Mutagenetix > Incidental Mutation

Incidental Mutation 'R1779:Pnpla6'

197351

Institutional Source

Beutler Lab

Gene Symbol

Pnpla6

Ensembl Gene

ENSMUSG00000004565

Gene Name

patatin-like phospholipase domain containing 6

Synonyms

Nte, Swiss-cheese, MSws

MMRRC Submission

039810-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1779 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

3565384-3594267 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 3591404 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tryptophan to Arginine at position 1151 (W1151R)

Ref Sequence

ENSEMBL: ENSMUSP00000146680 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000004681] [ENSMUST00000111070] [ENSMUST00000207421] [ENSMUST00000207941] [ENSMUST00000208002]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000004681
AA Change: W1133R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000004681
Gene: ENSMUSG00000004565
AA Change: W1133R

Domain	Start	End	E-Value	Type
transmembrane domain	9	31	N/A	INTRINSIC
low complexity region	67	83	N/A	INTRINSIC
low complexity region	87	101	N/A	INTRINSIC
cNMP	147	272	3.17e-13	SMART
cNMP	465	584	3.17e-4	SMART
cNMP	587	703	3.45e-5	SMART
Blast:cNMP	742	777	7e-11	BLAST
Pfam:Patatin	933	1099	5e-26	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000111070
AA Change: W1133R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000106699
Gene: ENSMUSG00000004565
AA Change: W1133R

Domain	Start	End	E-Value	Type
transmembrane domain	9	31	N/A	INTRINSIC
low complexity region	67	83	N/A	INTRINSIC
low complexity region	87	101	N/A	INTRINSIC
cNMP	147	272	3.17e-13	SMART
cNMP	465	584	3.17e-4	SMART
cNMP	587	703	3.45e-5	SMART
Blast:cNMP	742	777	7e-11	BLAST
Pfam:Patatin	933	1099	1.4e-25	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207299

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207317

Predicted Effect

unknown
Transcript: ENSMUST00000207336
AA Change: W55R

Predicted Effect

probably benign
Transcript: ENSMUST00000207421

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207929

Predicted Effect

probably damaging
Transcript: ENSMUST00000207941
AA Change: W1122R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Predicted Effect

probably damaging
Transcript: ENSMUST00000208002
AA Change: W1151R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208370

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208851

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208691

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208914

Meta Mutation Damage Score

0.8357

Coding Region Coverage

1x: 97.5%
3x: 96.9%
10x: 95.5%
20x: 93.0%

Validation Efficiency

97% (101/104)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a phospholipase that deacetylates intracellular phosphatidylcholine to produce glycerophosphocholine. It is thought to function in neurite outgrowth and process elongation during neuronal differentiation. The protein is anchored to the cytoplasmic face of the endoplasmic reticulum in both neurons and non-neuronal cells. Mutations in this gene result in autosomal recessive spastic paraplegia, and the protein is the target for neurodegeneration induced by organophosphorus compounds and chemical warfare agents. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]
PHENOTYPE: Homozygous mutation of this gene results in embryonic lethality during early gestation. Conditional inactivation in the central nervous system leads to neurodegeneration. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 103 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006A11Rik	T	G	3: 124,200,163 (GRCm39)	L476F	probably damaging	Het
4930432E11Rik	A	T	7: 29,278,591 (GRCm39)		noncoding transcript	Het
A930011G23Rik	A	T	5: 99,370,897 (GRCm39)		probably benign	Het
Abcd3	A	G	3: 121,575,612 (GRCm39)	Y217H	probably damaging	Het
Abraxas1	A	T	5: 100,965,822 (GRCm39)		probably benign	Het
Acsbg1	T	C	9: 54,523,346 (GRCm39)	Y427C	probably damaging	Het
Acsbg3	T	A	17: 57,192,169 (GRCm39)	Y577*	probably null	Het
Adam10	T	A	9: 70,683,651 (GRCm39)		probably benign	Het
Adam24	G	A	8: 41,134,004 (GRCm39)	V491I	possibly damaging	Het
Adamts2	T	G	11: 50,647,524 (GRCm39)	V299G	probably damaging	Het
Adh7	A	G	3: 137,929,752 (GRCm39)	T143A	probably damaging	Het
Ahcyl1	A	G	3: 107,581,419 (GRCm39)	S81P	probably benign	Het
Arhgap20	C	A	9: 51,761,215 (GRCm39)	T986K	probably benign	Het
Atp13a5	A	T	16: 29,133,478 (GRCm39)	I391N	possibly damaging	Het
Atp6v0a1	C	A	11: 100,917,511 (GRCm39)	A143E	probably benign	Het
Calcrl	A	G	2: 84,181,629 (GRCm39)	I173T	probably damaging	Het
Casz1	A	G	4: 149,017,394 (GRCm39)	T228A	probably benign	Het
Cckar	A	G	5: 53,857,321 (GRCm39)	I292T	probably damaging	Het
Ccn5	G	A	2: 163,670,906 (GRCm39)	V138M	probably damaging	Het
Cfhr2	T	A	1: 139,786,383 (GRCm39)		probably null	Het
Chkb	T	C	15: 89,313,260 (GRCm39)	I109V	possibly damaging	Het
Clec2i	T	C	6: 128,865,069 (GRCm39)		probably null	Het
Clec4a4	T	A	6: 123,000,934 (GRCm39)	W216R	probably damaging	Het
Cntnap1	A	C	11: 101,077,337 (GRCm39)	I1000L	probably damaging	Het
Cp	C	A	3: 20,011,549 (GRCm39)	D34E	possibly damaging	Het
Cse1l	T	C	2: 166,782,044 (GRCm39)		probably null	Het
Dennd3	T	C	15: 73,394,357 (GRCm39)		probably null	Het
Dnah7a	A	G	1: 53,616,382 (GRCm39)	V1193A	probably benign	Het
Eaf2	A	G	16: 36,630,832 (GRCm39)		probably null	Het
Efcab3	T	A	11: 104,611,765 (GRCm39)	S536T	probably benign	Het
Ephb2	T	C	4: 136,421,136 (GRCm39)	T405A	possibly damaging	Het
Fam117a	G	A	11: 95,269,779 (GRCm39)	V348M	probably damaging	Het
Fh1	T	C	1: 175,428,990 (GRCm39)	*167W	probably null	Het
Fmo9	T	A	1: 166,490,868 (GRCm39)	I486F	probably benign	Het
Gabbr1	T	A	17: 37,365,771 (GRCm39)	I150N	probably damaging	Het
Gfpt1	T	C	6: 87,054,179 (GRCm39)	V478A	possibly damaging	Het
Gm2663	A	T	6: 40,974,894 (GRCm39)	V59E	probably damaging	Het
Gm4868	T	A	5: 125,925,176 (GRCm39)		noncoding transcript	Het
Heatr4	T	A	12: 84,026,934 (GRCm39)	T108S	probably benign	Het
Hells	G	T	19: 38,935,286 (GRCm39)	A319S	probably benign	Het
Helz2	A	G	2: 180,876,780 (GRCm39)	V1238A	probably benign	Het
Helz2	T	A	2: 180,880,252 (GRCm39)	Q488L	possibly damaging	Het
Hkdc1	A	G	10: 62,227,162 (GRCm39)	F765S	probably damaging	Het
Hspg2	T	A	4: 137,245,820 (GRCm39)	W938R	probably damaging	Het
Itpr2	G	A	6: 146,060,399 (GRCm39)	R2473*	probably null	Het
Kctd1	C	T	18: 15,194,839 (GRCm39)	V595I	probably benign	Het
Krt7	A	G	15: 101,321,290 (GRCm39)	Y369C	probably damaging	Het
Krt72	T	C	15: 101,689,364 (GRCm39)	T323A	probably benign	Het
Krt76	A	G	15: 101,801,122 (GRCm39)	L58P	unknown	Het
Liph	C	A	16: 21,786,800 (GRCm39)	R272L	probably benign	Het
Lrrc9	A	T	12: 72,502,772 (GRCm39)	K248*	probably null	Het
Mei4	T	A	9: 81,809,195 (GRCm39)	S93T	probably damaging	Het
Mgll	T	A	6: 88,790,930 (GRCm39)	Y183*	probably null	Het
Myo5b	A	G	18: 74,875,218 (GRCm39)	M1541V	probably benign	Het
Napg	A	G	18: 63,115,762 (GRCm39)	E66G	probably benign	Het
Npr3	T	C	15: 11,851,572 (GRCm39)	D406G	probably damaging	Het
Nr2c2	A	G	6: 92,136,224 (GRCm39)	T355A	possibly damaging	Het
Or13j1	G	A	4: 43,706,041 (GRCm39)	H176Y	probably damaging	Het
Or4a71	A	T	2: 89,357,989 (GRCm39)	I255K	probably benign	Het
Or51m1	G	T	7: 103,578,668 (GRCm39)	V213L	probably benign	Het
Or51v8	A	G	7: 103,319,845 (GRCm39)	I131T	probably benign	Het
Or52z13	A	T	7: 103,247,107 (GRCm39)	I195F	probably damaging	Het
Or5b107	T	C	19: 13,142,404 (GRCm39)	Y9H	probably benign	Het
Or8d1	A	G	9: 38,766,846 (GRCm39)	M163V	possibly damaging	Het
Orai2	T	C	5: 136,179,793 (GRCm39)	E80G	probably damaging	Het
Pcdhb14	T	A	18: 37,582,535 (GRCm39)	V547E	probably damaging	Het
Pcdhb15	T	C	18: 37,609,084 (GRCm39)	I772T	possibly damaging	Het
Pcnt	T	C	10: 76,244,630 (GRCm39)	Q1150R	probably damaging	Het
Pdcd6	A	G	13: 74,453,700 (GRCm39)	I146T	probably damaging	Het
Phldb2	T	A	16: 45,621,988 (GRCm39)	D664V	probably damaging	Het
Pik3ap1	A	T	19: 41,320,673 (GRCm39)	V182E	probably damaging	Het
Pip4k2a	A	G	2: 18,852,433 (GRCm39)	V283A	probably benign	Het
Pkdrej	A	G	15: 85,705,372 (GRCm39)	V188A	possibly damaging	Het
Ppp1r14c	A	G	10: 3,316,890 (GRCm39)	Y75C	probably damaging	Het
Prl2b1	C	T	13: 27,567,452 (GRCm39)	D224N	probably benign	Het
Ptgis	A	G	2: 167,056,778 (GRCm39)	S270P	probably benign	Het
Rgs11	C	A	17: 26,429,640 (GRCm39)	A446D	probably damaging	Het
Rims2	A	G	15: 39,545,098 (GRCm39)	T1531A	probably damaging	Het
Sbno1	A	T	5: 124,526,580 (GRCm39)		probably benign	Het
Scarb2	C	G	5: 92,596,416 (GRCm39)	M409I	probably benign	Het
Scube3	C	T	17: 28,387,353 (GRCm39)		probably benign	Het
Slc44a4	T	C	17: 35,140,901 (GRCm39)	I180T	probably damaging	Het
Slc9a2	T	C	1: 40,781,803 (GRCm39)	M344T	probably damaging	Het
Smc3	A	T	19: 53,627,800 (GRCm39)	T860S	probably benign	Het
Snrpa	A	G	7: 26,891,174 (GRCm39)	I99T	probably benign	Het
Sorcs1	A	G	19: 50,163,481 (GRCm39)		probably benign	Het
Sorl1	C	T	9: 41,902,778 (GRCm39)		probably null	Het
Suds3	T	C	5: 117,243,309 (GRCm39)	K143R	probably benign	Het
Supt20	A	T	3: 54,622,164 (GRCm39)	M424L	probably benign	Het
Tgtp2	T	C	11: 48,949,751 (GRCm39)	M274V	probably benign	Het
Tmem158	T	A	9: 123,088,974 (GRCm39)	M213L	probably benign	Het
Tnks	C	A	8: 35,324,672 (GRCm39)	R639L	probably benign	Het
Tns2	C	T	15: 102,017,369 (GRCm39)	R281C	probably damaging	Het
Trmt10c	A	C	16: 55,854,938 (GRCm39)	N232K	possibly damaging	Het
Trpm6	C	T	19: 18,833,581 (GRCm39)	R1587W	probably damaging	Het
Trrap	G	A	5: 144,765,400 (GRCm39)	V2539I	probably benign	Het
Tsg101	A	G	7: 46,556,835 (GRCm39)	S115P	probably benign	Het
Ttll13	G	T	7: 79,910,256 (GRCm39)	V800L	probably benign	Het
Vmn1r57	A	G	7: 5,223,576 (GRCm39)	T34A	possibly damaging	Het
Vmn2r118	T	A	17: 55,918,530 (GRCm39)	T121S	probably benign	Het
Wdr35	A	G	12: 9,035,772 (GRCm39)	I238M	possibly damaging	Het
Zfp81	T	A	17: 33,554,080 (GRCm39)	T245S	probably benign	Het
Zfyve26	G	T	12: 79,325,237 (GRCm39)	P824Q	probably damaging	Het

Other mutations in Pnpla6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00227:Pnpla6	APN	8	3,573,808 (GRCm39)	missense	probably damaging	1.00
IGL00820:Pnpla6	APN	8	3,582,358 (GRCm39)	missense	possibly damaging	0.95
IGL00839:Pnpla6	APN	8	3,592,299 (GRCm39)	missense	probably benign	0.05
IGL01732:Pnpla6	APN	8	3,572,616 (GRCm39)	missense	probably damaging	0.99
IGL01973:Pnpla6	APN	8	3,567,619 (GRCm39)	missense	probably damaging	1.00
IGL02267:Pnpla6	APN	8	3,567,327 (GRCm39)	missense	probably benign	0.00
IGL03246:Pnpla6	APN	8	3,581,530 (GRCm39)	missense	probably benign	0.01
IGL03286:Pnpla6	APN	8	3,581,473 (GRCm39)	missense	probably damaging	0.99
Immemorial	UTSW	8	3,581,677 (GRCm39)	missense	probably benign	0.38
Mammilary	UTSW	8	3,571,384 (GRCm39)	missense	probably benign	0.01
I0000:Pnpla6	UTSW	8	3,592,322 (GRCm39)	missense	probably benign
R0141:Pnpla6	UTSW	8	3,582,117 (GRCm39)	critical splice donor site	probably null
R0180:Pnpla6	UTSW	8	3,574,250 (GRCm39)	critical splice acceptor site	probably null
R0377:Pnpla6	UTSW	8	3,591,501 (GRCm39)	missense	probably damaging	1.00
R0563:Pnpla6	UTSW	8	3,573,333 (GRCm39)	missense	possibly damaging	0.51
R0660:Pnpla6	UTSW	8	3,572,269 (GRCm39)	unclassified	probably benign
R0786:Pnpla6	UTSW	8	3,573,317 (GRCm39)	missense	probably benign
R0827:Pnpla6	UTSW	8	3,567,618 (GRCm39)	missense	possibly damaging	0.71
R0882:Pnpla6	UTSW	8	3,567,081 (GRCm39)	missense	probably damaging	1.00
R1512:Pnpla6	UTSW	8	3,585,459 (GRCm39)	splice site	probably benign
R1552:Pnpla6	UTSW	8	3,572,403 (GRCm39)	missense	probably damaging	1.00
R1609:Pnpla6	UTSW	8	3,567,135 (GRCm39)	missense	probably damaging	1.00
R1770:Pnpla6	UTSW	8	3,584,634 (GRCm39)	missense	possibly damaging	0.94
R1987:Pnpla6	UTSW	8	3,592,370 (GRCm39)	missense	probably benign	0.00
R3079:Pnpla6	UTSW	8	3,591,512 (GRCm39)	missense	probably benign	0.25
R3125:Pnpla6	UTSW	8	3,584,670 (GRCm39)	missense	probably null	1.00
R4171:Pnpla6	UTSW	8	3,593,997 (GRCm39)	missense	probably benign	0.09
R4281:Pnpla6	UTSW	8	3,571,513 (GRCm39)	missense	probably damaging	1.00
R4674:Pnpla6	UTSW	8	3,571,412 (GRCm39)	missense	probably damaging	1.00
R4776:Pnpla6	UTSW	8	3,573,818 (GRCm39)	missense	probably benign	0.01
R4779:Pnpla6	UTSW	8	3,572,838 (GRCm39)	missense	probably benign	0.00
R5114:Pnpla6	UTSW	8	3,572,613 (GRCm39)	missense	probably damaging	0.98
R5459:Pnpla6	UTSW	8	3,585,829 (GRCm39)	missense	probably benign	0.01
R5510:Pnpla6	UTSW	8	3,571,397 (GRCm39)	missense	probably damaging	0.99
R5538:Pnpla6	UTSW	8	3,581,508 (GRCm39)	missense	probably benign	0.01
R5664:Pnpla6	UTSW	8	3,587,478 (GRCm39)	missense	probably damaging	0.98
R6063:Pnpla6	UTSW	8	3,574,156 (GRCm39)	missense	probably benign	0.21
R6314:Pnpla6	UTSW	8	3,571,572 (GRCm39)	missense	probably benign	0.39
R6321:Pnpla6	UTSW	8	3,594,015 (GRCm39)	missense	probably benign
R6454:Pnpla6	UTSW	8	3,587,986 (GRCm39)	missense	probably damaging	0.99
R6477:Pnpla6	UTSW	8	3,586,627 (GRCm39)	missense	probably benign	0.00
R6524:Pnpla6	UTSW	8	3,584,519 (GRCm39)	splice site	probably null
R6809:Pnpla6	UTSW	8	3,584,611 (GRCm39)	missense	possibly damaging	0.72
R6975:Pnpla6	UTSW	8	3,588,068 (GRCm39)	missense	probably damaging	1.00
R7293:Pnpla6	UTSW	8	3,588,068 (GRCm39)	missense	probably damaging	1.00
R7389:Pnpla6	UTSW	8	3,593,981 (GRCm39)	nonsense	probably null
R7426:Pnpla6	UTSW	8	3,566,540 (GRCm39)	splice site	probably null
R7520:Pnpla6	UTSW	8	3,587,508 (GRCm39)	missense	probably damaging	1.00
R7666:Pnpla6	UTSW	8	3,591,591 (GRCm39)	missense	probably benign	0.01
R7733:Pnpla6	UTSW	8	3,572,660 (GRCm39)	missense	probably benign	0.01
R7743:Pnpla6	UTSW	8	3,586,594 (GRCm39)	missense	possibly damaging	0.77
R7744:Pnpla6	UTSW	8	3,581,677 (GRCm39)	missense	probably benign	0.38
R7923:Pnpla6	UTSW	8	3,581,737 (GRCm39)	nonsense	probably null
R7980:Pnpla6	UTSW	8	3,586,562 (GRCm39)	missense	probably damaging	0.97
R8141:Pnpla6	UTSW	8	3,571,384 (GRCm39)	missense	probably benign	0.01
R8191:Pnpla6	UTSW	8	3,592,382 (GRCm39)	missense	probably benign	0.12
R8251:Pnpla6	UTSW	8	3,582,399 (GRCm39)	missense	probably benign	0.29
R8881:Pnpla6	UTSW	8	3,581,489 (GRCm39)	missense	probably benign	0.00
R8917:Pnpla6	UTSW	8	3,567,637 (GRCm39)	missense	possibly damaging	0.50
R8939:Pnpla6	UTSW	8	3,571,319 (GRCm39)	missense	possibly damaging	0.86
R8988:Pnpla6	UTSW	8	3,567,401 (GRCm39)	missense	possibly damaging	0.51
R9037:Pnpla6	UTSW	8	3,592,379 (GRCm39)	nonsense	probably null
R9264:Pnpla6	UTSW	8	3,573,294 (GRCm39)	missense	probably benign
R9265:Pnpla6	UTSW	8	3,573,294 (GRCm39)	missense	probably benign
R9386:Pnpla6	UTSW	8	3,571,417 (GRCm39)	critical splice donor site	probably null
X0018:Pnpla6	UTSW	8	3,567,337 (GRCm39)	missense	probably damaging	1.00
Z1177:Pnpla6	UTSW	8	3,586,979 (GRCm39)	missense	possibly damaging	0.76

Predicted Primers

PCR Primer
(F):5'- AGGCAGTCAGGTATTTCCTTGGGC -3'
(R):5'- TCTTGAAGCAGTCAATGGATGGACG -3'

Sequencing Primer
(F):5'- TTGGCTCTGTAGTACACAGAC -3'
(R):5'- TCAATGGATGGACGAAGGTACTC -3'

Posted On

2014-05-23