5e-17	SMART
low complexity region	505	514	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000107069
AA Change: E128G

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

SMART Domains

Protein: ENSMUSP00000102684
Gene: ENSMUSG00000038298
AA Change: E128G

Domain	Start	End	E-Value	Type
PDZ	18	90	2.41e-17	SMART
PDZ	143	215	1e-14	SMART
PDZ	251	323	2.81e-18	SMART
PDZ	386	458	4.5e-17	SMART
low complexity region	505	514	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000107070
AA Change: E128G

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

SMART Domains

Protein: ENSMUSP00000102685
Gene: ENSMUSG00000038298
AA Change: E128G

Domain	Start	End	E-Value	Type
PDZ	18	90	2.41e-17	SMART
PDZ	143	215	1e-14	SMART
PDZ	251	323	2.81e-18	SMART
PDZ	386	458	4.5e-17	SMART
low complexity region	505	514	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000128789

SMART Domains

Protein: ENSMUSP00000123166
Gene: ENSMUSG00000038298

Domain	Start	End	E-Value	Type
PDB:2EDZ\|A	1	50	3e-32	PDB
SCOP:d1qaua_	6	50	4e-12	SMART
Blast:PDZ	18	50	7e-17	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000135031

SMART Domains

Protein: ENSMUSP00000114157
Gene: ENSMUSG00000038298

Domain	Start	End	E-Value	Type
PDZ	18	90	2.41e-17	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000138014
AA Change: E128G

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000115584
Gene: ENSMUSG00000038298
AA Change: E128G

Domain	Start	End	E-Value	Type
PDZ	18	90	2.41e-17	SMART
PDB:2EEI\|A	125	153	2e-7	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000153256
AA Change: E128G

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

SMART Domains

Protein: ENSMUSP00000118846
Gene: ENSMUSG00000038298
AA Change: E128G

Domain	Start	End	E-Value	Type
PDZ	18	90	2.41e-17	SMART
PDZ	143	215	1e-14	SMART
PDZ	251	323	2.81e-18	SMART
PDZ	386	458	4.5e-17	SMART
low complexity region	505	514	N/A	INTRINSIC

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.1%
20x: 94.3%

Validation Efficiency

98% (60/61)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a PDZ domain-containing scaffolding protein. PDZ domain-containing molecules bind to and mediate the subcellular localization of target proteins. The encoded protein mediates the localization of cell surface proteins and plays a critical role in cholesterol metabolism by regulating the HDL receptor, scavenger receptor class B type 1. Single nucleotide polymorphisms in this gene may be associated with metabolic syndrome, and overexpression of this gene may play a role in drug resistance of multiple myeloma. Pseudogenes of this gene are located on the long arm of chromosome 1. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]
PHENOTYPE: Homozygous mutation of this gene results in increased serum cholesterol levels. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921539E11Rik	G	A	4: 103,088,520 (GRCm39)	H229Y	probably benign	Het
Aadacl2fm2	A	C	3: 59,659,570 (GRCm39)	D341A	probably damaging	Het
Abcd2	A	G	15: 91,062,439 (GRCm39)	F500L	probably benign	Het
Adgb	A	G	10: 10,253,770 (GRCm39)	L1190P	probably damaging	Het
Adgrv1	A	G	13: 81,545,473 (GRCm39)	V5604A	probably benign	Het
Ank2	T	A	3: 126,736,669 (GRCm39)	T3072S	possibly damaging	Het
Arhgap39	A	G	15: 76,611,601 (GRCm39)		probably null	Het
C6	T	C	15: 4,764,654 (GRCm39)	C117R	probably damaging	Het
Cacna1a	A	G	8: 85,365,475 (GRCm39)	E2206G	probably damaging	Het
Cd2bp2	A	T	7: 126,793,007 (GRCm39)	F338L	probably damaging	Het
Cemip2	A	T	19: 21,803,490 (GRCm39)	Q841L	probably benign	Het
Cngb1	T	C	8: 95,997,470 (GRCm39)	D575G	probably damaging	Het
Cplane2	T	A	4: 140,945,473 (GRCm39)	V108D	probably benign	Het
Crat	A	G	2: 30,293,553 (GRCm39)	F63S	probably damaging	Het
Crybg3	T	C	16: 59,364,417 (GRCm39)	T2402A	probably benign	Het
Ctsq	A	G	13: 61,186,572 (GRCm39)		probably null	Het
Cux1	T	C	5: 136,361,564 (GRCm39)	R248G	probably damaging	Het
D7Ertd443e	T	C	7: 133,899,961 (GRCm39)	H420R	probably benign	Het
Deup1	A	G	9: 15,472,552 (GRCm39)	F587L	possibly damaging	Het
Dnah6	T	C	6: 73,063,149 (GRCm39)	K2651R	probably benign	Het
Dnah7b	A	G	1: 46,124,762 (GRCm39)	I144V	probably benign	Het
Dnajc1	T	C	2: 18,236,511 (GRCm39)		probably null	Het
Fscb	T	C	12: 64,521,094 (GRCm39)	N124S	possibly damaging	Het
Gabbr2	A	G	4: 46,787,641 (GRCm39)	Y341H	probably damaging	Het
Greb1	T	A	12: 16,731,395 (GRCm39)	I1648F	probably damaging	Het
Hace1	A	T	10: 45,562,758 (GRCm39)	N758Y	probably damaging	Het
Irs2	A	C	8: 11,056,805 (GRCm39)	D542E	probably benign	Het
Kat6a	T	A	8: 23,429,053 (GRCm39)	H1469Q	possibly damaging	Het
Kif15	G	A	9: 122,840,687 (GRCm39)	R36K	probably damaging	Het
Krt42	C	T	11: 100,157,886 (GRCm39)	V193M	probably damaging	Het
Limch1	A	T	5: 67,188,203 (GRCm39)	E878V	probably benign	Het
Med18	G	T	4: 132,187,024 (GRCm39)	D158E	probably benign	Het
Med6	T	C	12: 81,638,097 (GRCm39)	N38S	probably damaging	Het
Mup13	T	C	4: 61,183,596 (GRCm39)	T76A	probably benign	Het
Nlrp4b	T	A	7: 10,448,640 (GRCm39)	L281*	probably null	Het
Or5h23	A	T	16: 58,906,509 (GRCm39)	C112*	probably null	Het
Or7g28	C	A	9: 19,272,640 (GRCm39)	G4*	probably null	Het
Or9r3	A	T	10: 129,948,481 (GRCm39)	H59Q	probably benign	Het
Pde4d	A	T	13: 109,169,119 (GRCm39)	R54*	probably null	Het
Pdpk1	A	T	17: 24,317,109 (GRCm39)	Y251*	probably null	Het
Phf12	A	G	11: 77,918,996 (GRCm39)		probably null	Het
Pnliprp2	A	G	19: 58,748,884 (GRCm39)	E63G	possibly damaging	Het
Prkcd	T	C	14: 30,329,254 (GRCm39)	E62G	possibly damaging	Het
Prl7b1	G	T	13: 27,790,161 (GRCm39)	D77E	probably benign	Het
Rbck1	G	T	2: 152,165,094 (GRCm39)	C85*	probably null	Het
Rfx3	A	T	19: 27,779,795 (GRCm39)	M481K	probably damaging	Het
Rmdn3	A	G	2: 118,983,906 (GRCm39)	F159L	probably damaging	Het
Rpusd3	A	C	6: 113,394,802 (GRCm39)		probably null	Het
Ska1	T	C	18: 74,335,671 (GRCm39)	T100A	probably benign	Het
Slc1a3	T	C	15: 8,675,177 (GRCm39)	E276G	probably damaging	Het
Slc27a6	T	A	18: 58,731,732 (GRCm39)	Y361N	probably damaging	Het
Smc1b	A	G	15: 85,005,896 (GRCm39)	L336S	probably damaging	Het
St7	A	G	6: 17,694,347 (GRCm39)	D46G	possibly damaging	Het
Supt5	A	G	7: 28,014,622 (GRCm39)	I1059T	probably benign	Het
Syne1	A	T	10: 5,297,926 (GRCm39)	S1124T	possibly damaging	Het
Szt2	A	G	4: 118,260,185 (GRCm39)	S54P	probably damaging	Het
Tanc2	G	A	11: 105,758,543 (GRCm39)	R768Q	probably damaging	Het
Tbc1d7	A	C	13: 43,312,836 (GRCm39)	M19R	probably damaging	Het
Tbpl2	T	C	2: 23,985,004 (GRCm39)	N47D	possibly damaging	Het
Tgfbr3	C	T	5: 107,266,351 (GRCm39)	A790T	probably damaging	Het
Tnr	T	C	1: 159,740,324 (GRCm39)	V1166A	probably damaging	Het
Ttn	G	A	2: 76,676,654 (GRCm39)		probably benign	Het

Other mutations in Pdzk1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00730:Pdzk1	APN	3	96,775,742 (GRCm39)	missense	probably benign
IGL01895:Pdzk1	APN	3	96,776,417 (GRCm39)	missense	possibly damaging	0.96
IGL01995:Pdzk1	APN	3	96,764,687 (GRCm39)	missense	probably benign	0.01
IGL02027:Pdzk1	APN	3	96,761,989 (GRCm39)	splice site	probably benign
R1762:Pdzk1	UTSW	3	96,758,889 (GRCm39)	missense	probably benign	0.01
R2044:Pdzk1	UTSW	3	96,763,164 (GRCm39)	splice site	probably benign
R4721:Pdzk1	UTSW	3	96,776,518 (GRCm39)	nonsense	probably null
R4831:Pdzk1	UTSW	3	96,775,751 (GRCm39)	missense	probably benign
R5070:Pdzk1	UTSW	3	96,757,637 (GRCm39)	missense	probably benign	0.05
R6020:Pdzk1	UTSW	3	96,775,742 (GRCm39)	missense	probably benign
R6816:Pdzk1	UTSW	3	96,761,886 (GRCm39)	missense	probably benign	0.13
R7065:Pdzk1	UTSW	3	96,775,748 (GRCm39)	missense	probably benign
R7134:Pdzk1	UTSW	3	96,763,246 (GRCm39)	missense	probably benign	0.16
R7779:Pdzk1	UTSW	3	96,764,589 (GRCm39)	missense	probably damaging	1.00
R8097:Pdzk1	UTSW	3	96,757,556 (GRCm39)	missense	probably benign	0.00
R8350:Pdzk1	UTSW	3	96,759,024 (GRCm39)	missense	probably benign	0.01
R8450:Pdzk1	UTSW	3	96,759,024 (GRCm39)	missense	probably benign	0.01
R8805:Pdzk1	UTSW	3	96,758,910 (GRCm39)	missense	possibly damaging	0.94
R9448:Pdzk1	UTSW	3	96,761,922 (GRCm39)	missense	probably damaging	1.00
R9718:Pdzk1	UTSW	3	96,763,174 (GRCm39)	missense
Z1088:Pdzk1	UTSW	3	96,761,873 (GRCm39)	missense	probably benign
Z1176:Pdzk1	UTSW	3	96,761,873 (GRCm39)	missense	probably benign
Z1177:Pdzk1	UTSW	3	96,761,873 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- ACGATGAGCATCTTCCTCCTG -3'
(R):5'- TGCGCATACGTAGCAACTG -3'

Sequencing Primer
(F):5'- ATCTTCCTCCTGCAGTTGATGTGG -3'
(R):5'- TACGTAGCAACTGCAGCG -3'

Posted On

2017-07-14