Incidental Mutation 'R5510:Pnpla6'
| ID |
431155 |
| 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 |
043071-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5510 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
3565384-3594267 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 3571397 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Phenylalanine
at position 140
(Y140F)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000106699
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004681]
[ENSMUST00000111070]
[ENSMUST00000207146]
[ENSMUST00000207424]
[ENSMUST00000207941]
[ENSMUST00000208002]
[ENSMUST00000208310]
[ENSMUST00000208762]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000004681
AA Change: Y140F
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000004681
Gene: ENSMUSG00000004565
AA Change: Y140F
| 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: Y140F
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000106699
Gene: ENSMUSG00000004565
AA Change: Y140F
| 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: ENSMUST00000207146
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000207424
AA Change: Y140F
PolyPhen 2
Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000207430
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000207941
AA Change: Y172F
PolyPhen 2
Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000208002
AA Change: Y162F
PolyPhen 2
Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000208006
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000208310
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000208315
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000208851
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000208762
|
| Meta Mutation Damage Score |
0.4466 |
| Coding Region Coverage |
- 1x: 98.5%
- 3x: 97.3%
- 10x: 95.1%
- 20x: 90.1%
|
| Validation Efficiency |
99% (91/92) |
| 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: 73 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgrl4 |
T |
G |
3: 151,203,467 (GRCm39) |
I59R |
possibly damaging |
Het |
| Adgrv1 |
T |
A |
13: 81,593,363 (GRCm39) |
D4208V |
probably damaging |
Het |
| Aimp2 |
A |
T |
5: 143,843,347 (GRCm39) |
|
probably benign |
Het |
| Ank3 |
G |
A |
10: 69,838,395 (GRCm39) |
R1566K |
possibly damaging |
Het |
| Ankib1 |
A |
G |
5: 3,779,693 (GRCm39) |
V392A |
probably benign |
Het |
| Ap2b1 |
A |
G |
11: 83,227,563 (GRCm39) |
|
probably null |
Het |
| Arsg |
A |
G |
11: 109,418,700 (GRCm39) |
E232G |
probably benign |
Het |
| Axdnd1 |
A |
G |
1: 156,162,920 (GRCm39) |
F144S |
probably benign |
Het |
| Bud13 |
T |
A |
9: 46,203,498 (GRCm39) |
M111K |
probably damaging |
Het |
| Cav2 |
T |
C |
6: 17,287,012 (GRCm39) |
F152S |
possibly damaging |
Het |
| Ccdc180 |
A |
G |
4: 45,928,046 (GRCm39) |
T1194A |
probably damaging |
Het |
| Ccdc192 |
G |
A |
18: 57,671,156 (GRCm39) |
|
probably null |
Het |
| Ccdc88c |
T |
C |
12: 100,911,290 (GRCm39) |
K848R |
probably damaging |
Het |
| Ceacam15 |
A |
G |
7: 16,406,024 (GRCm39) |
W176R |
probably damaging |
Het |
| Cenpf |
A |
T |
1: 189,415,100 (GRCm39) |
D136E |
probably benign |
Het |
| Dclk2 |
T |
C |
3: 86,813,344 (GRCm39) |
I201V |
possibly damaging |
Het |
| Defa24 |
T |
A |
8: 22,224,612 (GRCm39) |
D20E |
probably damaging |
Het |
| Dgcr8 |
T |
C |
16: 18,095,039 (GRCm39) |
N566D |
probably damaging |
Het |
| Dido1 |
C |
A |
2: 180,326,966 (GRCm39) |
V386L |
probably benign |
Het |
| Dnah2 |
C |
T |
11: 69,349,746 (GRCm39) |
R2399Q |
probably benign |
Het |
| Dtx3 |
G |
A |
10: 127,028,807 (GRCm39) |
P141S |
probably benign |
Het |
| Fmn1 |
T |
C |
2: 113,426,714 (GRCm39) |
Y1144H |
probably damaging |
Het |
| Gabbr2 |
A |
G |
4: 46,734,113 (GRCm39) |
L535P |
probably damaging |
Het |
| Gimap3 |
T |
A |
6: 48,742,183 (GRCm39) |
E249V |
possibly damaging |
Het |
| Git2 |
A |
T |
5: 114,881,835 (GRCm39) |
|
probably null |
Het |
| Gm4922 |
T |
C |
10: 18,659,745 (GRCm39) |
T326A |
probably benign |
Het |
| Gsdmc2 |
T |
G |
15: 63,700,045 (GRCm39) |
E242D |
probably benign |
Het |
| Hdgfl2 |
G |
A |
17: 56,389,118 (GRCm39) |
G31S |
possibly damaging |
Het |
| Herc2 |
A |
T |
7: 55,856,519 (GRCm39) |
I3956F |
probably damaging |
Het |
| Hsf2bp |
G |
A |
17: 32,165,721 (GRCm39) |
R134C |
unknown |
Het |
| Igf1r |
G |
C |
7: 67,843,107 (GRCm39) |
R739S |
probably benign |
Het |
| Igkv4-51 |
T |
C |
6: 69,658,443 (GRCm39) |
E102G |
probably damaging |
Het |
| Kif1a |
T |
G |
1: 92,969,414 (GRCm39) |
I1156L |
possibly damaging |
Het |
| Kti12 |
T |
C |
4: 108,705,821 (GRCm39) |
L245S |
probably damaging |
Het |
| Med17 |
A |
G |
9: 15,181,700 (GRCm39) |
S17P |
probably benign |
Het |
| Mllt6 |
G |
A |
11: 97,560,326 (GRCm39) |
S210N |
possibly damaging |
Het |
| Mrps18b |
A |
G |
17: 36,225,215 (GRCm39) |
|
probably benign |
Het |
| Ms4a8a |
A |
G |
19: 11,056,828 (GRCm39) |
S85P |
probably benign |
Het |
| Msln |
T |
C |
17: 25,968,847 (GRCm39) |
Q487R |
probably benign |
Het |
| Myh13 |
A |
G |
11: 67,228,549 (GRCm39) |
N363S |
probably benign |
Het |
| Myo6 |
T |
C |
9: 80,152,942 (GRCm39) |
F192L |
probably damaging |
Het |
| Nfkbiz |
T |
C |
16: 55,634,383 (GRCm39) |
D688G |
probably damaging |
Het |
| Nsun4 |
C |
T |
4: 115,908,974 (GRCm39) |
V529I |
possibly damaging |
Het |
| Or12d15 |
A |
T |
17: 37,694,192 (GRCm39) |
M245L |
probably benign |
Het |
| Or1j16 |
G |
A |
2: 36,530,975 (GRCm39) |
R308K |
probably benign |
Het |
| Or5p70 |
G |
A |
7: 107,994,332 (GRCm39) |
A2T |
probably benign |
Het |
| Phf11a |
C |
A |
14: 59,516,834 (GRCm39) |
C208F |
probably damaging |
Het |
| Plekhh2 |
G |
A |
17: 84,874,275 (GRCm39) |
C520Y |
probably benign |
Het |
| Plxna4 |
C |
A |
6: 32,155,293 (GRCm39) |
M1550I |
probably damaging |
Het |
| Ppp1r12a |
T |
A |
10: 108,085,488 (GRCm39) |
S478T |
possibly damaging |
Het |
| Prkcz |
C |
A |
4: 155,357,393 (GRCm39) |
|
probably null |
Het |
| Prss55 |
T |
A |
14: 64,314,574 (GRCm39) |
M199L |
probably damaging |
Het |
| Qrich1 |
G |
A |
9: 108,433,659 (GRCm39) |
V651I |
possibly damaging |
Het |
| Ralyl |
T |
C |
3: 13,842,005 (GRCm39) |
V47A |
probably damaging |
Het |
| Raph1 |
A |
T |
1: 60,562,105 (GRCm39) |
|
probably benign |
Het |
| Rgs12 |
T |
C |
5: 35,123,383 (GRCm39) |
Y389H |
probably damaging |
Het |
| Sec24b |
C |
A |
3: 129,834,544 (GRCm39) |
G82V |
probably damaging |
Het |
| Sema4a |
A |
G |
3: 88,357,293 (GRCm39) |
|
probably null |
Het |
| Slc25a11 |
A |
T |
11: 70,536,361 (GRCm39) |
W149R |
probably damaging |
Het |
| Slc2a7 |
T |
G |
4: 150,244,551 (GRCm39) |
S340A |
probably benign |
Het |
| Slc32a1 |
T |
A |
2: 158,456,716 (GRCm39) |
M457K |
probably damaging |
Het |
| Spata31d1e |
T |
C |
13: 59,890,234 (GRCm39) |
|
probably null |
Het |
| Spint4 |
C |
T |
2: 164,542,812 (GRCm39) |
T135M |
probably damaging |
Het |
| Sult2a2 |
A |
C |
7: 13,472,228 (GRCm39) |
N142H |
probably damaging |
Het |
| Tbc1d1 |
G |
A |
5: 64,490,738 (GRCm39) |
G863D |
probably damaging |
Het |
| Tmem156 |
G |
A |
5: 65,232,917 (GRCm39) |
T151M |
probably benign |
Het |
| Trip12 |
T |
C |
1: 84,746,401 (GRCm39) |
Q459R |
probably damaging |
Het |
| Vmn2r116 |
G |
A |
17: 23,605,095 (GRCm39) |
C136Y |
probably damaging |
Het |
| Vmn2r51 |
C |
T |
7: 9,836,545 (GRCm39) |
V79M |
possibly damaging |
Het |
| Vmn2r67 |
A |
T |
7: 84,801,023 (GRCm39) |
D304E |
probably benign |
Het |
| Wdr93 |
T |
A |
7: 79,399,779 (GRCm39) |
F123I |
probably damaging |
Het |
| Zfp672 |
A |
T |
11: 58,207,456 (GRCm39) |
C288* |
probably null |
Het |
| Zp1 |
T |
C |
19: 10,896,769 (GRCm39) |
Y90C |
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 |
|
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 |
|
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'- AAGGATTAAATGGGTGTCTTAGTTC -3'
(R):5'- AGACGCTGGAAGACCATGTG -3'
Sequencing Primer
(F):5'- TAAGGCCATCTGCATGTCAG -3'
(R):5'- AAGACCATGTGCCGGCAG -3'
|
| Posted On |
2016-10-05 |
Incidental Mutation