NIPAL4 (NIPA like domain containing 4)

Gene

• Entrez ID: 348938
• Gene name: NIPA like domain containing 4
• Gene symbol: NIPAL4
• Synonyms: ARCI6, ICHTHYIN, ICHYN, NIPA4, SLC57A6
• Chromosome: 5
• Chromosome location: 5q33.3
• Summary: This gene likely encodes a membrane receptor. Mutations in this gene have been associated with autosomal recessive congenital ichthyosis. [provided by RefSeq, Feb 2010]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs188020393	C>G,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant, 5 prime UTR variant
rs199422216	C>A,T	Pathogenic	Synonymous variant, coding sequence variant, 5 prime UTR variant, stop gained
rs199422217	C>A,G	Pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant
rs370356566	G>A	Pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant
rs371608909	A>C,G	Pathogenic	Synonymous variant, missense variant, coding sequence variant, 5 prime UTR variant
rs373501601	C>A,T	Pathogenic	Coding sequence variant, synonymous variant, stop gained
rs375688767	G>A,C	Pathogenic	Coding sequence variant, missense variant
rs376074083	G>A,T	Pathogenic	Intron variant
rs750991783	C>G	Pathogenic	Coding sequence variant, missense variant
rs757041309	G>A	Pathogenic	Missense variant, coding sequence variant
rs775903553	G>A,T	Pathogenic	Coding sequence variant, missense variant, 5 prime UTR variant
rs777992589	C>G,T	Pathogenic	Coding sequence variant, stop gained, synonymous variant, 5 prime UTR variant
rs886060339	C>A,T	Uncertain-significance, pathogenic	Coding sequence variant, missense variant, synonymous variant
rs900769357	G>A	Pathogenic	5 prime UTR variant, intron variant, missense variant, coding sequence variant
rs1027052344	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs1212378071	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs1255386092	G>A,T	Likely-pathogenic	Stop gained, coding sequence variant, missense variant
rs1561831443	ATACATG>-	Pathogenic	Frameshift variant, coding sequence variant
rs1561831582	G>A	Pathogenic	Splice donor variant
rs1581265561	C>-	Pathogenic	5 prime UTR variant, coding sequence variant, frameshift variant
rs1581265715	T>A	Pathogenic	5 prime UTR variant, missense variant, coding sequence variant
rs1581269752	G>A	Pathogenic	Splice donor variant
rs1581271844	C>-	Pathogenic	Intron variant
rs1581271869	C>T	Pathogenic	5 prime UTR variant, missense variant, coding sequence variant
rs1581272003	C>G	Pathogenic	5 prime UTR variant, missense variant, coding sequence variant
rs1581272834	C>G	Pathogenic	Missense variant, coding sequence variant
rs1581273254	A>-	Pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1185681	hsa-miR-122	CLIP-seq
MIRT1185682	hsa-miR-1237	CLIP-seq
MIRT1185683	hsa-miR-3135b	CLIP-seq
MIRT1185684	hsa-miR-3179	CLIP-seq
MIRT1185685	hsa-miR-3202	CLIP-seq
MIRT1185686	hsa-miR-3616-3p	CLIP-seq
MIRT1185687	hsa-miR-3652	CLIP-seq
MIRT1185688	hsa-miR-3936	CLIP-seq
MIRT1185689	hsa-miR-423-3p	CLIP-seq
MIRT1185690	hsa-miR-4263	CLIP-seq
MIRT1185691	hsa-miR-4271	CLIP-seq
MIRT1185692	hsa-miR-4297	CLIP-seq
MIRT1185693	hsa-miR-4430	CLIP-seq
MIRT1185694	hsa-miR-4436b-3p	CLIP-seq
MIRT1185695	hsa-miR-4654	CLIP-seq
MIRT1185696	hsa-miR-4659a-3p	CLIP-seq
MIRT1185697	hsa-miR-4659b-3p	CLIP-seq
MIRT1185698	hsa-miR-4716-3p	CLIP-seq
MIRT1185699	hsa-miR-4718	CLIP-seq
MIRT1185700	hsa-miR-4725-3p	CLIP-seq
MIRT1185701	hsa-miR-4727-5p	CLIP-seq
MIRT1185702	hsa-miR-4733-5p	CLIP-seq
MIRT1185703	hsa-miR-4747-5p	CLIP-seq
MIRT1185704	hsa-miR-4755-3p	CLIP-seq
MIRT1185705	hsa-miR-4769-3p	CLIP-seq
MIRT1185706	hsa-miR-4769-5p	CLIP-seq
MIRT1185707	hsa-miR-515-5p	CLIP-seq
MIRT1185708	hsa-miR-541	CLIP-seq
MIRT1185709	hsa-miR-542-5p	CLIP-seq
MIRT1185710	hsa-miR-576-5p	CLIP-seq
MIRT1185711	hsa-miR-605	CLIP-seq
MIRT1185712	hsa-miR-625	CLIP-seq
MIRT1185713	hsa-miR-654-5p	CLIP-seq
MIRT1185714	hsa-miR-942	CLIP-seq
MIRT1185715	hsa-miR-4268	CLIP-seq
MIRT1185716	hsa-miR-4448	CLIP-seq
MIRT1185701	hsa-miR-4727-5p	CLIP-seq
MIRT1185702	hsa-miR-4733-5p	CLIP-seq
MIRT1185705	hsa-miR-4769-3p	CLIP-seq
MIRT1185711	hsa-miR-605	CLIP-seq
MIRT1551758	hsa-miR-138	CLIP-seq
MIRT1551759	hsa-miR-3157-5p	CLIP-seq
MIRT1551760	hsa-miR-4676-5p	CLIP-seq
MIRT1551761	hsa-miR-4691-3p	CLIP-seq
MIRT1551762	hsa-miR-575	CLIP-seq
MIRT1551763	hsa-miR-622	CLIP-seq
MIRT2053831	hsa-miR-3158-5p	CLIP-seq
MIRT2053832	hsa-miR-3166	CLIP-seq
MIRT2053833	hsa-miR-3180-5p	CLIP-seq
MIRT1185701	hsa-miR-4727-5p	CLIP-seq
MIRT1185705	hsa-miR-4769-3p	CLIP-seq
MIRT2053834	hsa-miR-4771	CLIP-seq
MIRT2053835	hsa-miR-642a	CLIP-seq
MIRT2053836	hsa-miR-665	CLIP-seq
MIRT2283000	hsa-miR-1296	CLIP-seq
MIRT2283001	hsa-miR-2909	CLIP-seq
MIRT2053831	hsa-miR-3158-5p	CLIP-seq
MIRT2053832	hsa-miR-3166	CLIP-seq
MIRT2283002	hsa-miR-4512	CLIP-seq
MIRT1185701	hsa-miR-4727-5p	CLIP-seq
MIRT2053834	hsa-miR-4771	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	32296183
GO:0015095	Function	Magnesium ion transmembrane transporter activity	IEA
GO:0015693	Process	Magnesium ion transport	IBA	21873635
GO:0016020	Component	Membrane	IBA	21873635
GO:0016021	Component	Integral component of membrane	IEA
GO:1903830	Process	Magnesium ion transmembrane transport	IEA

Other IDs

• MIM: 609383
• HGNC: 28018
• e!Ensembl: ENSG00000172548

Protein

• UniProt ID: Q0D2K0
• Protein name: Magnesium transporter NIPA4 (Ichthyin) (NIPA-like protein 4) (Non-imprinted in Prader-Willi/Angelman syndrome region protein 4)
• Protein function: Acts as a Mg(2+) transporter. Can also transport other divalent cations such as Ba(2+), Sr(2+) and Fe(2+) but to a much less extent than Mg(2+) (By similarity). May be a receptor for ligands (trioxilins A3 and B3) from the hepoxilin pathway (Pub
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF05653	Mg_trans_NIPA	116 → 410	Magnesium transporter NIPA	Family

• Sequence:

  MPGDSSPGTLPLWDASLSPPLGPDPGGFSRASHAGDKSRPPAPELGSPGAVRPRVGSCAP
  GPMELRVSNTSCENGSLLHLYCSSQEVLCQIVNDLSPEVPSNATFHSWQERIRQNYGFYI
  GLGLAFLSSFLIGSSVILKKKGLLRLVATGATRAVDGGFGYLKDAMWWAGFLTMAAGEVA
  NFGAYAFAPATVVTPLGALSVLISAILSSYFLRESLNLLGKLGCVICVAGSTVMVIHAPE
  EEKVTTIMEMASKMKDTGFIVFAVLLLVSCLILIFVIAPRYGQRNILIYIIICSVIGAFS
  VAAVKGLGITIKNFFQGLPVVRHPLPYILSLILALSLSTQVNFLNRALDIFNTSLVFPIY
  YVFFTTVVVTSSIILFKEWYSMSAVDIAGTLSGFVTIILGVFMLHAFKDLDISCASLPHM
  HKNPPPSPAPEPTVIRLEDKNVLVDNIELASTSSPEEKPKVFIIHS

• Sequence length: 466

Pathways

Reactome:

Miscellaneous transport and binding events

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Hypotrichosis	Hypotrichosis	rs121434306, rs121434307, rs121434308, rs121434309, rs1325804776, rs267606775, rs786200875, rs1568062215, rs267606776, rs1462595806, rs267606777, rs267606659, rs2147483647, rs559648418, rs121917819, rs121917820, rs387906382, rs267606867, rs267606868, rs267606869, rs201868115, rs587776925, rs587777527, rs587777545, rs766783183, rs879255262, rs201249971, rs768448663, rs1566212378, rs1249530918, rs1260995701, rs1569039353, rs1827030121
Ichthyosis	Ichthyoses	rs199766569, rs587776996, rs587777262, rs863223405, rs370031870, rs1569044747, rs200806519
Ichthyosis with hypotrichosis	ICHTHYOSIS, CONGENITAL, AUTOSOMAL RECESSIVE 6	rs1114167426, rs1114167425, rs1114167424, rs762765702, rs530109812, rs774363396, rs760309815, rs140526640, rs1303127476	17557927, 20016120, 15317751, 25458912, 26762237, 26456858, 24397709, 22622417
Keratitis	Keratitis	rs587776571
Lamellar ichthyosis	Lamellar ichthyosis	rs118203935, rs118203937, rs199422216, rs199422217, rs28940270, rs137853289, rs137853134, rs121918716, rs121918717, rs121918718, rs121918720, rs121918722, rs121918723, rs121918725, rs121918731, rs121918732, rs397514525, rs143473912, rs397514532, rs199766569, rs587779765, rs587776384, rs370031870, rs757520757, rs752509098, rs142634031, rs886041250, rs200491579, rs147149459, rs781006633, rs370356566, rs781053760, rs199503269, rs367699137, rs938583000, rs1554138062, rs771820315, rs760429286, rs781631629, rs760309815, rs779287673, rs1322979131, rs1296165092, rs118091316, rs369811073, rs1382435790, rs768098854, rs767352854, rs769229606, rs1567982673, rs761068277, rs538068583, rs543521135, rs1230140208, rs1311967606, rs1296095311, rs375688767
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
Renal insufficiency	Renal Insufficiency	rs1596536873

Unknown
Disease name	Disease term	dbSNP ID	References
Alopecia	Alopecia
Congenital nonbullous ichthyosiform erythroderma	Congenital Nonbullous Ichthyosiform Erythroderma, Congenital non-bullous ichthyosiform erythroderma		20016120, 22739337
Corneal erosion	Corneal erosion
Dwarfism	Dwarfism
Ectropion	Ectropion
Exfoliative dermatitis	Exfoliative dermatitis
Gangrene	Gangrene
Hyperkeratosis	Hyperkeratosis
Hypohidrosis	Hypohidrosis
Impaired cognition	Impaired cognition
Otitis media	Chronic otitis media	rs601338, rs1047781, rs1800028
Parakeratosis	Parakeratosis