Incidental Mutation 'R4779:Pnpla6'
ID 368157
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 045240-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4779 (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 3572838 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 345 (V345A)
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: V323A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000004681
Gene: ENSMUSG00000004565
AA Change: V323A

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: V323A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000106699
Gene: ENSMUSG00000004565
AA Change: V323A

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: V355A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Predicted Effect probably benign
Transcript: ENSMUST00000208002
AA Change: V345A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208006
Predicted Effect probably benign
Transcript: ENSMUST00000208762
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208851
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208315
Meta Mutation Damage Score 0.0699 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.8%
Validation Efficiency 98% (95/97)
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: 87 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930562C15Rik T A 16: 4,667,613 (GRCm39) S335T unknown Het
4933421I07Rik T A 7: 42,097,455 (GRCm39) H13L possibly damaging Het
6030468B19Rik A G 11: 117,696,834 (GRCm39) T185A probably benign Het
Abcc1 T A 16: 14,228,635 (GRCm39) V294E probably benign Het
Abhd16b A G 2: 181,135,253 (GRCm39) T52A possibly damaging Het
Actl7a A T 4: 56,743,632 (GRCm39) N53I probably benign Het
Ankmy1 T C 1: 92,814,445 (GRCm39) E354G probably benign Het
Arap1 T C 7: 101,053,574 (GRCm39) F1301S probably damaging Het
Arfgef1 A T 1: 10,223,958 (GRCm39) W1447R probably damaging Het
Atoh7 ATGGCGCT AT 10: 62,936,187 (GRCm39) probably benign Het
Ccl24 T A 5: 135,601,811 (GRCm39) T6S possibly damaging Het
Cep152 G T 2: 125,410,812 (GRCm39) P1292Q possibly damaging Het
Cfap46 T C 7: 139,239,731 (GRCm39) probably benign Het
Chd6 A T 2: 160,791,477 (GRCm39) S2627T probably damaging Het
Chd8 A T 14: 52,468,963 (GRCm39) S552T probably damaging Het
Ciita C A 16: 10,329,230 (GRCm39) L502M probably damaging Het
Clic1 T C 17: 35,271,463 (GRCm39) F31S probably damaging Het
Cntnap1 T A 11: 101,068,898 (GRCm39) I147N possibly damaging Het
Cplane1 T C 15: 8,248,322 (GRCm39) S1624P probably benign Het
Crispld1 T A 1: 17,819,831 (GRCm39) D276E probably benign Het
Cspg4 A T 9: 56,793,092 (GRCm39) N276Y probably damaging Het
Cspg4b A T 13: 113,504,870 (GRCm39) N2000Y possibly damaging Het
Cwf19l2 A G 9: 3,410,035 (GRCm39) M55V possibly damaging Het
Cyp2c69 T C 19: 39,866,038 (GRCm39) N185S probably benign Het
Dop1b T C 16: 93,553,969 (GRCm39) I301T probably damaging Het
Epg5 T C 18: 78,034,580 (GRCm39) V1443A probably benign Het
Ephb4 T C 5: 137,363,964 (GRCm39) V612A probably benign Het
Fcgbp T A 7: 27,794,362 (GRCm39) C1189S probably damaging Het
Fgfr2 T G 7: 129,786,923 (GRCm39) probably benign Het
Fmn2 A G 1: 174,437,461 (GRCm39) E1144G probably damaging Het
Fmo3 T C 1: 162,796,407 (GRCm39) Y55C probably damaging Het
Frmpd1 A G 4: 45,229,865 (GRCm39) T11A probably damaging Het
Ghdc G T 11: 100,660,929 (GRCm39) Q79K possibly damaging Het
Gm11677 C T 11: 111,615,537 (GRCm39) noncoding transcript Het
Gm5591 T C 7: 38,221,680 (GRCm39) T130A probably damaging Het
Heg1 T G 16: 33,540,142 (GRCm39) D367E probably benign Het
Igkv13-84 C T 6: 68,916,894 (GRCm39) P64S probably damaging Het
Il10rb T A 16: 91,211,545 (GRCm39) S128T possibly damaging Het
Il15ra T A 2: 11,723,117 (GRCm39) I47N probably damaging Het
Il33 C A 19: 29,936,311 (GRCm39) S207* probably null Het
Itgb7 A G 15: 102,132,848 (GRCm39) Y155H possibly damaging Het
Kdm5a A G 6: 120,346,060 (GRCm39) probably benign Het
Kif11 G A 19: 37,406,397 (GRCm39) V987I probably benign Het
Krtap19-2 G A 16: 88,670,762 (GRCm39) probably benign Het
Krtap24-1 T A 16: 88,408,417 (GRCm39) R236S probably damaging Het
L3mbtl2 A G 15: 81,566,813 (GRCm39) I406V probably benign Het
Lrp2 A T 2: 69,290,059 (GRCm39) H3593Q possibly damaging Het
Mavs G T 2: 131,082,285 (GRCm39) W56C probably damaging Het
Mn1 C T 5: 111,567,526 (GRCm39) P499S probably damaging Het
Ntn5 T A 7: 45,340,895 (GRCm39) C178S probably damaging Het
Nufip2 A G 11: 77,577,154 (GRCm39) H34R unknown Het
Or5p51 T A 7: 107,444,755 (GRCm39) M62L possibly damaging Het
Or6f2 T A 7: 139,756,363 (GRCm39) L110Q probably damaging Het
Osbpl10 C T 9: 114,938,598 (GRCm39) S86L probably damaging Het
Pitpna T A 11: 75,511,153 (GRCm39) M242K possibly damaging Het
Polk A G 13: 96,632,999 (GRCm39) probably null Het
Polr3k A G 2: 181,506,340 (GRCm39) Y30C probably damaging Het
Pramel6 A G 2: 87,339,941 (GRCm39) H235R probably benign Het
Ptpra G A 2: 130,379,537 (GRCm39) V364I probably damaging Het
Recql A G 6: 142,309,426 (GRCm39) probably benign Het
Ring1 T C 17: 34,241,263 (GRCm39) probably benign Het
Rufy4 T C 1: 74,186,822 (GRCm39) C537R probably damaging Het
Samsn1 C A 16: 75,744,177 (GRCm39) noncoding transcript Het
Scara5 A G 14: 65,968,198 (GRCm39) H157R probably benign Het
Sdc3 C T 4: 130,546,376 (GRCm39) P245L probably damaging Het
Slc18b1 T A 10: 23,696,767 (GRCm39) M318K possibly damaging Het
Slc26a10 C T 10: 127,009,224 (GRCm39) A638T possibly damaging Het
Slc35f2 T A 9: 53,717,013 (GRCm39) W259R possibly damaging Het
Spata13 G A 14: 60,991,356 (GRCm39) W366* probably null Het
Sptlc3 A G 2: 139,431,509 (GRCm39) T344A probably benign Het
Tap1 T C 17: 34,412,865 (GRCm39) V560A probably damaging Het
Tbc1d1 T C 5: 64,435,389 (GRCm39) probably null Het
Tlr11 A G 14: 50,598,707 (GRCm39) Y231C possibly damaging Het
Tmem245 A T 4: 56,936,468 (GRCm39) S230T possibly damaging Het
Tnnt3 C T 7: 142,068,020 (GRCm39) probably benign Het
Traf7 C G 17: 24,729,412 (GRCm39) probably benign Het
Tshz2 A G 2: 169,804,601 (GRCm39) probably benign Het
Tshz3 T C 7: 36,468,397 (GRCm39) S129P probably damaging Het
Ttc6 A T 12: 57,776,237 (GRCm39) N1727I probably damaging Het
Ttc7b A G 12: 100,369,621 (GRCm39) S383P probably damaging Het
Tulp3 T A 6: 128,300,083 (GRCm39) I448F probably damaging Het
Ube3b T C 5: 114,542,778 (GRCm39) probably null Het
Vav1 G A 17: 57,603,552 (GRCm39) V84I probably damaging Het
Vav3 A T 3: 109,416,110 (GRCm39) K243I possibly damaging Het
Vmn1r25 T A 6: 57,956,011 (GRCm39) I93F probably damaging Het
Vmn2r73 C T 7: 85,520,923 (GRCm39) W348* probably null Het
Zdbf2 A G 1: 63,342,397 (GRCm39) R259G possibly 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
R4776:Pnpla6 UTSW 8 3,573,818 (GRCm39) missense probably benign 0.01
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'- CTTCAGTCATGTGAGTTGGACAG -3'
(R):5'- CACTGCTTTCTACGGCCATG -3'

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