PNPLA1 (patatin like domain 1, omega-hydroxyceramide transacylase)

Gene

• Entrez ID: 285848
• Gene name: Patatin like domain 1, omega-hydroxyceramide transacylase
• Gene symbol: PNPLA1
• Synonyms: ARCI10, dJ50J22.1
• Chromosome: 6
• Chromosome location: 6p21.31
• Summary: The protein encoded by this gene belongs to the patatin-like phospholipase (PNPLA) family, which is characterized by the presence of a highly conserved patatin domain. PNPLA family members have diverse lipolytic and acyltransferase activities, and are key

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs140585347	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, upstream transcript variant, coding sequence variant, genic upstream transcript variant
rs200806519	C>A,T	Pathogenic	Genic upstream transcript variant, coding sequence variant, upstream transcript variant, synonymous variant, missense variant
rs369445146	C>A	Pathogenic, likely-pathogenic	Genic upstream transcript variant, missense variant, coding sequence variant, upstream transcript variant
rs371307766	C>G,T	Likely-pathogenic	Genic upstream transcript variant, missense variant, coding sequence variant, upstream transcript variant
rs373148099	G>A	Pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant
rs376245108	C>A,T	Pathogenic	Missense variant, coding sequence variant
rs533584507	C>A,T	Likely-pathogenic	Missense variant, coding sequence variant, intron variant, genic upstream transcript variant
rs746575171	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant
rs753687060	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs766188849	C>T	Pathogenic	5 prime UTR variant, coding sequence variant, missense variant
rs766215523	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs767462752	->GTACGAGGATGCAGTTTTGT	Likely-pathogenic	Coding sequence variant, frameshift variant
rs781053760	T>C	Pathogenic-likely-pathogenic, pathogenic	Genic upstream transcript variant, missense variant, coding sequence variant, upstream transcript variant
rs922934422	C>T	Likely-pathogenic	Upstream transcript variant, missense variant, coding sequence variant, genic upstream transcript variant, 5 prime UTR variant
rs938583000	C>-	Likely-pathogenic	Coding sequence variant, intron variant, genic upstream transcript variant, frameshift variant
rs1170446813	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1182312612	G>A,C	Pathogenic	Coding sequence variant, intron variant, genic upstream transcript variant, missense variant
rs1207879599	C>G,T	Pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant, intron variant
rs1231123861	C>A,T	Pathogenic	Coding sequence variant, intron variant, missense variant, genic upstream transcript variant
rs1373230987	C>G,T	Likely-pathogenic	Coding sequence variant, missense variant, genic upstream transcript variant, intron variant
rs1407871103	A>C,G	Pathogenic	Upstream transcript variant, coding sequence variant, genic upstream transcript variant, missense variant
rs1554138062	T>C	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs1554139129	->GTCA	Pathogenic	Coding sequence variant, frameshift variant
rs1561853847	C>T	Pathogenic	Genic upstream transcript variant, missense variant, coding sequence variant, intron variant
rs1561864453	G>T	Pathogenic	Upstream transcript variant, coding sequence variant, stop gained, genic upstream transcript variant
rs1582046125	T>C	Pathogenic	Genic upstream transcript variant, missense variant, coding sequence variant, intron variant
rs1582078740	A>G	Pathogenic	Genic upstream transcript variant, upstream transcript variant, coding sequence variant, missense variant
rs1582081682	T>C	Pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant
rs1582086407	TAC>-	Pathogenic	Coding sequence variant, inframe deletion

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1245377	hsa-miR-1266	CLIP-seq
MIRT1245378	hsa-miR-1273f	CLIP-seq
MIRT1245379	hsa-miR-197	CLIP-seq
MIRT1245380	hsa-miR-24	CLIP-seq
MIRT1245381	hsa-miR-2467-5p	CLIP-seq
MIRT1245382	hsa-miR-3612	CLIP-seq
MIRT1245383	hsa-miR-411	CLIP-seq
MIRT1245384	hsa-miR-4270	CLIP-seq
MIRT1245385	hsa-miR-4441	CLIP-seq
MIRT1245386	hsa-miR-4443	CLIP-seq
MIRT1245387	hsa-miR-4518	CLIP-seq
MIRT1245388	hsa-miR-4534	CLIP-seq
MIRT1245389	hsa-miR-4653-3p	CLIP-seq
MIRT1245390	hsa-miR-4694-3p	CLIP-seq
MIRT1245391	hsa-miR-4700-3p	CLIP-seq
MIRT1245392	hsa-miR-4716-5p	CLIP-seq
MIRT1245393	hsa-miR-4781-3p	CLIP-seq
MIRT1245394	hsa-miR-4802-5p	CLIP-seq
MIRT1245395	hsa-miR-5095	CLIP-seq
MIRT1245396	hsa-miR-5096	CLIP-seq
MIRT1245397	hsa-miR-650	CLIP-seq
MIRT1245398	hsa-miR-1254	CLIP-seq
MIRT1245399	hsa-miR-1343	CLIP-seq
MIRT1245379	hsa-miR-197	CLIP-seq
MIRT1245400	hsa-miR-198	CLIP-seq
MIRT1245401	hsa-miR-2116	CLIP-seq
MIRT1245402	hsa-miR-3116	CLIP-seq
MIRT1245403	hsa-miR-3152-5p	CLIP-seq
MIRT1245404	hsa-miR-3155	CLIP-seq
MIRT1245405	hsa-miR-3155b	CLIP-seq
MIRT1245406	hsa-miR-3176	CLIP-seq
MIRT1245407	hsa-miR-3922-3p	CLIP-seq
MIRT1245408	hsa-miR-4438	CLIP-seq
MIRT1245388	hsa-miR-4534	CLIP-seq
MIRT1245389	hsa-miR-4653-3p	CLIP-seq
MIRT1245409	hsa-miR-4677-5p	CLIP-seq
MIRT1245410	hsa-miR-4687-3p	CLIP-seq
MIRT1245392	hsa-miR-4716-5p	CLIP-seq
MIRT1245411	hsa-miR-4740-3p	CLIP-seq
MIRT1245412	hsa-miR-4753-3p	CLIP-seq
MIRT1245413	hsa-miR-4772-3p	CLIP-seq
MIRT1245393	hsa-miR-4781-3p	CLIP-seq
MIRT1245414	hsa-miR-484	CLIP-seq
MIRT1245415	hsa-miR-498	CLIP-seq
MIRT1245395	hsa-miR-5095	CLIP-seq
MIRT1245396	hsa-miR-5096	CLIP-seq
MIRT1245416	hsa-miR-661	CLIP-seq
MIRT2299723	hsa-miR-122	CLIP-seq
MIRT1245378	hsa-miR-1273f	CLIP-seq
MIRT2299724	hsa-miR-130a	CLIP-seq
MIRT2299725	hsa-miR-130b	CLIP-seq
MIRT1245379	hsa-miR-197	CLIP-seq
MIRT2299726	hsa-miR-301a	CLIP-seq
MIRT2299727	hsa-miR-301b	CLIP-seq
MIRT2299728	hsa-miR-3135b	CLIP-seq
MIRT2299729	hsa-miR-3149	CLIP-seq
MIRT1245403	hsa-miR-3152-5p	CLIP-seq
MIRT2299730	hsa-miR-3605-3p	CLIP-seq
MIRT2299731	hsa-miR-3652	CLIP-seq
MIRT2299732	hsa-miR-3666	CLIP-seq
MIRT2299733	hsa-miR-3907	CLIP-seq
MIRT1245383	hsa-miR-411	CLIP-seq
MIRT2299734	hsa-miR-4295	CLIP-seq
MIRT2299735	hsa-miR-4423-5p	CLIP-seq
MIRT2299736	hsa-miR-4430	CLIP-seq
MIRT2299737	hsa-miR-4492	CLIP-seq
MIRT2299738	hsa-miR-4498	CLIP-seq
MIRT1245388	hsa-miR-4534	CLIP-seq
MIRT2299739	hsa-miR-454	CLIP-seq
MIRT1245389	hsa-miR-4653-3p	CLIP-seq
MIRT2299740	hsa-miR-4654	CLIP-seq
MIRT1245392	hsa-miR-4716-5p	CLIP-seq
MIRT1245411	hsa-miR-4740-3p	CLIP-seq
MIRT2299741	hsa-miR-4769-5p	CLIP-seq
MIRT2299742	hsa-miR-4775	CLIP-seq
MIRT1245393	hsa-miR-4781-3p	CLIP-seq
MIRT1245396	hsa-miR-5096	CLIP-seq
MIRT2299743	hsa-miR-590-3p	CLIP-seq
MIRT2299744	hsa-miR-595	CLIP-seq
MIRT2299745	hsa-miR-652	CLIP-seq
MIRT2299746	hsa-miR-762	CLIP-seq
MIRT1245378	hsa-miR-1273f	CLIP-seq
MIRT2456792	hsa-miR-3170	CLIP-seq
MIRT2299735	hsa-miR-4423-5p	CLIP-seq
MIRT2299737	hsa-miR-4492	CLIP-seq
MIRT2299738	hsa-miR-4498	CLIP-seq
MIRT1245395	hsa-miR-5095	CLIP-seq
MIRT2456793	hsa-miR-552	CLIP-seq
MIRT2299746	hsa-miR-762	CLIP-seq
MIRT2456794	hsa-miR-764	CLIP-seq
MIRT1245399	hsa-miR-1343	CLIP-seq
MIRT1245403	hsa-miR-3152-5p	CLIP-seq
MIRT1245411	hsa-miR-4740-3p	CLIP-seq
MIRT1245412	hsa-miR-4753-3p	CLIP-seq
MIRT1245415	hsa-miR-498	CLIP-seq
MIRT2299733	hsa-miR-3907	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004806	Function	Triglyceride lipase activity	IBA	21873635
GO:0005737	Component	Cytoplasm	IBA	21873635
GO:0005737	Component	Cytoplasm	IDA	22246504
GO:0005811	Component	Lipid droplet	IBA	21873635
GO:0016020	Component	Membrane	IBA	21873635
GO:0016747	Function	Transferase activity, transferring acyl groups other than amino-acyl groups	IDA	28248318
GO:0016747	Function	Transferase activity, transferring acyl groups other than amino-acyl groups	IMP	27751867
GO:0019433	Process	Triglyceride catabolic process	IBA	21873635
GO:0030280	Function	Structural constituent of skin epidermis	IC	28248318
GO:0046513	Process	Ceramide biosynthetic process	IMP	27751867, 28248318
GO:0055088	Process	Lipid homeostasis	IBA	21873635

Other IDs

• MIM: 612121
• HGNC: 21246
• e!Ensembl: ENSG00000180316

Protein

• UniProt ID: Q8N8W4
• Protein name: Omega-hydroxyceramide transacylase (EC 2.3.1.296) (Patatin-like phospholipase domain-containing protein 1)
• Protein function: Omega-hydroxyceramide transacylase involved in the synthesis of omega-O-acylceramides (esterified omega-hydroxyacyl-sphingosine; EOS), which are extremely hydrophobic lipids involved in skin barrier formation (PubMed:27751867, PubMed:28248318).
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01734	Patatin	16 → 84	Patatin-like phospholipase	Family

• Sequence:

  MEEQVFKGDPDTPHSISFSGSGFLSFYQAGAVDALRDLAPRMLETAHRFAGTSAGAVIAA
  LAICGIEMDEYLRVLNVGVAEVKKSFLGPLSPSCKMVQMMRQFLYRVLPEDSYKVTTGKL
  HVSLTRLTDGENVVVSEFTSKEELIEALYCSCFVPVYCGLIPPTYRGVRYIDGGFTGMQP
  CAFWTDAITISTFSGQQDICPRDCPAIFHDFRMFNCSFQFSLENIARMTHALFPPDLVIL
  HDYYYRGYEDAVLYLRRLNAVYLNSSSKRVIFPRVEVYCQIELALGNECPERSQPSLRAR
  QASLEGATQPHKEWVPKGDGRGSHGPPVSQPVQTLEFTCESPVSAPVSPLEQPPAQPLAS
  STPLSLSGMPPVSFPAVHKPPSSTPGSSLPTPPPGLSPLSPQQQVQPSGSPARSLHSQAP
  TSPRPSLGPSTVGAPQTLPRSSLSAFPAQPPVEELGQEQPQAVALLVSSKPKSAVPLVHV
  KETVSKPYVTESPAEDSNWVNKVFKKNKQKTSGTRKGFPRHSGSKKPSSKVQ

• Sequence length: 532

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Congenital ichthyosis	Congenital ichthyosis	rs118203935, rs118203936, rs118203937, rs199422216, rs199422217, rs1561831582, rs28940268, rs28940269, rs28940568, rs28940270, rs387906284, rs387906285, rs137853289, rs267606622, rs121434232, rs121434233, rs121434234, rs137852931, rs137852932, rs137853131, rs387906349, rs137853023, rs137853024, rs2139023508, rs121918719, rs121918728, rs121918716, rs121918717, rs121918718, rs121918720, rs121918721, rs121918722, rs121918723, rs2139018490, rs121918725, rs121918726, rs121918727, rs121918730, rs121918731, rs121918732, rs398122900, rs397514522, rs398122901, rs878853259, rs397514523, rs397514524, rs397514525, rs143473912, rs398122902, rs398122903, rs398122904, rs398122905, rs397514526, rs397514527, rs397514528, rs397514529, rs1598181810, rs397514532, rs199766569, rs397514533, rs786205120, rs745480657, rs1355284797, rs1561864453, rs1561853847, rs587776996, rs762679102, rs141340759, rs587777262, rs587777263, rs199545653, rs863223405, rs370031870, rs864321707, rs753798494, rs114863111, rs11891778, rs780990272, rs886039654, rs752509098, rs750066836, rs142634031, rs886041250, rs886041950, rs200491579, rs147149459, rs531800013, rs781006633, rs370356566, rs201868387, rs1057517836, rs904122716, rs151054393, rs531650682, rs139208806, rs959284348, rs1170446813, rs781053760, rs369445146, rs922934422, rs202128350, rs745368359, rs139375856, rs199503269, rs1064794422, rs367699137, rs762667660, rs1114167426, rs1114167425, rs1114167424, rs762765702, rs1131692156, rs1555643304, rs775524204, rs1554138062, rs771820315, rs1555306238, rs760429286, rs1553520468, rs774363396, rs1555305836, rs1220151696, rs1555306172, rs140000324, rs752349623, rs1555305725, rs1555305783, rs1555306113, rs779287673, rs1437822062, rs776068111, rs1555306117, rs1322979131, rs199678720, rs1211601030, rs147916609, rs1156392436, rs773303931, rs1044429462, rs1555306089, rs1555306102, rs1296165092, rs1199770893, rs972054392, rs201432046, rs758568142, rs118091316, rs369811073, rs1568357749, rs773886415, rs1382435790, rs770500550, rs776275777, rs1568360348, rs1568360387, rs1568360475, rs1568360526, rs1568360554, rs1568361250, rs751937099, rs768098854, rs767352854, rs755885838, rs370734976, rs1568362605, rs1568362644, rs769229606, rs201129618, rs1568364101, rs1568364107, rs1568364117, rs200581968, rs144961059, rs1568365205, rs1167473603, rs1360295659, rs1187032187, rs1559120651, rs200806519, rs1566380103, rs1182312612, rs761068277, rs764355087, rs1559134341, rs1561831443, rs373501601, rs1373230987, rs533584507, rs1582086407, rs746575171, rs538068583, rs1566377068, rs1202280089, rs1381998109, rs543521135, rs1247223599, rs773777400, rs1230140208, rs1566381457, rs1567644030, rs1567980596, rs746723399, rs1028050037, rs1567985231, rs1567985261, rs1311967606, rs1296095311, rs765682032, rs1568005543, rs1449980834, rs745942843, rs112419023, rs1566378425, rs1581262988, rs1581265561, rs775903553, rs900769357, rs371608909, rs777992589, rs1581271869, rs1581272003, rs1212378071, rs1027052344, rs375688767, rs1581272834, rs886060339, rs1581273254, rs1452328130, rs1581269752, rs1581271844, rs1207879599, rs1582078740, rs766188849, rs753687060, rs1594571148, rs1598181642, rs1574984736, rs1596772428, rs867950920, rs1594568541, rs760428119
Ichthyosis	Ichthyoses	rs199766569, rs587776996, rs587777262, rs863223405, rs370031870, rs1569044747, rs200806519	22246504
Ichthyosis with hypotrichosis	ICHTHYOSIS, CONGENITAL, AUTOSOMAL RECESSIVE 10	rs1114167426, rs1114167425, rs1114167424, rs762765702, rs530109812, rs774363396, rs760309815, rs140526640, rs1303127476	26778108, 22246504, 28369476
Keratitis	Keratitis	rs587776571
Palmoplantar keratoderma	Keratoderma, Palmoplantar	rs59616921, rs1568039793, rs746488412, rs200564757, rs1567027297, rs781596375, rs1567027610, rs398123054, rs398123055, rs398123056, rs398123057, rs398122949, rs398122950, rs397515639, rs398122951, rs397515640, rs397515641, rs142859678, rs797044479, rs577442939, rs672601344, rs568609861, rs1057518846, rs1182196436, rs1567037561

Unknown
Disease name	Disease term	dbSNP ID	References
Alopecia	Alopecia
Congenital nonbullous ichthyosiform erythroderma	Congenital Nonbullous Ichthyosiform Erythroderma, Congenital non-bullous ichthyosiform erythroderma		22246504
Corneal erosion	Corneal erosion
Dwarfism	Dwarfism
Ectropion	Ectropion
Exfoliative dermatitis	Exfoliative dermatitis
Hypohidrosis	Hypohidrosis
Ichthyosis congenita	Ichthyosiform Erythroderma, Congenital		28403545
Xeroderma	Xeroderma		22246504