Mutagenetix > Incidental Mutation

Incidental Mutation 'R4776:Pnpla6'

367937

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

042413-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4776 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

3515384-3544267 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 3523818 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 422 (V422A)

Ref Sequence

ENSEMBL: ENSMUSP00000146680 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000004681] [ENSMUST00000111070] [ENSMUST00000207424] [ENSMUST00000207941] [ENSMUST00000208002] [ENSMUST00000208762]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000004681
AA Change: V400A

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000004681
Gene: ENSMUSG00000004565
AA Change: V400A

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 benign
Transcript: ENSMUST00000111070
AA Change: V400A

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000106699
Gene: ENSMUSG00000004565
AA Change: V400A

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

probably benign
Transcript: ENSMUST00000207424

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207430

Predicted Effect

probably benign
Transcript: ENSMUST00000207941
AA Change: V432A

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

Predicted Effect

probably benign
Transcript: ENSMUST00000208002
AA Change: V422A

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208006

Predicted Effect

probably benign
Transcript: ENSMUST00000208762

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000208851

Meta Mutation Damage Score

0.0613

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.8%
20x: 93.9%

Validation Efficiency

98% (94/96)

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: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310035C23Rik	T	A	1: 105,719,535	Y683*	probably null	Het
2610028H24Rik	A	T	10: 76,457,512	M156L	probably benign	Het
4930470P17Rik	C	T	2: 170,579,724	A79T	unknown	Het
4930522L14Rik	A	G	5: 109,736,873	I373T	probably benign	Het
A830010M20Rik	C	A	5: 107,510,451	A1117E	probably damaging	Het
Amotl1	G	A	9: 14,593,373	Q217*	probably null	Het
Ankrd28	A	T	14: 31,732,054	C254S	probably damaging	Het
Ap2a1	A	G	7: 44,901,546		probably benign	Het
Arfgef3	A	T	10: 18,654,247	S245T	probably benign	Het
Arntl	A	T	7: 113,285,037	K94I	probably damaging	Het
Atp1b2	A	T	11: 69,601,561	D224E	probably damaging	Het
Boc	G	A	16: 44,487,721	R924W	probably damaging	Het
Car14	C	T	3: 95,898,873	G292D	probably benign	Het
Cenpb	T	C	2: 131,178,183		probably benign	Het
Ces1b	A	T	8: 93,063,030	D423E	possibly damaging	Het
Cfap54	T	A	10: 92,972,694	N1373I	possibly damaging	Het
Chrdl2	T	C	7: 100,006,541		probably benign	Het
Cic	T	G	7: 25,282,883	S12A	possibly damaging	Het
Csmd2	A	T	4: 128,442,892	Q1421L	probably benign	Het
D630039A03Rik	T	C	4: 57,910,452	H120R	possibly damaging	Het
Dicer1	T	A	12: 104,692,446	D1779V	probably damaging	Het
Dock9	G	T	14: 121,610,097	H1016N	possibly damaging	Het
Dxo	T	C	17: 34,838,998	L352P	probably damaging	Het
Eif2b5	T	A	16: 20,500,233	F78I	probably damaging	Het
Eri2	A	G	7: 119,784,946		probably benign	Het
Fam208b	A	G	13: 3,570,391	F2170S	probably damaging	Het
Fbxw7	T	G	3: 84,925,689	L13V	possibly damaging	Het
Fgf7	T	A	2: 126,035,783	C23*	probably null	Het
Fubp1	T	A	3: 152,222,068		probably null	Het
Gm2663	A	T	6: 40,995,953	I240N	probably damaging	Het
Gnb1l	C	T	16: 18,548,096	Q140*	probably null	Het
Gnptab	G	A	10: 88,436,528	R1010Q	probably damaging	Het
Gtf2h1	G	A	7: 46,822,878	W544*	probably null	Het
Gucy2c	C	T	6: 136,722,514	E586K	probably damaging	Het
Hc	T	A	2: 35,039,734	E232V	probably benign	Het
Ifi207	T	A	1: 173,730,056	D372V	unknown	Het
Igkv8-28	A	T	6: 70,144,118	V15E	probably benign	Het
Il1rap	A	G	16: 26,692,799	S198G	possibly damaging	Het
Lct	A	G	1: 128,300,387	I1123T	probably damaging	Het
Lhcgr	T	C	17: 88,742,697	E467G	probably damaging	Het
Macf1	C	T	4: 123,476,015	R86K	probably benign	Het
Maml3	T	A	3: 51,856,532	Q337L	probably benign	Het
March10	T	A	11: 105,390,037	D474V	probably benign	Het
March2	G	T	17: 33,709,916	T2K	probably damaging	Het
Mast1	A	G	8: 84,937,193		probably null	Het
Med12l	T	C	3: 59,233,212	I868T	probably damaging	Het
Msrb1	T	C	17: 24,740,173	S100P	probably damaging	Het
Nlrp4c	T	C	7: 6,066,126	L342P	probably benign	Het
Nrxn3	T	A	12: 90,331,956	V417E	possibly damaging	Het
Ntng1	T	A	3: 109,934,713	D248V	probably damaging	Het
Oaz3	T	C	3: 94,434,998	Q117R	probably benign	Het
Olfr1311	A	G	2: 112,020,931	Y308H	probably benign	Het
Olfr444	A	G	6: 42,955,521	I8V	probably benign	Het
Olfr589	A	G	7: 103,155,414	L111P	probably benign	Het
Osbpl3	A	C	6: 50,300,973	S767A	probably benign	Het
Pafah1b1	A	T	11: 74,685,871		probably benign	Het
Pard6b	A	G	2: 168,098,788	T232A	probably damaging	Het
Paxip1	A	T	5: 27,765,206	C596S	probably damaging	Het
Psmd6	A	T	14: 14,120,932		probably benign	Het
Rock2	T	A	12: 16,977,740	C1353S	probably damaging	Het
Rpl31-ps17	C	T	12: 54,701,612		noncoding transcript	Het
Sel1l	T	A	12: 91,813,893	H658L	probably damaging	Het
Sh3yl1	T	A	12: 30,940,314	L105Q	probably damaging	Het
Shroom3	G	T	5: 92,943,086	V1151F	probably damaging	Het
Sirt1	T	C	10: 63,335,722	K227E	probably benign	Het
Slc25a34	A	T	4: 141,623,588	F37I	possibly damaging	Het
Slc39a5	T	A	10: 128,397,049	I378F	probably damaging	Het
Smarcad1	A	T	6: 65,098,824	D731V	probably null	Het
Sox6	T	G	7: 115,541,670	K483N	probably damaging	Het
Sp140	T	A	1: 85,610,828	D95E	possibly damaging	Het
Srgap1	G	T	10: 121,792,351	D882E	probably benign	Het
Syne4	T	C	7: 30,316,833		probably benign	Het
Tec	T	C	5: 72,768,776	Y289C	probably benign	Het
Tmem102	A	T	11: 69,804,802	Y115N	probably damaging	Het
Tns2	C	T	15: 102,108,934	R281C	probably damaging	Het
Trav17	T	A	14: 53,806,640	M1K	probably null	Het
Trdn	T	A	10: 33,399,082		probably null	Het
Trp53	A	T	11: 69,586,921	I8F	probably benign	Het
Ttn	T	A	2: 76,754,662	D22064V	probably damaging	Het
Ube3c	G	A	5: 29,632,838		probably null	Het
Ulk1	C	T	5: 110,788,947		probably null	Het
Upp1	T	C	11: 9,135,976	V271A	probably damaging	Het
Vmn2r4	T	C	3: 64,388,661	E901G	probably damaging	Het
Vmn2r96	G	A	17: 18,597,508	G449D	probably damaging	Het
Vps37b	T	C	5: 124,006,612	K165E	probably damaging	Het
Vwf	A	T	6: 125,566,305	I185F	possibly damaging	Het
Wasf2	A	G	4: 133,185,004	T56A	probably benign	Het
Zdhhc23	C	G	16: 43,973,589	D241H	possibly damaging	Het
Zfp276	T	C	8: 123,254,884	S57P	probably benign	Het
Zxdc	A	G	6: 90,370,518	H287R	probably damaging	Het

Other mutations in Pnpla6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00227:Pnpla6	APN	8	3523808	missense	probably damaging	1.00
IGL00820:Pnpla6	APN	8	3532358	missense	possibly damaging	0.95
IGL00839:Pnpla6	APN	8	3542299	missense	probably benign	0.05
IGL01732:Pnpla6	APN	8	3522616	missense	probably damaging	0.99
IGL01973:Pnpla6	APN	8	3517619	missense	probably damaging	1.00
IGL02267:Pnpla6	APN	8	3517327	missense	probably benign	0.00
IGL03246:Pnpla6	APN	8	3531530	missense	probably benign	0.01
IGL03286:Pnpla6	APN	8	3531473	missense	probably damaging	0.99
Immemorial	UTSW	8	3531677	missense	probably benign	0.38
Mammilary	UTSW	8	3521384	missense	probably benign	0.01
I0000:Pnpla6	UTSW	8	3542322	missense	probably benign
R0141:Pnpla6	UTSW	8	3532117	critical splice donor site	probably null
R0180:Pnpla6	UTSW	8	3524250	critical splice acceptor site	probably null
R0377:Pnpla6	UTSW	8	3541501	missense	probably damaging	1.00
R0563:Pnpla6	UTSW	8	3523333	missense	possibly damaging	0.51
R0660:Pnpla6	UTSW	8	3522269	unclassified	probably benign
R0786:Pnpla6	UTSW	8	3523317	missense	probably benign
R0827:Pnpla6	UTSW	8	3517618	missense	possibly damaging	0.71
R0882:Pnpla6	UTSW	8	3517081	missense	probably damaging	1.00
R1512:Pnpla6	UTSW	8	3535459	splice site	probably benign
R1552:Pnpla6	UTSW	8	3522403	missense	probably damaging	1.00
R1609:Pnpla6	UTSW	8	3517135	missense	probably damaging	1.00
R1770:Pnpla6	UTSW	8	3534634	missense	possibly damaging	0.94
R1779:Pnpla6	UTSW	8	3541404	missense	probably damaging	1.00
R1987:Pnpla6	UTSW	8	3542370	missense	probably benign	0.00
R3079:Pnpla6	UTSW	8	3541512	missense	probably benign	0.25
R3125:Pnpla6	UTSW	8	3534670	missense	probably null	1.00
R4171:Pnpla6	UTSW	8	3543997	missense	probably benign	0.09
R4281:Pnpla6	UTSW	8	3521513	missense	probably damaging	1.00
R4674:Pnpla6	UTSW	8	3521412	missense	probably damaging	1.00
R4779:Pnpla6	UTSW	8	3522838	missense	probably benign	0.00
R5114:Pnpla6	UTSW	8	3522613	missense	probably damaging	0.98
R5459:Pnpla6	UTSW	8	3535829	missense	probably benign	0.01
R5510:Pnpla6	UTSW	8	3521397	missense	probably damaging	0.99
R5538:Pnpla6	UTSW	8	3531508	missense	probably benign	0.01
R5664:Pnpla6	UTSW	8	3537478	missense	probably damaging	0.98
R6063:Pnpla6	UTSW	8	3524156	missense	probably benign	0.21
R6314:Pnpla6	UTSW	8	3521572	missense	probably benign	0.39
R6321:Pnpla6	UTSW	8	3544015	missense	probably benign
R6454:Pnpla6	UTSW	8	3537986	missense	probably damaging	0.99
R6477:Pnpla6	UTSW	8	3536627	missense	probably benign	0.00
R6524:Pnpla6	UTSW	8	3534519	splice site	probably null
R6809:Pnpla6	UTSW	8	3534611	missense	possibly damaging	0.72
R6975:Pnpla6	UTSW	8	3538068	missense	probably damaging	1.00
R7293:Pnpla6	UTSW	8	3538068	missense	probably damaging	1.00
R7389:Pnpla6	UTSW	8	3543981	nonsense	probably null
R7426:Pnpla6	UTSW	8	3516540	splice site	probably null
R7520:Pnpla6	UTSW	8	3537508	missense	probably damaging	1.00
R7666:Pnpla6	UTSW	8	3541591	missense	probably benign	0.01
R7733:Pnpla6	UTSW	8	3522660	missense	probably benign	0.01
R7743:Pnpla6	UTSW	8	3536594	missense	possibly damaging	0.77
R7744:Pnpla6	UTSW	8	3531677	missense	probably benign	0.38
R7923:Pnpla6	UTSW	8	3531737	nonsense	probably null
R7980:Pnpla6	UTSW	8	3536562	missense	probably damaging	0.97
R8141:Pnpla6	UTSW	8	3521384	missense	probably benign	0.01
R8191:Pnpla6	UTSW	8	3542382	missense	probably benign	0.12
R8251:Pnpla6	UTSW	8	3532399	missense	probably benign	0.29
R8881:Pnpla6	UTSW	8	3531489	missense	probably benign	0.00
R8917:Pnpla6	UTSW	8	3517637	missense	possibly damaging	0.50
R8939:Pnpla6	UTSW	8	3521319	missense	possibly damaging	0.86
R8988:Pnpla6	UTSW	8	3517401	missense	possibly damaging	0.51
R9037:Pnpla6	UTSW	8	3542379	nonsense	probably null
R9264:Pnpla6	UTSW	8	3523294	missense	probably benign
R9265:Pnpla6	UTSW	8	3523294	missense	probably benign
R9386:Pnpla6	UTSW	8	3521417	critical splice donor site	probably null
X0018:Pnpla6	UTSW	8	3517337	missense	probably damaging	1.00
Z1177:Pnpla6	UTSW	8	3536979	missense	possibly damaging	0.76

Predicted Primers

PCR Primer
(F):5'- TGGTCGCAGCATTAAATGGAG -3'
(R):5'- CAGGACTAGTGATTTCCCATGTG -3'

Sequencing Primer
(F):5'- ATTGGTATAGCTGTGGTCACTAAC -3'
(R):5'- ATGTGCCCTCCCAACTGAC -3'

Posted On

2015-12-29