Mutagenetix > Incidental Mutation

Incidental Mutation 'R2025:Pdss2'

220464

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

040034-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2025 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

43097482-43340878 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 43269871 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Isoleucine at position 238 (N238I)

Ref Sequence

ENSEMBL: ENSMUSP00000124046 (fasta)

Gene Model

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

AlphaFold

Q33DR3

Predicted Effect

possibly damaging
Transcript: ENSMUST00000095725
AA Change: N238I

PolyPhen 2 Score 0.814 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000093393
Gene: ENSMUSG00000038240
AA Change: N238I

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

possibly damaging
Transcript: ENSMUST00000159139
AA Change: N238I

PolyPhen 2 Score 0.814 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000124864
Gene: ENSMUSG00000038240
AA Change: N238I

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

possibly damaging
Transcript: ENSMUST00000160823
AA Change: N238I

PolyPhen 2 Score 0.814 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000124046
Gene: ENSMUSG00000038240
AA Change: N238I

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

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.1%
20x: 94.6%

Validation Efficiency

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc4	T	C	14: 118,790,737 (GRCm39)	M757V	probably benign	Het
Abitram	T	A	4: 56,805,916 (GRCm39)	I138N	probably damaging	Het
Acan	T	G	7: 78,750,970 (GRCm39)	S1914A	probably benign	Het
Axin2	T	A	11: 108,833,904 (GRCm39)	V617D	probably damaging	Het
Bhlhe22	A	G	3: 18,109,975 (GRCm39)	S342G	probably benign	Het
Cald1	AAGAGAGAGAGAGAG	AAGAGAGAGAGAG	6: 34,723,108 (GRCm39)		probably null	Het
Ccdc34	A	G	2: 109,862,731 (GRCm39)	K179E	possibly damaging	Het
Clasp1	A	G	1: 118,432,629 (GRCm39)	T208A	probably damaging	Het
Crabp1	C	T	9: 54,675,752 (GRCm39)	R112*	probably null	Het
Cstdc1	T	C	2: 148,624,148 (GRCm39)	F41L	probably damaging	Het
D130040H23Rik	A	G	8: 69,755,525 (GRCm39)	N310S	probably benign	Het
Dalrd3	T	C	9: 108,448,284 (GRCm39)	I278T	probably benign	Het
Dbp	C	A	7: 45,357,700 (GRCm39)	D89E	probably benign	Het
Dennd2c	A	G	3: 103,039,005 (GRCm39)	D51G	possibly damaging	Het
Dido1	A	T	2: 180,330,974 (GRCm39)	L158*	probably null	Het
Disp1	G	T	1: 182,869,767 (GRCm39)	F884L	probably damaging	Het
Dmrtb1	T	C	4: 107,540,782 (GRCm39)	D193G	probably damaging	Het
Dnah8	A	G	17: 30,950,133 (GRCm39)	D1984G	probably damaging	Het
Dpf2	T	C	19: 5,952,781 (GRCm39)	Y218C	possibly damaging	Het
Dsg4	C	T	18: 20,599,693 (GRCm39)	Q770*	probably null	Het
Efemp1	A	T	11: 28,864,696 (GRCm39)	Y250F	possibly damaging	Het
Erbin	A	T	13: 103,966,703 (GRCm39)	I1249N	probably benign	Het
F5	A	G	1: 164,037,044 (GRCm39)	K1928E	probably benign	Het
Fhip1b	A	G	7: 105,038,143 (GRCm39)	V260A	probably damaging	Het
Gdf11	T	A	10: 128,727,314 (GRCm39)	I81F	probably damaging	Het
Gm10518	T	A	1: 179,631,483 (GRCm39)		probably benign	Het
Grb10	G	C	11: 11,920,576 (GRCm39)	S14*	probably null	Het
Greb1l	A	T	18: 10,515,221 (GRCm39)	Y562F	possibly damaging	Het
Gtf2ird1	T	C	5: 134,392,788 (GRCm39)	E789G	probably damaging	Het
Hook3	T	C	8: 26,528,126 (GRCm39)	E588G	probably damaging	Het
Hpx	A	G	7: 105,244,311 (GRCm39)	S266P	probably damaging	Het
Hs6st3	A	G	14: 120,106,801 (GRCm39)	D403G	probably damaging	Het
Igf2bp1	A	G	11: 95,864,996 (GRCm39)	V151A	possibly damaging	Het
Itga11	C	T	9: 62,670,093 (GRCm39)	T739I	probably damaging	Het
Kalrn	T	C	16: 34,010,106 (GRCm39)	I702V	probably damaging	Het
Kif2b	C	T	11: 91,468,172 (GRCm39)	S37N	probably damaging	Het
Kng2	T	A	16: 22,819,325 (GRCm39)	D237V	probably benign	Het
Krtap27-1	C	A	16: 88,468,173 (GRCm39)	V124L	possibly damaging	Het
Lig4	A	T	8: 10,022,436 (GRCm39)	L448Q	probably damaging	Het
Macf1	C	T	4: 123,265,711 (GRCm39)	A4821T	probably damaging	Het
Msh5	T	A	17: 35,251,768 (GRCm39)	I431F	possibly damaging	Het
Ndufa10	A	G	1: 92,367,614 (GRCm39)	Y339H	probably damaging	Het
Nin	T	A	12: 70,076,782 (GRCm39)	Q1091L	probably damaging	Het
Nom1	A	C	5: 29,651,849 (GRCm39)	D729A	probably damaging	Het
Or52e8	C	A	7: 104,624,451 (GRCm39)	G247V	probably benign	Het
P2ry14	A	T	3: 59,022,866 (GRCm39)	V207E	probably damaging	Het
Pkn1	A	G	8: 84,398,007 (GRCm39)	V795A	probably damaging	Het
Pla2g6	A	C	15: 79,170,964 (GRCm39)	L804R	probably damaging	Het
Poglut1	A	T	16: 38,358,267 (GRCm39)		probably null	Het
Prkcz	A	T	4: 155,374,167 (GRCm39)	V83D	probably damaging	Het
Prss50	T	C	9: 110,690,328 (GRCm39)	F157S	probably benign	Het
Psors1c2	A	G	17: 35,845,099 (GRCm39)		probably benign	Het
Ptch1	T	G	13: 63,672,773 (GRCm39)	E944A	probably benign	Het
Ptpro	T	A	6: 137,420,592 (GRCm39)	V1007D	probably damaging	Het
Pwwp4a	G	T	X: 72,171,261 (GRCm39)	G218C	probably damaging	Het
Rab7	G	A	6: 87,981,161 (GRCm39)	L174F	probably damaging	Het
Rapgef4	A	G	2: 72,073,083 (GRCm39)	T790A	probably benign	Het
Rb1cc1	G	T	1: 6,315,533 (GRCm39)	V503L	probably damaging	Het
Sbf1	T	A	15: 89,186,933 (GRCm39)	E815V	probably damaging	Het
Setd3	T	A	12: 108,126,526 (GRCm39)	E104V	probably damaging	Het
Slc39a5	A	T	10: 128,234,279 (GRCm39)	L208Q	probably damaging	Het
Slc39a5	G	T	10: 128,234,280 (GRCm39)	L208M	probably damaging	Het
Slc3a1	T	G	17: 85,340,273 (GRCm39)	Y232D	probably damaging	Het
Slc8a1	T	A	17: 81,956,541 (GRCm39)	S166C	probably damaging	Het
Stard9	T	A	2: 120,532,879 (GRCm39)	D3045E	probably benign	Het
Stk4	C	A	2: 163,938,751 (GRCm39)	D206E	probably damaging	Het
Syn3	T	C	10: 86,302,846 (GRCm39)	D103G	probably damaging	Het
Tbc1d30	T	A	10: 121,115,051 (GRCm39)	Y369F	probably benign	Het
Tenm2	G	T	11: 35,938,091 (GRCm39)	Y1527*	probably null	Het
Tfg	T	C	16: 56,525,988 (GRCm39)	K85R	possibly damaging	Het
Timp3	T	C	10: 86,136,749 (GRCm39)	L11P	probably damaging	Het
Tmem144	A	T	3: 79,735,018 (GRCm39)		probably null	Het
Tmtc4	T	C	14: 123,158,677 (GRCm39)	N682S	probably benign	Het
Tnks2	C	T	19: 36,843,466 (GRCm39)	L464F	probably damaging	Het
Trank1	T	C	9: 111,221,107 (GRCm39)	F2615L	probably benign	Het
Trio	T	C	15: 27,744,223 (GRCm39)	K2570E	probably damaging	Het
Trio	T	A	15: 27,774,013 (GRCm39)	D673V	probably damaging	Het
Ublcp1	A	T	11: 44,356,458 (GRCm39)	C87S	probably benign	Het
Unc13a	C	T	8: 72,092,412 (GRCm39)	E1386K	possibly damaging	Het
Wdr41	C	T	13: 95,155,456 (GRCm39)	H404Y	probably damaging	Het
Zfp280b	T	C	10: 75,874,328 (GRCm39)	L69S	probably damaging	Het
Zfp346	T	C	13: 55,280,121 (GRCm39)	S282P	probably damaging	Het
Zfp579	C	A	7: 4,996,520 (GRCm39)	E464*	probably null	Het
Zfp78	T	A	7: 6,378,513 (GRCm39)		probably null	Het
Zswim9	T	C	7: 13,003,292 (GRCm39)	E186G	probably damaging	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
R2026:Pdss2	UTSW	10	43,269,871 (GRCm39)	missense	possibly damaging	0.81
R4077:Pdss2	UTSW	10	43,278,518 (GRCm39)	missense	probably benign
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'- GAGTGTTGCTAGTCCGTCCTTAC -3'
(R):5'- ATACCTTGTGACTCATGGCC -3'

Sequencing Primer
(F):5'- TTGTTTATTTACTACTGTGGGCTAAC -3'
(R):5'- TGACTCATGGCCATGTGC -3'

Posted On

2014-08-25