Mutagenetix > Incidental Mutation

Incidental Mutation 'R4962:Pdss2'

381851

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

042559-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4962 (G1)

Quality Score

195

Status

Not validated

Chromosome

Chromosomal Location

43097482-43340878 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 43174908 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Threonine at position 138 (M138T)

Ref Sequence

ENSEMBL: ENSMUSP00000124046 (fasta)

Gene Model

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

AlphaFold

Q33DR3

Predicted Effect

probably benign
Transcript: ENSMUST00000095725
AA Change: M138T

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000093393
Gene: ENSMUSG00000038240
AA Change: M138T

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
AA Change: M138T

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000124864
Gene: ENSMUSG00000038240
AA Change: M138T

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

noncoding transcript
Transcript: ENSMUST00000160108

Predicted Effect

possibly damaging
Transcript: ENSMUST00000160823
AA Change: M138T

PolyPhen 2 Score 0.473 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000124046
Gene: ENSMUSG00000038240
AA Change: M138T

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

noncoding transcript
Transcript: ENSMUST00000162758

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.6%

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921509C19Rik	A	G	2: 151,314,728 (GRCm39)	F317L	possibly damaging	Het
Abcc4	A	G	14: 118,905,811 (GRCm39)	I85T	probably benign	Het
Acoxl	G	T	2: 127,917,810 (GRCm39)	C498F	probably damaging	Het
Akap13	C	T	7: 75,399,178 (GRCm39)	T2752I	probably damaging	Het
Anks6	C	T	4: 47,030,795 (GRCm39)	G601S	probably damaging	Het
Ap2a2	T	G	7: 141,210,061 (GRCm39)	F836C	probably damaging	Het
Atp2c1	A	G	9: 105,320,149 (GRCm39)	V404A	probably benign	Het
Atp7b	G	T	8: 22,510,901 (GRCm39)	A415E	probably damaging	Het
Babam2	A	T	5: 31,942,927 (GRCm39)	I71L	possibly damaging	Het
Bean1	A	G	8: 104,943,606 (GRCm39)	T54A	probably damaging	Het
Cacna1b	T	A	2: 24,508,330 (GRCm39)	I1816F	probably damaging	Het
Cacna1b	C	T	2: 24,547,378 (GRCm39)	G1202D	probably damaging	Het
Casp8ap2	A	G	4: 32,640,554 (GRCm39)	E536G	probably damaging	Het
Cfap57	A	G	4: 118,470,262 (GRCm39)	V206A	probably benign	Het
Clca3a2	A	T	3: 144,783,640 (GRCm39)	D658E	probably damaging	Het
Cwc22	A	T	2: 77,726,653 (GRCm39)	S809T	probably benign	Het
Cyp2c54	C	T	19: 40,060,585 (GRCm39)	R132Q	possibly damaging	Het
Ddx20	A	T	3: 105,587,921 (GRCm39)	D386E	possibly damaging	Het
Ddx50	T	C	10: 62,478,632 (GRCm39)	T185A	probably damaging	Het
Decr1	G	A	4: 15,930,976 (GRCm39)	R119*	probably null	Het
Dennd4a	T	C	9: 64,813,285 (GRCm39)	S1415P	probably benign	Het
Dnah12	A	T	14: 26,437,855 (GRCm39)	I495L	probably benign	Het
Dnah2	G	A	11: 69,346,799 (GRCm39)	Q2596*	probably null	Het
Dnajb13	A	G	7: 100,156,707 (GRCm39)	L123S	probably benign	Het
Drgx	G	T	14: 32,369,101 (GRCm39)		probably benign	Het
Elavl3	G	A	9: 21,948,107 (GRCm39)	P19L	probably benign	Het
Fer1l6	T	C	15: 58,443,250 (GRCm39)	S518P	probably benign	Het
Fgd3	T	C	13: 49,420,105 (GRCm39)	S591G	probably benign	Het
Galnt18	C	A	7: 111,071,271 (GRCm39)	R566L	probably benign	Het
Galnt6	A	T	15: 100,594,455 (GRCm39)	Y525*	probably null	Het
Gm10036	A	T	18: 15,966,359 (GRCm39)	Y170F	probably benign	Het
Hacd2	A	G	16: 34,842,921 (GRCm39)	D24G	unknown	Het
Idh3a	T	C	9: 54,503,325 (GRCm39)	M128T	possibly damaging	Het
Ido1	C	T	8: 25,074,565 (GRCm39)	M359I	probably benign	Het
Ikbkb	T	C	8: 23,171,693 (GRCm39)	T185A	probably damaging	Het
Insl6	C	T	19: 29,299,019 (GRCm39)	G131D	probably damaging	Het
Irgm1	A	C	11: 48,757,159 (GRCm39)	S217R	possibly damaging	Het
Itga11	T	A	9: 62,668,850 (GRCm39)	Y702*	probably null	Het
Itgb4	C	T	11: 115,874,983 (GRCm39)	R447W	probably benign	Het
Kansl2	T	C	15: 98,429,724 (GRCm39)	M103V	probably benign	Het
Kcnq2	T	C	2: 180,753,836 (GRCm39)	N258S	possibly damaging	Het
Kdm5d	A	T	Y: 940,624 (GRCm39)	D1045V	probably damaging	Het
Lats2	A	G	14: 57,937,049 (GRCm39)	L480P	probably damaging	Het
Lin28b	T	A	10: 45,296,736 (GRCm39)	K87N	possibly damaging	Het
Lpgat1	T	A	1: 191,451,682 (GRCm39)	W103R	probably damaging	Het
Lpl	G	T	8: 69,347,345 (GRCm39)	G166C	probably damaging	Het
Ly75	A	T	2: 60,182,469 (GRCm39)	Y569N	probably damaging	Het
Mcm8	A	T	2: 132,680,689 (GRCm39)	E564D	probably damaging	Het
Me2	G	T	18: 73,918,847 (GRCm39)	N411K	probably damaging	Het
Mn1	A	G	5: 111,602,652 (GRCm39)	T1297A	possibly damaging	Het
Mphosph8	T	A	14: 56,916,046 (GRCm39)	F447L	probably benign	Het
Nacad	T	A	11: 6,549,169 (GRCm39)	D1294V	probably damaging	Het
Neu3	A	T	7: 99,472,615 (GRCm39)	F41I	probably damaging	Het
Nlrp6	G	T	7: 140,503,497 (GRCm39)	L534F	probably damaging	Het
Nrap	A	G	19: 56,366,575 (GRCm39)	M338T	probably damaging	Het
Nuak1	T	C	10: 84,210,979 (GRCm39)	K370E	probably damaging	Het
Or10ab4	T	A	7: 107,654,647 (GRCm39)	C153S	probably benign	Het
Or4d10	T	A	19: 12,051,639 (GRCm39)	D119V	probably damaging	Het
Or5w8	A	G	2: 87,687,632 (GRCm39)	T38A	probably benign	Het
Or6c212	C	T	10: 129,558,592 (GRCm39)	V274M	probably damaging	Het
P3h3	T	C	6: 124,818,736 (GRCm39)	S701G	probably benign	Het
Piezo1	C	T	8: 123,213,220 (GRCm39)	E1848K	probably benign	Het
Prmt3	T	G	7: 49,476,557 (GRCm39)	S389A	probably benign	Het
Prune2	T	A	19: 17,099,637 (GRCm39)	F1714I	probably benign	Het
Ptgis	A	G	2: 167,067,194 (GRCm39)		probably null	Het
Ptpn20	T	C	14: 33,336,416 (GRCm39)	V85A	probably benign	Het
Rabepk	A	T	2: 34,670,669 (GRCm39)	Y264N	probably damaging	Het
Ralgapa2	A	T	2: 146,276,754 (GRCm39)	C495*	probably null	Het
Satb2	A	G	1: 56,930,327 (GRCm39)	I232T	probably benign	Het
Selenbp2	A	T	3: 94,610,856 (GRCm39)	L307F	probably damaging	Het
Sgpl1	T	G	10: 60,949,863 (GRCm39)	Y112S	probably damaging	Het
Slitrk5	T	C	14: 111,918,679 (GRCm39)	S768P	probably benign	Het
Smc3	T	A	19: 53,619,948 (GRCm39)	Y615N	probably damaging	Het
Spag17	A	G	3: 99,934,939 (GRCm39)	N715S	probably benign	Het
Spats2	A	G	15: 99,110,157 (GRCm39)	E518G	probably benign	Het
Spats2l	A	G	1: 57,924,983 (GRCm39)	H127R	possibly damaging	Het
Tenm3	T	A	8: 48,731,996 (GRCm39)	K1287*	probably null	Het
Thoc1	T	A	18: 9,962,387 (GRCm39)	S91T	probably benign	Het
Thoc6	C	T	17: 23,888,911 (GRCm39)	G166S	probably damaging	Het
Tmem107	C	A	11: 68,962,087 (GRCm39)	T42N	possibly damaging	Het
Tmprss11c	A	G	5: 86,385,569 (GRCm39)	I288T	probably damaging	Het
Tnrc18	A	G	5: 142,725,248 (GRCm39)	F1827S	unknown	Het
Trmt112	C	A	19: 6,887,566 (GRCm39)	T5N	probably damaging	Het
Trp53bp1	A	T	2: 121,101,027 (GRCm39)	M57K	probably benign	Het
Ttbk2	C	A	2: 120,575,631 (GRCm39)	Q1115H	probably damaging	Het
Ttn	C	A	2: 76,559,989 (GRCm39)	E27725*	probably null	Het
Ttn	A	G	2: 76,774,453 (GRCm39)	M2151T	probably damaging	Het
Usp9y	A	T	Y: 1,384,336 (GRCm39)	D727E	probably damaging	Het
Vps13c	A	G	9: 67,781,173 (GRCm39)	T221A	probably damaging	Het
Zbtb20	A	G	16: 43,439,055 (GRCm39)	D725G	probably damaging	Het
Zfp341	A	T	2: 154,468,734 (GRCm39)	I126F	possibly damaging	Het
Zfyve16	C	T	13: 92,650,402 (GRCm39)	A861T	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
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
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
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'- TTGATCTGTCCAGCCTTGGG -3'
(R):5'- GGTAACTCACAAAGGACTAGTGAC -3'

Sequencing Primer
(F):5'- CCTTGGGAAAGTGTGTCACCTC -3'
(R):5'- GGAAATTTTACTGCTGAGCCACC -3'

Posted On

2016-04-27