Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	84879
Gene name Gene Name - the full gene name approved by the HGNC.	MFSD2 lysolipid transporter A, lysophospholipid
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	MFSD2A
Synonyms (NCBI Gene) Gene synonyms aliases	HsMFSD2A, MCPH15, MFSD2, NEDMISBA, NLS1, SLC59A1
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1p34.2
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene is a transmembrane protein and sodium-dependent lysophosphatidylcholine transporter. The encoded protein is involved in the establishment of the blood-brain barrier and is required for brain growth and function. Defects in

Show/Hide all(5)

SNP ID	Visualize variation	Clinical significance	Consequence
rs571640983	C>A,T	Likely-pathogenic	Missense variant, intron variant, coding sequence variant
rs1057517688	C>T	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs1057517689	C>T	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs1057519087	C>T	Pathogenic	Missense variant, intron variant, coding sequence variant
rs1570238098	TGT>-	Pathogenic	Intron variant, inframe deletion, coding sequence variant

Show/Hide all(126)

miRTarBase ID	miRNA	Experiments	Reference
MIRT673141	hsa-miR-106a-5p	HITS-CLIP	23824327
MIRT673140	hsa-miR-106b-5p	HITS-CLIP	23824327
MIRT673139	hsa-miR-17-5p	HITS-CLIP	23824327
MIRT673138	hsa-miR-20a-5p	HITS-CLIP	23824327
MIRT673137	hsa-miR-20b-5p	HITS-CLIP	23824327
MIRT673136	hsa-miR-519d-3p	HITS-CLIP	23824327
MIRT673135	hsa-miR-526b-3p	HITS-CLIP	23824327
MIRT673134	hsa-miR-93-5p	HITS-CLIP	23824327
MIRT673133	hsa-miR-302a-3p	HITS-CLIP	23824327
MIRT673132	hsa-miR-302b-3p	HITS-CLIP	23824327
MIRT673131	hsa-miR-302c-3p	HITS-CLIP	23824327
MIRT673130	hsa-miR-302d-3p	HITS-CLIP	23824327
MIRT673129	hsa-miR-302e	HITS-CLIP	23824327
MIRT673128	hsa-miR-372-3p	HITS-CLIP	23824327
MIRT673127	hsa-miR-373-3p	HITS-CLIP	23824327
MIRT673126	hsa-miR-520a-3p	HITS-CLIP	23824327
MIRT673125	hsa-miR-520b	HITS-CLIP	23824327
MIRT673124	hsa-miR-520c-3p	HITS-CLIP	23824327
MIRT673123	hsa-miR-520d-3p	HITS-CLIP	23824327
MIRT673122	hsa-miR-520e	HITS-CLIP	23824327
MIRT673121	hsa-miR-512-3p	HITS-CLIP	23824327
MIRT673120	hsa-miR-520g-3p	HITS-CLIP	23824327
MIRT673119	hsa-miR-520h	HITS-CLIP	23824327
MIRT673118	hsa-miR-125a-3p	HITS-CLIP	23824327
MIRT673117	hsa-miR-764	HITS-CLIP	23824327
MIRT673116	hsa-miR-3934-5p	HITS-CLIP	23824327
MIRT673115	hsa-miR-186-3p	HITS-CLIP	23824327
MIRT673114	hsa-miR-1234-3p	HITS-CLIP	23824327
MIRT673113	hsa-miR-7107-5p	HITS-CLIP	23824327
MIRT673112	hsa-miR-150-5p	HITS-CLIP	23824327
MIRT673111	hsa-miR-1913	HITS-CLIP	23824327
MIRT673110	hsa-miR-324-3p	HITS-CLIP	23824327
MIRT673109	hsa-miR-18a-3p	HITS-CLIP	23824327
MIRT673108	hsa-miR-619-5p	HITS-CLIP	23824327
MIRT673106	hsa-miR-6506-5p	HITS-CLIP	23824327
MIRT673107	hsa-miR-4707-3p	HITS-CLIP	23824327
MIRT673105	hsa-miR-6778-3p	HITS-CLIP	23824327
MIRT673104	hsa-miR-4731-5p	HITS-CLIP	23824327
MIRT673103	hsa-miR-5589-5p	HITS-CLIP	23824327
MIRT673102	hsa-miR-5089-5p	HITS-CLIP	23824327
MIRT667423	hsa-miR-508-5p	HITS-CLIP	23824327
MIRT667422	hsa-miR-449b-3p	HITS-CLIP	23824327
MIRT667421	hsa-miR-4691-3p	HITS-CLIP	23824327
MIRT667420	hsa-miR-1273g-3p	HITS-CLIP	23824327
MIRT667419	hsa-miR-4793-3p	HITS-CLIP	23824327
MIRT667418	hsa-miR-5186	HITS-CLIP	23824327
MIRT667417	hsa-miR-4252	HITS-CLIP	23824327
MIRT667416	hsa-miR-7703	HITS-CLIP	23824327
MIRT673141	hsa-miR-106a-5p	HITS-CLIP	23824327
MIRT673140	hsa-miR-106b-5p	HITS-CLIP	23824327
MIRT673139	hsa-miR-17-5p	HITS-CLIP	23824327
MIRT673138	hsa-miR-20a-5p	HITS-CLIP	23824327
MIRT673137	hsa-miR-20b-5p	HITS-CLIP	23824327
MIRT673136	hsa-miR-519d-3p	HITS-CLIP	23824327
MIRT673135	hsa-miR-526b-3p	HITS-CLIP	23824327
MIRT673134	hsa-miR-93-5p	HITS-CLIP	23824327
MIRT673133	hsa-miR-302a-3p	HITS-CLIP	23824327
MIRT673132	hsa-miR-302b-3p	HITS-CLIP	23824327
MIRT673131	hsa-miR-302c-3p	HITS-CLIP	23824327
MIRT673130	hsa-miR-302d-3p	HITS-CLIP	23824327
MIRT673129	hsa-miR-302e	HITS-CLIP	23824327
MIRT673128	hsa-miR-372-3p	HITS-CLIP	23824327
MIRT673127	hsa-miR-373-3p	HITS-CLIP	23824327
MIRT673126	hsa-miR-520a-3p	HITS-CLIP	23824327
MIRT673125	hsa-miR-520b	HITS-CLIP	23824327
MIRT673124	hsa-miR-520c-3p	HITS-CLIP	23824327
MIRT673123	hsa-miR-520d-3p	HITS-CLIP	23824327
MIRT673122	hsa-miR-520e	HITS-CLIP	23824327
MIRT673121	hsa-miR-512-3p	HITS-CLIP	23824327
MIRT673120	hsa-miR-520g-3p	HITS-CLIP	23824327
MIRT673119	hsa-miR-520h	HITS-CLIP	23824327
MIRT673118	hsa-miR-125a-3p	HITS-CLIP	23824327
MIRT673117	hsa-miR-764	HITS-CLIP	23824327
MIRT673116	hsa-miR-3934-5p	HITS-CLIP	23824327
MIRT673115	hsa-miR-186-3p	HITS-CLIP	23824327
MIRT673114	hsa-miR-1234-3p	HITS-CLIP	23824327
MIRT673113	hsa-miR-7107-5p	HITS-CLIP	23824327
MIRT673112	hsa-miR-150-5p	HITS-CLIP	23824327
MIRT673111	hsa-miR-1913	HITS-CLIP	23824327
MIRT673110	hsa-miR-324-3p	HITS-CLIP	23824327
MIRT673109	hsa-miR-18a-3p	HITS-CLIP	23824327
MIRT673108	hsa-miR-619-5p	HITS-CLIP	23824327
MIRT673106	hsa-miR-6506-5p	HITS-CLIP	23824327
MIRT673107	hsa-miR-4707-3p	HITS-CLIP	23824327
MIRT673105	hsa-miR-6778-3p	HITS-CLIP	23824327
MIRT673104	hsa-miR-4731-5p	HITS-CLIP	23824327
MIRT673103	hsa-miR-5589-5p	HITS-CLIP	23824327
MIRT673102	hsa-miR-5089-5p	HITS-CLIP	23824327
MIRT667423	hsa-miR-508-5p	HITS-CLIP	23824327
MIRT667422	hsa-miR-449b-3p	HITS-CLIP	23824327
MIRT667421	hsa-miR-4691-3p	HITS-CLIP	23824327
MIRT667420	hsa-miR-1273g-3p	HITS-CLIP	23824327
MIRT667419	hsa-miR-4793-3p	HITS-CLIP	23824327
MIRT667418	hsa-miR-5186	HITS-CLIP	23824327
MIRT667417	hsa-miR-4252	HITS-CLIP	23824327
MIRT667416	hsa-miR-7703	HITS-CLIP	23824327
MIRT1146437	hsa-miR-1237	CLIP-seq
MIRT1146438	hsa-miR-1324	CLIP-seq
MIRT1146439	hsa-miR-188-5p	CLIP-seq
MIRT1146440	hsa-miR-3166	CLIP-seq
MIRT1146441	hsa-miR-3182	CLIP-seq
MIRT1146442	hsa-miR-1910	CLIP-seq
MIRT1146443	hsa-miR-3189-3p	CLIP-seq
MIRT1146444	hsa-miR-455-3p	CLIP-seq
MIRT1146445	hsa-miR-4642	CLIP-seq
MIRT1146437	hsa-miR-1237	CLIP-seq
MIRT2041724	hsa-miR-128	CLIP-seq
MIRT2271228	hsa-miR-1827	CLIP-seq
MIRT2271229	hsa-miR-1915	CLIP-seq
MIRT2271230	hsa-miR-2467-3p	CLIP-seq
MIRT2271231	hsa-miR-3158-3p	CLIP-seq
MIRT2271232	hsa-miR-328	CLIP-seq
MIRT2271233	hsa-miR-3607-3p	CLIP-seq
MIRT2271234	hsa-miR-3612	CLIP-seq
MIRT2271235	hsa-miR-3686	CLIP-seq
MIRT2271236	hsa-miR-4255	CLIP-seq
MIRT2271237	hsa-miR-4323	CLIP-seq
MIRT2271238	hsa-miR-4477a	CLIP-seq
MIRT2271239	hsa-miR-4514	CLIP-seq
MIRT2271240	hsa-miR-4672	CLIP-seq
MIRT2271241	hsa-miR-4685-5p	CLIP-seq
MIRT2271242	hsa-miR-4692	CLIP-seq
MIRT2271243	hsa-miR-4758-3p	CLIP-seq
MIRT2271244	hsa-miR-650	CLIP-seq
MIRT2271245	hsa-miR-760	CLIP-seq
MIRT2271246	hsa-miR-940	CLIP-seq

Transcription factors

Show/Hide all(3)

Transcription factor	Regulation	Reference
AHR	Unknown	21736709
ARNT	Unknown	21736709
GCM1	Unknown	20484742

Show/Hide all(100)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003406	Process	Retinal pigment epithelium development	IEA
GO:0003406	Process	Retinal pigment epithelium development	ISS
GO:0005324	Function	Long-chain fatty acid transmembrane transporter activity	IEA
GO:0005324	Function	Long-chain fatty acid transmembrane transporter activity	IMP	26005865
GO:0005324	Function	Long-chain fatty acid transmembrane transporter activity	ISS
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005548	Function	Phospholipid transporter activity	TAS
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA	26005865, 26005868
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	ISS
GO:0005886	Component	Plasma membrane	RCA	26005868
GO:0005886	Component	Plasma membrane	TAS
GO:0006656	Process	Phosphatidylcholine biosynthetic process	TAS
GO:0006869	Process	Lipid transport	IEA
GO:0007420	Process	Brain development	IEA
GO:0007420	Process	Brain development	IEA
GO:0007420	Process	Brain development	IMP	26005865, 26005868
GO:0007420	Process	Brain development	ISS
GO:0008594	Process	Photoreceptor cell morphogenesis	IEA
GO:0008594	Process	Photoreceptor cell morphogenesis	ISS
GO:0008643	Process	Carbohydrate transport	IEA
GO:0009267	Process	Cellular response to starvation	IEA
GO:0009267	Process	Cellular response to starvation	ISS
GO:0010867	Process	Positive regulation of triglyceride biosynthetic process	IEA
GO:0010867	Process	Positive regulation of triglyceride biosynthetic process	ISS
GO:0015245	Function	Fatty acid transmembrane transporter activity	IBA
GO:0015245	Function	Fatty acid transmembrane transporter activity	IEA
GO:0015245	Function	Fatty acid transmembrane transporter activity	ISS	24828044
GO:0015293	Function	Symporter activity	IEA
GO:0015908	Process	Fatty acid transport	IBA
GO:0015908	Process	Fatty acid transport	IEA
GO:0015908	Process	Fatty acid transport	IMP	26005865
GO:0015908	Process	Fatty acid transport	ISS
GO:0015909	Process	Long-chain fatty acid transport	IEA
GO:0015909	Process	Long-chain fatty acid transport	ISS
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	26005865
GO:0021766	Process	Hippocampus development	IEA
GO:0021766	Process	Hippocampus development	ISS	24828044
GO:0030307	Process	Positive regulation of cell growth	IEA
GO:0030307	Process	Positive regulation of cell growth	ISS
GO:0031999	Process	Negative regulation of fatty acid beta-oxidation	IEA
GO:0031999	Process	Negative regulation of fatty acid beta-oxidation	ISS
GO:0034204	Process	Lipid translocation	IEA
GO:0034379	Process	Very-low-density lipoprotein particle assembly	IEA
GO:0034379	Process	Very-low-density lipoprotein particle assembly	ISS
GO:0035633	Process	Maintenance of blood-brain barrier	IEA
GO:0035633	Process	Maintenance of blood-brain barrier	ISS
GO:0035633	Process	Maintenance of blood-brain barrier	ISS	26005868
GO:0035845	Process	Photoreceptor cell outer segment organization	IEA
GO:0035845	Process	Photoreceptor cell outer segment organization	ISS
GO:0036464	Component	Cytoplasmic ribonucleoprotein granule	IDA
GO:0040014	Process	Regulation of multicellular organism growth	IEA
GO:0040014	Process	Regulation of multicellular organism growth	ISS
GO:0045056	Process	Transcytosis	IEA
GO:0045056	Process	Transcytosis	ISS
GO:0050773	Process	Regulation of dendrite development	IEA
GO:0050773	Process	Regulation of dendrite development	ISS
GO:0050890	Process	Cognition	IMP	26005868
GO:0051977	Process	Lysophospholipid transport	IDA	24828044
GO:0051977	Process	Lysophospholipid transport	IEA
GO:0051977	Process	Lysophospholipid transport	IMP	26005868
GO:0051977	Process	Lysophospholipid transport	ISS
GO:0051978	Function	Lysophospholipid:sodium symporter activity	IBA
GO:0051978	Function	Lysophospholipid:sodium symporter activity	IDA	24828044, 34135507
GO:0051978	Function	Lysophospholipid:sodium symporter activity	IEA
GO:0055085	Process	Transmembrane transport	IBA
GO:0060042	Process	Retina morphogenesis in camera-type eye	IEA
GO:0060042	Process	Retina morphogenesis in camera-type eye	ISS
GO:0060856	Process	Establishment of blood-brain barrier	ISS
GO:0060856	Process	Establishment of blood-brain barrier	ISS
GO:0061744	Process	Motor behavior	IEA
GO:0061744	Process	Motor behavior	ISS
GO:0097009	Process	Energy homeostasis	IEA
GO:0097009	Process	Energy homeostasis	ISS
GO:0140329	Process	Lysophospholipid translocation	IBA
GO:0140329	Process	Lysophospholipid translocation	IMP	26005865
GO:0140348	Function	Lysophosphatidylcholine flippase activity	IEA
GO:0150011	Process	Regulation of neuron projection arborization	IEA
GO:0150011	Process	Regulation of neuron projection arborization	ISS
GO:0150104	Process	Transport across blood-brain barrier	NAS	26590417, 30280653
GO:0150172	Process	Regulation of phosphatidylcholine metabolic process	IEA
GO:0150172	Process	Regulation of phosphatidylcholine metabolic process	IEA
GO:0150172	Process	Regulation of phosphatidylcholine metabolic process	IMP	26005868
GO:0150172	Process	Regulation of phosphatidylcholine metabolic process	ISS
GO:0150175	Process	Regulation of phosphatidylethanolamine metabolic process	IEA
GO:0150175	Process	Regulation of phosphatidylethanolamine metabolic process	ISS
GO:0150178	Process	Regulation of phosphatidylserine metabolic process	IEA
GO:0150178	Process	Regulation of phosphatidylserine metabolic process	ISS
GO:1901480	Function	Oleate transmembrane transporter activity	IMP	26005865
GO:1990379	Process	Lipid transport across blood-brain barrier	IBA
GO:1990379	Process	Lipid transport across blood-brain barrier	IEA
GO:1990379	Process	Lipid transport across blood-brain barrier	IMP	26005865
GO:1990379	Process	Lipid transport across blood-brain barrier	ISS
GO:1990403	Process	Embryonic brain development	ISS
GO:1990963	Process	Establishment of blood-retinal barrier	ISS

MIM	HGNC	e!Ensembl
614397	25897	ENSG00000168389

Protein

UniProt ID

Q8NA29

Protein name

Sodium-dependent lysophosphatidylcholine symporter 1 (NLS1) (Sodium-dependent LPC symporter 1) (Major facilitator superfamily domain-containing protein 2A) (HsMFSD2A) (MFSD2a)

Protein function

Sodium-dependent lysophosphatidylcholine (LPC) symporter, which plays an essential role for blood-brain barrier formation and function (PubMed:24828040, PubMed:32572202, PubMed:34135507). Specifically expressed in endothelium of the blood-brain

PDB

7OIX

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13347	MFS_2	48 → 509		Family

Tissue specificity

TISSUE SPECIFICITY: In placenta, associated with trophoblast cells. {ECO:0000269|PubMed:18988732}.

Sequence

MAKGEGAESGSAAGLLPTSILQSTERPAQVKKEPKKKKQQLSVCNKLCYALGGAPYQVTG
CALGFFLQIYLLDVAQKDEEVVFCFSSFQVGPFSASIILFVGRAWDAITDPLVGLCISKS
PWTCLGRLMPWIIFSTPLAVIAYFLIWFVPDFPHGQTYWYLLFYCLFETMVTCFHVPYSA
LTMFISTEQTERDSATAYRMTVEVLGTVLGTAIQGQIVGQADTPCFQDLNSSTVASQSAN
HTHGTTSHRETQKAYLLAAGVIVCIYIICAVILILGVREQREPYEAQQSEPIAYFRGLRL
VMSHGPYIKLITGFLFTSLAFMLVEGNFVLFCTYTLGFRNEFQNLLLAIMLSATLTIPIW
QWFLTRFGKKTAVYVGISSAVPFLILVALMESNLIITYAVAVAAGISVAAAFLLPWSMLP
DVIDDFHLKQPHFHGTEPIFFSFYVFFTKFASGVSLGISTLSLDFAGYQTRGCSQPERVK
FTLNMLVTMAPIVLILLGLLLFKMYPIDEERRRQNKKALQALRDEASSSGCSETDSTELA
SIL

Sequence length

543

Interactions

View interactions

	Reactome
			Synthesis of PC

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Microcephaly	microcephaly 15, primary, autosomal recessive	rs1057517688, rs1057519087, rs571640983	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Metabolic Syndrome	Metabolic syndrome	N/A	N/A	GWAS

Show/Hide Text Mining Associations (23)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenocarcinoma of Lung	Associate	30353687
Alzheimer Disease	Associate	31861865, 36334414
Attention Deficit and Disruptive Behavior Disorders	Associate	32572202
Autosomal Recessive Primary Microcephaly	Associate	32572202
Breast Neoplasms	Associate	40644891
Carcinoma Hepatocellular	Associate	31584009
Cardiomegaly	Associate	32572202
COVID 19	Associate	36334414
Dementia	Inhibit	36334414
Developmental Disabilities	Associate	32572202
Diabetes Gestational	Inhibit	32117064
Hepatitis B Chronic	Inhibit	31584009
Lewy Body Disease	Associate	37463072
Lung Neoplasms	Associate	17145094, 21736709
Mental Retardation Autosomal Recessive 1	Associate	32117064
Microcephaly	Associate	32117064, 32572202
Mucocutaneous Lymph Node Syndrome	Associate	37894766
Neoplasms	Inhibit	21736709
Neoplasms	Associate	30353687
Obesity	Stimulate	33321178
Obesity	Inhibit	36371454
Osteogenesis imperfecta type 2A	Inhibit	32572202
Osteogenesis imperfecta type 2A	Associate	32572202

MFSD2A (MFSD2 lysolipid transporter A, lysophospholipid)