Mutagenetix > Incidental Mutation

Incidental Mutation 'R4721:Pdzk1'

354444

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

041986-MU

Accession Numbers

Essential gene?

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

Stock #

R4721 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

96736772-96778242 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

G to T at 96776518 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Stop codon at position 493 (E493*)

Ref Sequence

ENSEMBL: ENSMUSP00000118846 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029738] [ENSMUST00000058865] [ENSMUST00000107069] [ENSMUST00000107070] [ENSMUST00000153256]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000029738

SMART Domains

Protein: ENSMUSP00000029738
Gene: ENSMUSG00000028096

Domain	Start	End	E-Value	Type
transmembrane domain	4	26	N/A	INTRINSIC
transmembrane domain	38	60	N/A	INTRINSIC
transmembrane domain	75	97	N/A	INTRINSIC
transmembrane domain	110	127	N/A	INTRINSIC
Pfam:GPHR_N	140	207	1.1e-31	PFAM
Pfam:ABA_GPCR	276	446	4.9e-46	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000058865
AA Change: E493*

SMART Domains

Protein: ENSMUSP00000058936
Gene: ENSMUSG00000038298
AA Change: E493*

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 null
Transcript: ENSMUST00000107069
AA Change: E493*

SMART Domains

Protein: ENSMUSP00000102684
Gene: ENSMUSG00000038298
AA Change: E493*

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 null
Transcript: ENSMUST00000107070
AA Change: E493*

SMART Domains

Protein: ENSMUSP00000102685
Gene: ENSMUSG00000038298
AA Change: E493*

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

noncoding transcript
Transcript: ENSMUST00000135533

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146645

Predicted Effect

probably null
Transcript: ENSMUST00000153256
AA Change: E493*

SMART Domains

Protein: ENSMUSP00000118846
Gene: ENSMUSG00000038298
AA Change: E493*

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

0.9755

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.2%

Validation Efficiency

98% (90/92)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3425401B19Rik	T	C	14: 32,385,107 (GRCm39)	D286G	probably benign	Het
Abca15	G	A	7: 119,949,998 (GRCm39)	E491K	probably benign	Het
Acsl5	A	G	19: 55,268,962 (GRCm39)	T208A	probably benign	Het
Adamts10	T	A	17: 33,764,511 (GRCm39)		probably null	Het
Ahcyl1	T	C	3: 107,577,233 (GRCm39)	Q313R	possibly damaging	Het
Ccdc71	C	T	9: 108,340,622 (GRCm39)	S145L	possibly damaging	Het
Cep250	A	G	2: 155,812,119 (GRCm39)	T472A	probably damaging	Het
Copa	T	C	1: 171,931,841 (GRCm39)		probably benign	Het
Crybg1	C	A	10: 43,873,883 (GRCm39)	R1075L	probably damaging	Het
Ddr2	T	A	1: 169,832,809 (GRCm39)	K84*	probably null	Het
Ddx59	C	T	1: 136,344,844 (GRCm39)	P172S	probably benign	Het
Dhx34	T	A	7: 15,931,307 (GRCm39)	Q1118L	possibly damaging	Het
Dkkl1	T	A	7: 44,857,232 (GRCm39)	I112F	probably damaging	Het
Dnah8	T	A	17: 30,944,140 (GRCm39)	C1786S	probably damaging	Het
Eml6	T	A	11: 29,788,525 (GRCm39)	D520V	possibly damaging	Het
Ergic1	T	A	17: 26,857,750 (GRCm39)	V192E	probably damaging	Het
Fat3	T	C	9: 15,941,262 (GRCm39)	E1343G	probably damaging	Het
Fxr1	T	C	3: 34,118,381 (GRCm39)	S535P	possibly damaging	Het
Gkn3	C	T	6: 87,360,507 (GRCm39)	A163T	probably damaging	Het
Gm15446	C	T	5: 110,090,866 (GRCm39)	H373Y	probably damaging	Het
Gpr157	A	T	4: 150,183,420 (GRCm39)	N197Y	probably benign	Het
Grid2	G	A	6: 64,643,185 (GRCm39)	M982I	probably benign	Het
Hey2	G	T	10: 30,710,304 (GRCm39)	R150S	possibly damaging	Het
Hmcn1	T	C	1: 150,648,322 (GRCm39)		probably null	Het
Ighv3-3	G	A	12: 114,160,156 (GRCm39)	R85*	probably null	Het
Ighv5-4	A	T	12: 113,561,060 (GRCm39)		probably benign	Het
Igsf21	A	G	4: 139,834,621 (GRCm39)	S84P	probably benign	Het
Kif20b	A	G	19: 34,915,773 (GRCm39)	T517A	probably benign	Het
Krt87	T	C	15: 101,385,863 (GRCm39)	E244G	probably damaging	Het
Lrp1	T	C	10: 127,390,928 (GRCm39)	T2990A	possibly damaging	Het
Lrp1b	T	A	2: 40,605,381 (GRCm39)		probably null	Het
Lrrc42	A	T	4: 107,091,050 (GRCm39)	S382T	probably benign	Het
Magi2	C	T	5: 20,739,467 (GRCm39)	R737W	probably damaging	Het
Mcc	A	G	18: 44,652,623 (GRCm39)	L267P	probably damaging	Het
Mzf1	T	A	7: 12,777,223 (GRCm39)	Q727L	possibly damaging	Het
Mzf1	C	T	7: 12,777,448 (GRCm39)	R652Q	possibly damaging	Het
Nkain3	C	T	4: 20,485,015 (GRCm39)	A21T	probably damaging	Het
Nlrp4e	T	A	7: 23,020,521 (GRCm39)	V336E	possibly damaging	Het
Nptn	C	T	9: 58,548,059 (GRCm39)	R155C	probably damaging	Het
Nr2c2	T	C	6: 92,116,828 (GRCm39)	I10T	possibly damaging	Het
Or12e13	T	A	2: 87,663,515 (GRCm39)	I44N	probably damaging	Het
Or1e26	C	T	11: 73,480,273 (GRCm39)	C97Y	probably damaging	Het
Or1j13	T	C	2: 36,369,836 (GRCm39)	Y102C	probably benign	Het
Plekhh1	GTCAAA	G	12: 79,122,194 (GRCm39)		probably null	Het
Polr3b	T	C	10: 84,491,867 (GRCm39)	V342A	possibly damaging	Het
Prg3	T	C	2: 84,821,750 (GRCm39)	V125A	possibly damaging	Het
Raph1	G	A	1: 60,542,160 (GRCm39)		probably benign	Het
Rassf2	A	G	2: 131,846,358 (GRCm39)	V133A	probably benign	Het
Rbm22	G	A	18: 60,697,463 (GRCm39)	R56H	probably damaging	Het
Rbpjl	A	C	2: 164,246,447 (GRCm39)	S31R	probably benign	Het
Reln	A	G	5: 22,124,220 (GRCm39)	V2762A	probably damaging	Het
Rxrg	T	A	1: 167,452,621 (GRCm39)	I141N	probably damaging	Het
Scn7a	C	A	2: 66,514,529 (GRCm39)	G1082C	probably damaging	Het
Selenon	C	A	4: 134,270,387 (GRCm39)	E322*	probably null	Het
Sipa1	C	T	19: 5,710,413 (GRCm39)	R199Q	probably damaging	Het
Slc26a7	A	T	4: 14,510,261 (GRCm39)		probably null	Het
Slc37a4	T	C	9: 44,312,787 (GRCm39)	S314P	possibly damaging	Het
Smarce1	T	C	11: 99,111,543 (GRCm39)	I59V	probably benign	Het
Stk19	T	C	17: 35,042,120 (GRCm39)		probably null	Het
Susd2	C	T	10: 75,473,964 (GRCm39)	D544N	probably benign	Het
Tcf7l2	G	T	19: 55,919,886 (GRCm39)	R465L	possibly damaging	Het
Tfap2d	T	A	1: 19,174,984 (GRCm39)	S146T	possibly damaging	Het
Tmem156	A	G	5: 65,248,870 (GRCm39)	F10S	probably benign	Het
Tmem63c	G	T	12: 87,103,954 (GRCm39)	A68S	possibly damaging	Het
Tnfrsf21	T	C	17: 43,396,395 (GRCm39)	C560R	probably damaging	Het
Trav10n	C	T	14: 53,359,590 (GRCm39)	T7I	probably benign	Het
Ttc38	C	T	15: 85,722,947 (GRCm39)	R132W	probably benign	Het
Tvp23a	T	C	16: 10,245,275 (GRCm39)	K108R	probably benign	Het
Vmn1r233	T	C	17: 21,214,879 (GRCm39)	M24V	probably benign	Het
Vmn1r88	T	A	7: 12,912,451 (GRCm39)	L269*	probably null	Het
Vmn2r101	T	A	17: 19,832,287 (GRCm39)	M761K	probably damaging	Het
Vps13b	C	T	15: 35,910,864 (GRCm39)	Q3543*	probably null	Het
Wdr37	T	C	13: 8,904,065 (GRCm39)	E101G	possibly damaging	Het
Zc3hc1	A	G	6: 30,374,899 (GRCm39)	V214A	probably benign	Het
Zcchc9	A	T	13: 91,948,728 (GRCm39)		probably null	Het
Zdbf2	A	T	1: 63,347,951 (GRCm39)	Q2110L	possibly damaging	Het
Zfp516	T	G	18: 82,975,236 (GRCm39)	L478R	possibly damaging	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
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
R6049:Pdzk1	UTSW	3	96,758,979 (GRCm39)	missense	probably benign	0.00
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'- TGCAAGAGGAACCCTACGAC -3'
(R):5'- ATTTCACTTACTAACTGCCAACTGC -3'

Sequencing Primer
(F):5'- ACCCTACGACAGAGTGGTG -3'
(R):5'- GAGGATTGCAAGTTCTACACCAGC -3'

Posted On

2015-10-21