Incidental Mutation 'R4776:Pnpla6'
ID 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 8
Chromosomal Location 3565384-3594267 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 3573818 bp (GRCm39)
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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 question?
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
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610028H24Rik A T 10: 76,293,346 (GRCm39) M156L probably benign Het
4930470P17Rik C T 2: 170,421,644 (GRCm39) A79T unknown Het
4930522L14Rik A G 5: 109,884,739 (GRCm39) I373T probably benign Het
Amotl1 G A 9: 14,504,669 (GRCm39) Q217* probably null Het
Ankrd28 A T 14: 31,454,011 (GRCm39) C254S probably damaging Het
Ap2a1 A G 7: 44,550,970 (GRCm39) probably benign Het
Arfgef3 A T 10: 18,529,995 (GRCm39) S245T probably benign Het
Atp1b2 A T 11: 69,492,387 (GRCm39) D224E probably damaging Het
Bmal1 A T 7: 112,884,244 (GRCm39) K94I probably damaging Het
Boc G A 16: 44,308,084 (GRCm39) R924W probably damaging Het
Btbd8 C A 5: 107,658,317 (GRCm39) A1117E probably damaging Het
Car14 C T 3: 95,806,185 (GRCm39) G292D probably benign Het
Cenpb T C 2: 131,020,103 (GRCm39) probably benign Het
Ces1b A T 8: 93,789,658 (GRCm39) D423E possibly damaging Het
Cfap54 T A 10: 92,808,556 (GRCm39) N1373I possibly damaging Het
Chrdl2 T C 7: 99,655,748 (GRCm39) probably benign Het
Cic T G 7: 24,982,308 (GRCm39) S12A possibly damaging Het
Csmd2 A T 4: 128,336,685 (GRCm39) Q1421L probably benign Het
D630039A03Rik T C 4: 57,910,452 (GRCm39) H120R possibly damaging Het
Dicer1 T A 12: 104,658,705 (GRCm39) D1779V probably damaging Het
Dock9 G T 14: 121,847,509 (GRCm39) H1016N possibly damaging Het
Dxo T C 17: 35,057,974 (GRCm39) L352P probably damaging Het
Eif2b5 T A 16: 20,318,983 (GRCm39) F78I probably damaging Het
Eri2 A G 7: 119,384,169 (GRCm39) probably benign Het
Fbxw7 T G 3: 84,832,996 (GRCm39) L13V possibly damaging Het
Fgf7 T A 2: 125,877,703 (GRCm39) C23* probably null Het
Fubp1 T A 3: 151,927,705 (GRCm39) probably null Het
Gm2663 A T 6: 40,972,887 (GRCm39) I240N probably damaging Het
Gnb1l C T 16: 18,366,846 (GRCm39) Q140* probably null Het
Gnptab G A 10: 88,272,390 (GRCm39) R1010Q probably damaging Het
Gtf2h1 G A 7: 46,472,302 (GRCm39) W544* probably null Het
Gucy2c C T 6: 136,699,512 (GRCm39) E586K probably damaging Het
Hc T A 2: 34,929,746 (GRCm39) E232V probably benign Het
Ifi207 T A 1: 173,557,622 (GRCm39) D372V unknown Het
Igkv8-28 A T 6: 70,121,102 (GRCm39) V15E probably benign Het
Il1rap A G 16: 26,511,549 (GRCm39) S198G possibly damaging Het
Lct A G 1: 128,228,124 (GRCm39) I1123T probably damaging Het
Lhcgr T C 17: 89,050,125 (GRCm39) E467G probably damaging Het
Macf1 C T 4: 123,369,808 (GRCm39) R86K probably benign Het
Maml3 T A 3: 51,763,953 (GRCm39) Q337L probably benign Het
Marchf10 T A 11: 105,280,863 (GRCm39) D474V probably benign Het
Marchf2 G T 17: 33,928,890 (GRCm39) T2K probably damaging Het
Mast1 A G 8: 85,663,822 (GRCm39) probably null Het
Med12l T C 3: 59,140,633 (GRCm39) I868T probably damaging Het
Msrb1 T C 17: 24,959,147 (GRCm39) S100P probably damaging Het
Nlrp4c T C 7: 6,069,125 (GRCm39) L342P probably benign Het
Nrxn3 T A 12: 90,298,730 (GRCm39) V417E possibly damaging Het
Ntng1 T A 3: 109,842,029 (GRCm39) D248V probably damaging Het
Oaz3 T C 3: 94,342,305 (GRCm39) Q117R probably benign Het
Or2a56 A G 6: 42,932,455 (GRCm39) I8V probably benign Het
Or4f58 A G 2: 111,851,276 (GRCm39) Y308H probably benign Het
Or52e2 A G 7: 102,804,621 (GRCm39) L111P probably benign Het
Osbpl3 A C 6: 50,277,953 (GRCm39) S767A probably benign Het
Pafah1b1 A T 11: 74,576,697 (GRCm39) probably benign Het
Pard6b A G 2: 167,940,708 (GRCm39) T232A probably damaging Het
Paxip1 A T 5: 27,970,204 (GRCm39) C596S probably damaging Het
Psmd6 A T 14: 14,120,932 (GRCm38) probably benign Het
Relch T A 1: 105,647,260 (GRCm39) Y683* probably null Het
Rock2 T A 12: 17,027,741 (GRCm39) C1353S probably damaging Het
Rpl31-ps17 C T 12: 54,748,397 (GRCm39) noncoding transcript Het
Sel1l T A 12: 91,780,667 (GRCm39) H658L probably damaging Het
Sh3yl1 T A 12: 30,990,313 (GRCm39) L105Q probably damaging Het
Shroom3 G T 5: 93,090,945 (GRCm39) V1151F probably damaging Het
Sirt1 T C 10: 63,171,501 (GRCm39) K227E probably benign Het
Slc25a34 A T 4: 141,350,899 (GRCm39) F37I possibly damaging Het
Slc39a5 T A 10: 128,232,918 (GRCm39) I378F probably damaging Het
Smarcad1 A T 6: 65,075,808 (GRCm39) D731V probably null Het
Sox6 T G 7: 115,140,905 (GRCm39) K483N probably damaging Het
Sp140 T A 1: 85,538,549 (GRCm39) D95E possibly damaging Het
Srgap1 G T 10: 121,628,256 (GRCm39) D882E probably benign Het
Syne4 T C 7: 30,016,258 (GRCm39) probably benign Het
Tasor2 A G 13: 3,620,391 (GRCm39) F2170S probably damaging Het
Tec T C 5: 72,926,119 (GRCm39) Y289C probably benign Het
Tmem102 A T 11: 69,695,628 (GRCm39) Y115N probably damaging Het
Tns2 C T 15: 102,017,369 (GRCm39) R281C probably damaging Het
Trav17 T A 14: 54,044,097 (GRCm39) M1K probably null Het
Trdn T A 10: 33,275,078 (GRCm39) probably null Het
Trp53 A T 11: 69,477,747 (GRCm39) I8F probably benign Het
Ttn T A 2: 76,585,006 (GRCm39) D22064V probably damaging Het
Ube3c G A 5: 29,837,836 (GRCm39) probably null Het
Ulk1 C T 5: 110,936,813 (GRCm39) probably null Het
Upp1 T C 11: 9,085,976 (GRCm39) V271A probably damaging Het
Vmn2r4 T C 3: 64,296,082 (GRCm39) E901G probably damaging Het
Vmn2r96 G A 17: 18,817,770 (GRCm39) G449D probably damaging Het
Vps37b T C 5: 124,144,675 (GRCm39) K165E probably damaging Het
Vwf A T 6: 125,543,268 (GRCm39) I185F possibly damaging Het
Wasf2 A G 4: 132,912,315 (GRCm39) T56A probably benign Het
Zdhhc23 C G 16: 43,793,952 (GRCm39) D241H possibly damaging Het
Zfp276 T C 8: 123,981,623 (GRCm39) S57P probably benign Het
Zxdc A G 6: 90,347,500 (GRCm39) H287R probably damaging Het
Other mutations in Pnpla6
AlleleSourceChrCoordTypePredicted EffectPPH 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
R1779:Pnpla6 UTSW 8 3,591,404 (GRCm39) missense probably damaging 1.00
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
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'- TGGTCGCAGCATTAAATGGAG -3'
(R):5'- CAGGACTAGTGATTTCCCATGTG -3'

Sequencing Primer
(F):5'- ATTGGTATAGCTGTGGTCACTAAC -3'
(R):5'- ATGTGCCCTCCCAACTGAC -3'
Posted On 2015-12-29