Mutagenetix > Incidental Mutation

Incidental Mutation 'R4077:Pdss2'

316632

Institutional Source

Beutler Lab

Gene Symbol

Pdss2

Ensembl Gene

ENSMUSG00000038240

Gene Name

prenyl (solanesyl) diphosphate synthase, subunit 2

Synonyms

5430420P03Rik, kd, PLMP, mDLP1

MMRRC Submission

041622-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4077 (G1)

Quality Score

194

Status

Validated

Chromosome

Chromosomal Location

43097482-43340878 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 43278518 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Leucine at position 342 (M342L)

Ref Sequence

ENSEMBL: ENSMUSP00000124046 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000095725] [ENSMUST00000159139] [ENSMUST00000160823]

AlphaFold

Q33DR3

Predicted Effect

probably benign
Transcript: ENSMUST00000095725

SMART Domains

Protein: ENSMUSP00000093393
Gene: ENSMUSG00000038240

Domain	Start	End	E-Value	Type
low complexity region	2	18	N/A	INTRINSIC
low complexity region	32	46	N/A	INTRINSIC
Pfam:polyprenyl_synt	106	324	9e-20	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000159139

SMART Domains

Protein: ENSMUSP00000124864
Gene: ENSMUSG00000038240

Domain	Start	End	E-Value	Type
low complexity region	2	18	N/A	INTRINSIC
low complexity region	32	46	N/A	INTRINSIC
Pfam:polyprenyl_synt	103	323	7.9e-15	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000160823
AA Change: M342L

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

SMART Domains

Protein: ENSMUSP00000124046
Gene: ENSMUSG00000038240
AA Change: M342L

Domain	Start	End	E-Value	Type
low complexity region	2	18	N/A	INTRINSIC
low complexity region	32	46	N/A	INTRINSIC
Pfam:polyprenyl_synt	103	319	7.4e-15	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162008

SMART Domains

Protein: ENSMUSP00000124440
Gene: ENSMUSG00000038240

Domain	Start	End	E-Value	Type
SCOP:d1uby__	9	136	1e-16	SMART

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.5%
20x: 95.8%

Validation Efficiency

99% (81/82)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is an enzyme that synthesizes the prenyl side-chain of coenzyme Q, or ubiquinone, one of the key elements in the respiratory chain. The gene product catalyzes the formation of all trans-polyprenyl pyrophosphates from isopentyl diphosphate in the assembly of polyisoprenoid side chains, the first step in coenzyme Q biosynthesis. Defects in this gene are a cause of coenzyme Q10 deficiency.[provided by RefSeq, Oct 2009]
PHENOTYPE: Mutations in this gene result in renal abnormalities leading to early death. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abhd12	T	A	2: 150,690,379 (GRCm39)		probably null	Het
Adam33	T	C	2: 130,905,444 (GRCm39)		probably benign	Het
Adrm1b	A	C	3: 92,336,195 (GRCm39)		probably benign	Het
Akap8	C	T	17: 32,531,272 (GRCm39)	R380Q	probably damaging	Het
Arhgef12	T	C	9: 42,886,588 (GRCm39)	M1131V	probably damaging	Het
Atrn	T	C	2: 130,806,850 (GRCm39)		probably null	Het
Btaf1	A	G	19: 36,963,879 (GRCm39)	T817A	probably benign	Het
C3	C	T	17: 57,512,303 (GRCm39)	D1542N	possibly damaging	Het
Cadm3	A	G	1: 173,169,236 (GRCm39)	V293A	probably benign	Het
Cdk11b	C	T	4: 155,724,204 (GRCm39)		probably benign	Het
Cdnf	A	G	2: 3,522,060 (GRCm39)	Y84C	probably damaging	Het
Chdh	T	C	14: 29,757,297 (GRCm39)	S407P	probably damaging	Het
Cmtr1	C	A	17: 29,904,949 (GRCm39)	T300K	probably damaging	Het
Dennd2d	A	T	3: 106,389,939 (GRCm39)		probably benign	Het
Diaph1	T	A	18: 37,986,636 (GRCm39)	E1116D	possibly damaging	Het
Eif1ad3	A	G	12: 87,843,401 (GRCm39)	K16R	unknown	Het
Eif1ad3	A	T	12: 87,843,710 (GRCm39)	D119V	possibly damaging	Het
Enpp1	A	G	10: 24,544,905 (GRCm39)		probably null	Het
Erbb4	T	C	1: 68,079,496 (GRCm39)	T1195A	probably benign	Het
Ermard	T	A	17: 15,273,638 (GRCm39)	S408T	probably benign	Het
Etl4	A	T	2: 20,812,772 (GRCm39)	R1442S	probably damaging	Het
F13b	T	A	1: 139,429,508 (GRCm39)	F9I	unknown	Het
Fnbp4	C	T	2: 90,588,821 (GRCm39)	R531*	probably null	Het
Gdf6	A	G	4: 9,844,776 (GRCm39)	Y100C	probably damaging	Het
Gpr3	T	C	4: 132,938,226 (GRCm39)	T149A	probably damaging	Het
Grm8	T	C	6: 27,760,208 (GRCm39)	H374R	probably benign	Het
Hbs1l	T	C	10: 21,228,501 (GRCm39)	V493A	probably damaging	Het
Hgs	A	G	11: 120,368,202 (GRCm39)	K277E	probably damaging	Het
Hnrnpul1	C	T	7: 25,426,300 (GRCm39)	R517Q	probably damaging	Het
Hoxa11	A	T	6: 52,222,504 (GRCm39)	Y66N	probably damaging	Het
Hsh2d	G	A	8: 72,954,304 (GRCm39)	D229N	probably benign	Het
Igdcc4	T	A	9: 65,039,047 (GRCm39)	L944Q	probably damaging	Het
Ighv3-1	C	A	12: 113,928,107 (GRCm39)	S84I	probably damaging	Het
Iqgap2	T	C	13: 95,794,375 (GRCm39)	D1199G	probably damaging	Het
Kcnk10	A	T	12: 98,401,205 (GRCm39)	M490K	probably benign	Het
Kirrel1	A	G	3: 86,992,387 (GRCm39)		probably null	Het
Lias	A	T	5: 65,552,768 (GRCm39)	T124S	probably benign	Het
Lrig3	A	C	10: 125,845,656 (GRCm39)	E695A	probably damaging	Het
Lrpap1	A	G	5: 35,253,381 (GRCm39)	I261T	possibly damaging	Het
Lrrc37a	T	A	11: 103,388,808 (GRCm39)	T2206S	unknown	Het
Macf1	T	A	4: 123,365,884 (GRCm39)	Q2959L	probably benign	Het
Mis12	A	G	11: 70,916,134 (GRCm39)	T56A	probably benign	Het
Or10ag56	T	A	2: 87,139,208 (GRCm39)	M25K	probably null	Het
Or1l4	T	A	2: 37,092,024 (GRCm39)	I257N	possibly damaging	Het
Or4k41	A	G	2: 111,279,848 (GRCm39)	D121G	probably damaging	Het
Or5b99	T	C	19: 12,977,235 (GRCm39)	V295A	probably damaging	Het
Otof	A	T	5: 30,576,850 (GRCm39)	L134Q	possibly damaging	Het
Pds5b	T	A	5: 150,717,824 (GRCm39)	V1155E	possibly damaging	Het
Phyhipl	C	T	10: 70,404,903 (GRCm39)	V57I	probably damaging	Het
Plekha5	T	A	6: 140,501,647 (GRCm39)		probably null	Het
Pnck	A	T	X: 72,701,761 (GRCm39)	V93E	probably damaging	Het
Proser1	A	G	3: 53,385,962 (GRCm39)	T615A	probably damaging	Het
Ptprk	G	A	10: 28,139,508 (GRCm39)	V78I	probably benign	Het
Ptprv	A	G	1: 135,038,168 (GRCm39)		noncoding transcript	Het
Ranbp3l	A	G	15: 9,060,838 (GRCm39)	N233S	probably damaging	Het
Rassf2	G	A	2: 131,854,522 (GRCm39)	P7S	probably benign	Het
Sart1	A	T	19: 5,432,771 (GRCm39)	L521Q	possibly damaging	Het
Scgb1b21	T	A	7: 33,227,118 (GRCm39)		noncoding transcript	Het
Scyl2	A	T	10: 89,476,458 (GRCm39)	M889K	probably benign	Het
Secisbp2l	A	G	2: 125,593,785 (GRCm39)		probably benign	Het
Svil	A	G	18: 5,063,522 (GRCm39)	E931G	probably benign	Het
Syce1	C	A	7: 140,359,809 (GRCm39)	L83F	probably damaging	Het
Tdrd1	A	G	19: 56,819,505 (GRCm39)	M2V	probably benign	Het
Tjp2	A	T	19: 24,086,182 (GRCm39)	V780E	possibly damaging	Het
Tram1	A	G	1: 13,636,599 (GRCm39)	V358A	probably benign	Het
Unc13c	C	T	9: 73,643,821 (GRCm39)	W1214*	probably null	Het
Vps13b	T	C	15: 35,455,274 (GRCm39)	C728R	probably damaging	Het
Wwox	A	G	8: 115,166,481 (GRCm39)		probably benign	Het
Zbtb41	G	A	1: 139,357,064 (GRCm39)	V440I	probably benign	Het
Zfp777	T	C	6: 48,002,456 (GRCm39)	S589G	probably benign	Het
Zfp955a	A	G	17: 33,460,675 (GRCm39)	Y486H	probably benign	Het

Other mutations in Pdss2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02346:Pdss2	APN	10	43,221,639 (GRCm39)	missense	possibly damaging	0.80
IGL03337:Pdss2	APN	10	43,221,589 (GRCm39)	missense	probably damaging	1.00
IGL03340:Pdss2	APN	10	43,269,997 (GRCm39)	missense	probably benign	0.00
whup	UTSW	10	43,269,945 (GRCm39)	missense	possibly damaging	0.75
R0277:Pdss2	UTSW	10	43,248,172 (GRCm39)	missense	probably benign
R0323:Pdss2	UTSW	10	43,248,172 (GRCm39)	missense	probably benign
R0324:Pdss2	UTSW	10	43,269,924 (GRCm39)	missense	probably damaging	1.00
R0508:Pdss2	UTSW	10	43,097,927 (GRCm39)	small deletion	probably benign
R0654:Pdss2	UTSW	10	43,097,927 (GRCm39)	small deletion	probably benign
R1472:Pdss2	UTSW	10	43,289,533 (GRCm39)	missense	probably benign	0.00
R1801:Pdss2	UTSW	10	43,221,601 (GRCm39)	missense	probably benign	0.29
R2024:Pdss2	UTSW	10	43,269,871 (GRCm39)	missense	possibly damaging	0.81
R2025:Pdss2	UTSW	10	43,269,871 (GRCm39)	missense	possibly damaging	0.81
R2026:Pdss2	UTSW	10	43,269,871 (GRCm39)	missense	possibly damaging	0.81
R4079:Pdss2	UTSW	10	43,278,518 (GRCm39)	missense	probably benign
R4292:Pdss2	UTSW	10	43,097,834 (GRCm39)	missense	probably benign
R4518:Pdss2	UTSW	10	43,248,146 (GRCm39)	missense	probably damaging	0.99
R4603:Pdss2	UTSW	10	43,248,197 (GRCm39)	missense	probably damaging	0.99
R4962:Pdss2	UTSW	10	43,174,908 (GRCm39)	missense	possibly damaging	0.47
R5016:Pdss2	UTSW	10	43,098,001 (GRCm39)	missense	probably damaging	1.00
R5610:Pdss2	UTSW	10	43,315,828 (GRCm39)	missense	probably benign	0.00
R5888:Pdss2	UTSW	10	43,097,793 (GRCm39)	synonymous	silent
R5972:Pdss2	UTSW	10	43,174,922 (GRCm39)	missense	probably damaging	0.99
R7246:Pdss2	UTSW	10	43,248,172 (GRCm39)	missense	probably benign
R7697:Pdss2	UTSW	10	43,221,544 (GRCm39)	missense	probably damaging	1.00
R7765:Pdss2	UTSW	10	43,340,628 (GRCm39)	missense	probably benign	0.33
R8227:Pdss2	UTSW	10	43,221,577 (GRCm39)	missense	probably damaging	1.00
R8497:Pdss2	UTSW	10	43,289,521 (GRCm39)	missense	possibly damaging	0.89
R8897:Pdss2	UTSW	10	43,221,663 (GRCm39)	missense	probably damaging	1.00
R9101:Pdss2	UTSW	10	43,269,945 (GRCm39)	missense	possibly damaging	0.75
R9529:Pdss2	UTSW	10	43,269,990 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- ACATTTGCATGTGCTTGCTTAC -3'
(R):5'- TGAGACATCACACGGGTCTTCC -3'

Sequencing Primer
(F):5'- TGCTAGGCATAGTAGCATATGCC -3'
(R):5'- GGGTCTTCCAGCATCATGAACTAG -3'

Posted On

2015-05-15