Incidental Mutation 'R0141:Pnpla6'
ID 22325
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 038426-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0141 (G1)
Quality Score 220
Status Validated (trace)
Chromosome 8
Chromosomal Location 3565384-3594267 bp(+) (GRCm39)
Type of Mutation critical splice donor site (1 bp from exon)
DNA Base Change (assembly) G to T at 3582117 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
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 null
Transcript: ENSMUST00000004681
SMART Domains Protein: ENSMUSP00000004681
Gene: ENSMUSG00000004565

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 null
Transcript: ENSMUST00000111070
SMART Domains Protein: ENSMUSP00000106699
Gene: ENSMUSG00000004565

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 noncoding transcript
Transcript: ENSMUST00000207299
Predicted Effect probably benign
Transcript: ENSMUST00000207421
Predicted Effect noncoding transcript
Transcript: ENSMUST00000207929
Predicted Effect probably null
Transcript: ENSMUST00000207941
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208851
Predicted Effect probably null
Transcript: ENSMUST00000208002
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208370
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208914
Meta Mutation Damage Score 0.9594 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 98.0%
  • 10x: 95.5%
  • 20x: 89.9%
Validation Efficiency 88% (50/57)
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acot12 A C 13: 91,919,947 (GRCm39) D294A probably benign Het
Adamts9 T C 6: 92,920,066 (GRCm39) D24G probably benign Het
Ahnak G A 19: 8,984,044 (GRCm39) G1776D probably damaging Het
Arfgef3 C A 10: 18,473,155 (GRCm39) C1636F probably damaging Het
AW551984 A G 9: 39,501,940 (GRCm39) L722P probably damaging Het
Ccndbp1 T A 2: 120,842,903 (GRCm39) M188K probably damaging Het
Col27a1 A T 4: 63,183,870 (GRCm39) probably null Het
Cpt1c A G 7: 44,616,095 (GRCm39) Y306H probably damaging Het
Cyp3a57 A G 5: 145,298,912 (GRCm39) I71V probably benign Het
Def8 G A 8: 124,183,234 (GRCm39) A278T probably damaging Het
Dmrt2 A T 19: 25,655,655 (GRCm39) Q418L possibly damaging Het
Ebf1 T C 11: 44,798,827 (GRCm39) L284S probably damaging Het
Fam131a G A 16: 20,517,738 (GRCm39) A15T probably benign Het
Fbxo17 A G 7: 28,432,916 (GRCm39) T146A possibly damaging Het
Fer1l6 A G 15: 58,430,251 (GRCm39) E226G probably damaging Het
Galnt18 A T 7: 111,198,238 (GRCm39) I174N probably damaging Het
Gm44501 T C 17: 40,889,744 (GRCm39) I86T probably benign Het
Gtsf1l T C 2: 162,929,246 (GRCm39) Q79R probably benign Het
Hapln4 T C 8: 70,540,930 (GRCm39) L321P probably damaging Het
Herc2 A G 7: 55,771,309 (GRCm39) T1024A probably benign Het
Hps5 A G 7: 46,438,605 (GRCm39) S43P probably damaging Het
Igsf10 A G 3: 59,238,253 (GRCm39) Y643H probably damaging Het
Lama4 G A 10: 38,968,274 (GRCm39) R1472H probably benign Het
Lhx9 A G 1: 138,767,744 (GRCm39) Y73H possibly damaging Het
Loxl1 T A 9: 58,219,415 (GRCm39) Q252L probably damaging Het
Lrrc37 A C 11: 103,504,512 (GRCm39) I2485M probably damaging Het
Nfat5 C T 8: 108,065,707 (GRCm39) R156W probably damaging Het
Nr3c2 T A 8: 77,635,037 (GRCm39) V46D probably damaging Het
Or11h4 T C 14: 50,973,840 (GRCm39) S260G possibly damaging Het
Or4k77 T A 2: 111,199,835 (GRCm39) I286N probably damaging Het
Or5i1 C G 2: 87,613,049 (GRCm39) P55R possibly damaging Het
Or5p63 A C 7: 107,811,210 (GRCm39) N175K possibly damaging Het
Or5p70 A T 7: 107,994,575 (GRCm39) N83Y probably benign Het
Osbp T C 19: 11,951,223 (GRCm39) V256A possibly damaging Het
Pclo A T 5: 14,841,936 (GRCm39) D4737V unknown Het
Pkdrej A G 15: 85,699,831 (GRCm39) I2035T probably damaging Het
Plek2 A G 12: 78,941,278 (GRCm39) S185P probably damaging Het
Pou3f2 T C 4: 22,487,210 (GRCm39) T308A possibly damaging Het
Pramel22 T C 4: 143,381,138 (GRCm39) Y295C probably benign Het
Pxmp4 A G 2: 154,434,215 (GRCm39) V82A probably damaging Het
Rnf6 A T 5: 146,148,645 (GRCm39) N135K possibly damaging Het
Rtl1 A G 12: 109,559,382 (GRCm39) V819A probably damaging Het
Scn1a C A 2: 66,119,406 (GRCm39) V1355L probably damaging Het
Scn2a T A 2: 65,542,160 (GRCm39) N754K probably benign Het
Serpina3b A T 12: 104,097,030 (GRCm39) N104Y probably damaging Het
Sh3rf2 T C 18: 42,289,122 (GRCm39) S648P probably benign Het
Slc17a6 G A 7: 51,318,815 (GRCm39) V486I probably benign Het
Spata31e2 A T 1: 26,722,863 (GRCm39) N772K probably benign Het
Syne2 T G 12: 75,988,072 (GRCm39) D1743E probably damaging Het
Tex14 T G 11: 87,383,857 (GRCm39) probably null Het
Tfb1m T C 17: 3,605,232 (GRCm39) D87G probably damaging Het
Tll2 C T 19: 41,086,351 (GRCm39) G609S probably damaging Het
Tsc22d2 A T 3: 58,324,577 (GRCm39) probably benign Het
Tsen2 A G 6: 115,545,790 (GRCm39) D360G probably damaging Het
Ugt2b37 G A 5: 87,388,842 (GRCm39) P457L probably damaging Het
Vmn1r68 T C 7: 10,261,252 (GRCm39) N282S possibly damaging Het
Vmn2r58 G A 7: 41,511,309 (GRCm39) S498F probably benign Het
Zfp959 T C 17: 56,205,139 (GRCm39) I392T probably benign 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
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
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'- GGAGACCCAACCCCAACTTTAGTG -3'
(R):5'- TCTGGCTTAGCAGATGAATAAGGCG -3'

Sequencing Primer
(F):5'- TCCTTCCTGTGAGTCAGAAACAATC -3'
(R):5'- GAGACTGAAAGGTCTCACCTTTG -3'
Posted On 2013-04-16