Mutagenetix > Incidental Mutation

Incidental Mutation 'R9264:Pnpla6'

702428

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

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9264 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

3515384-3544267 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 3523294 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Proline to Leucine at position 386 (P386L)

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: P364L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000004681
Gene: ENSMUSG00000004565
AA Change: P364L

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: P364L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000106699
Gene: ENSMUSG00000004565
AA Change: P364L

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

probably benign
Transcript: ENSMUST00000207941
AA Change: P396L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

Predicted Effect

probably benign
Transcript: ENSMUST00000208002
AA Change: P386L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

Predicted Effect

probably benign
Transcript: ENSMUST00000208762

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

100% (58/58)

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: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017D01Rik	T	A	19: 11,116,466	M1L	probably benign	Het
Abca15	A	T	7: 120,401,833	I1531L	probably benign	Het
Adam28	T	C	14: 68,607,465	Y791C	probably benign	Het
Ankrd40	T	A	11: 94,338,361	I262N	probably damaging	Het
BC067074	G	A	13: 113,319,480	V687M		Het
Catsperg2	A	T	7: 29,698,188	N1033K	possibly damaging	Het
Cdh10	A	T	15: 18,963,995	D81V	probably damaging	Het
Cep290	T	C	10: 100,498,016	V310A	possibly damaging	Het
Cep78	T	C	19: 15,974,466	Y325C	probably damaging	Het
Clstn3	T	A	6: 124,459,768	D197V	probably damaging	Het
Col11a1	T	C	3: 114,212,160	I1647T	unknown	Het
Col5a1	G	A	2: 27,964,111	R569K	unknown	Het
Cyp4a10	T	C	4: 115,524,278	S180P	probably benign	Het
D630045J12Rik	T	C	6: 38,158,238	I1336V	probably benign	Het
Dchs2	G	A	3: 83,270,477	V946M	probably damaging	Het
Dnah10	A	G	5: 124,736,836	R347G	probably damaging	Het
Dnah11	T	A	12: 118,027,527	D2368V	probably damaging	Het
Ganab	T	C	19: 8,912,864	I719T	possibly damaging	Het
Gm10944	C	A	10: 10,681,839	A11D	unknown	Het
Gmcl1	T	C	6: 86,714,213	M267V	probably benign	Het
Inhbe	T	A	10: 127,350,558	D251V	probably damaging	Het
Kcnj1	G	A	9: 32,396,358	R26Q	probably benign	Het
Lama5	A	G	2: 180,196,478		probably benign	Het
Lin9	T	A	1: 180,667,347	D251E	probably damaging	Het
Magel2	T	A	7: 62,378,596	I416N	possibly damaging	Het
Mdga2	T	C	12: 66,513,283	N772S	probably damaging	Het
Msh3	G	T	13: 92,349,304	Q171K	probably benign	Het
Mslnl	T	G	17: 25,742,532		probably benign	Het
Mtpn	A	G	6: 35,512,241	L116P	possibly damaging	Het
Myh7	T	C	14: 54,975,997	T1351A	probably benign	Het
Nectin3	A	T	16: 46,454,635	I353N	probably damaging	Het
Nprl3	A	T	11: 32,233,948	N500K	probably benign	Het
Nup93	T	A	8: 94,292,720	I181N	probably benign	Het
Olfr1198	T	C	2: 88,746,432	H152R	probably damaging	Het
Olfr362	G	A	2: 37,104,789	T287I	probably damaging	Het
Optc	T	C	1: 133,905,240	I41V	probably benign	Het
Pcdh7	C	A	5: 58,129,321	N1246K	probably benign	Het
Pcdhb3	T	A	18: 37,302,113	D377E	probably benign	Het
Polr3a	T	C	14: 24,470,831	T587A	probably benign	Het
Pramel1	T	G	4: 143,398,529	L341R	probably damaging	Het
Rhot2	A	T	17: 25,841,766	N210K	probably damaging	Het
Slc37a1	A	G	17: 31,300,485	I12V	probably benign	Het
Spata48	T	A	11: 11,464,678	D141E		Het
Sstr3	G	T	15: 78,539,592	N318K	probably damaging	Het
Ssx2ip	T	C	3: 146,437,200	V511A	probably benign	Het
Stfa1	G	A	16: 36,280,568	V57I	unknown	Het
Syne1	T	G	10: 5,262,793	R3265S	probably damaging	Het
Tacc2	G	T	7: 130,626,803	K1739N	probably damaging	Het
Tas2r143	A	T	6: 42,400,739	M168L	probably benign	Het
Tm4sf1	A	T	3: 57,294,610		probably null	Het
Ttc16	A	G	2: 32,763,005	I604T	possibly damaging	Het
Ugt1a10	T	A	1: 88,055,671	W64R	possibly damaging	Het
Usp34	A	T	11: 23,489,064	H3561L		Het
Vasp	C	T	7: 19,259,451	V276I	unknown	Het
Vwa3a	A	G	7: 120,775,464	N333S	probably benign	Het
Wipf3	A	G	6: 54,483,881	N105D	probably benign	Het
Zfp760	T	C	17: 21,723,682	S613P	possibly 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
R4776:Pnpla6	UTSW	8	3523818	missense	probably benign	0.01
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
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'- CGGTCAGCATATTTACTCGCTG -3'
(R):5'- GGAGAACAATTGCAGAGCATATCC -3'

Sequencing Primer
(F):5'- CAGCATATTTACTCGCTGAGTCTAG -3'
(R):5'- CCAAGGAAGTAGGATCTATACACTC -3'

Posted On

2022-03-25