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    MFSD2A MFSD2 lysolipid transporter A, lysophospholipid [ Homo sapiens (human) ]

    Gene ID: 84879, updated on 11-Apr-2024

    Summary

    Official Symbol
    MFSD2Aprovided by HGNC
    Official Full Name
    MFSD2 lysolipid transporter A, lysophospholipidprovided by HGNC
    Primary source
    HGNC:HGNC:25897
    See related
    Ensembl:ENSG00000168389 MIM:614397; AllianceGenome:HGNC:25897
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NLS1; MFSD2; MCPH15; SLC59A1; HsMFSD2A; NEDMISBA
    Summary
    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 this gene are a cause of a progressive microcephaly syndrome. [provided by RefSeq, Mar 2017]
    Expression
    Broad expression in testis (RPKM 27.5), lung (RPKM 23.6) and 14 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See MFSD2A in Genome Data Viewer
    Location:
    1p34.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (39955145..39969956)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (39824591..39839402)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (40420817..40435628)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 821 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 822 Neighboring gene tRNA isopentenyltransferase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40348408-40349228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40349229-40350047 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:40353876-40354074 Neighboring gene MYCL antisense RNA 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:40363871-40364442 Neighboring gene Sharpr-MPRA regulatory region 6057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 716 Neighboring gene MYCL proto-oncogene, bHLH transcription factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:40409912-40410434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 823 Neighboring gene ribosomal protein S2 pseudogene 12 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40446045-40446898 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 718 Neighboring gene uncharacterized LOC105378669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 824 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40505419-40506052 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40506053-40506687 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:40518723-40519222 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:40524580-40525341 Neighboring gene cyclase associated actin cytoskeleton regulatory protein 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:40535511-40536710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 720 Neighboring gene Sharpr-MPRA regulatory region 13734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 829 Neighboring gene palmitoyl-protein thioesterase 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Microcephaly 15, primary, autosomal recessive
    MedGen: C4225310 OMIM: 616486 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Generalization of variants identified by genome-wide association studies for electrocardiographic traits in African Americans.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ14490, FLJ35904

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    acts_upstream_of_or_within brain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of brain development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in carbohydrate transport IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within cellular response to starvation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of cognition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT involved_in embryonic brain development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within energy homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT involved_in establishment of blood-brain barrier ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in establishment of blood-brain barrier ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT involved_in establishment of blood-retinal barrier ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in fatty acid transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in fatty acid transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in fatty acid transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in hippocampus development ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in lipid transport across blood-brain barrier IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in lipid transport across blood-brain barrier IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lipid transport across blood-brain barrier ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in long-chain fatty acid transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in lysophospholipid translocation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in lysophospholipid translocation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lysophospholipid transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in lysophospholipid transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lysophospholipid transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within maintenance of blood-brain barrier ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in maintenance of blood-brain barrier ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    acts_upstream_of_or_within motor behavior ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within negative regulation of fatty acid beta-oxidation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in phosphatidylcholine biosynthetic process TAS
    Traceable Author Statement
    more info
     
    acts_upstream_of_or_within photoreceptor cell morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within photoreceptor cell outer segment organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within positive regulation of cell growth ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within positive regulation of triglyceride biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of regulation of dendrite development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within regulation of multicellular organism growth ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of regulation of neuron projection arborization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of regulation of phosphatidylcholine metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of regulation of phosphatidylcholine metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of regulation of phosphatidylethanolamine metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of regulation of phosphatidylserine metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within retina morphogenesis in camera-type eye ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within retinal pigment epithelium development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in transcytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transport across blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within very-low-density lipoprotein particle assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    sodium-dependent lysophosphatidylcholine symporter 1
    Names
    major facilitator superfamily domain containing 2A
    major facilitator superfamily domain-containing protein 2A
    sodium-dependent LPC symporter 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_053084.1 RefSeqGene

      Range
      5034..19845
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001136493.3NP_001129965.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform 1

      See identical proteins and their annotated locations for NP_001129965.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK093223, BP321361, DB376308
      Consensus CDS
      CCDS44118.1
      UniProtKB/Swiss-Prot
      A8K675, Q6UWU5, Q8NA29, Q96F59, Q9BRC8
      UniProtKB/TrEMBL
      B4DNN7
      Related
      ENSP00000361895.5, ENST00000372809.5
      Conserved Domains (2) summary
      pfam13347
      Location:46509
      MFS_2; MFS/sugar transport protein
      cl21472
      Location:40511
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
    2. NM_001287808.2NP_001274737.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in its 5' UTR, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK093223, BP321361, DB376308
      Consensus CDS
      CCDS72762.1
      UniProtKB/TrEMBL
      B4DWH2, E7EPI8
      Related
      ENSP00000391261.2, ENST00000420632.6
      Conserved Domains (2) summary
      pfam13347
      Location:3340
      MFS_2; MFS/sugar transport protein
      cl21472
      Location:1342
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
    3. NM_001287809.2NP_001274738.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (4) is shorter, compared to isoform 1.
      Source sequence(s)
      AB073383, AK297991, DB376308, DC297497
      UniProtKB/TrEMBL
      B4DNN7
      Conserved Domains (2) summary
      pfam13347
      Location:32457
      MFS_2; MFS/sugar transport protein
      cl21472
      Location:51459
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
    4. NM_001349821.2NP_001336750.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) encodes isoform 6.
      Source sequence(s)
      AL663070
      UniProtKB/TrEMBL
      B4DNN7
      Conserved Domains (1) summary
      pfam13347
      Location:46494
      MFS_2; MFS/sugar transport protein
    5. NM_001349822.2NP_001336751.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform 7

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) encodes isoform 7.
      Source sequence(s)
      AL663070
      UniProtKB/TrEMBL
      B4DNN7
      Conserved Domains (1) summary
      pfam13347
      Location:48468
      MFS_2; MFS/sugar transport protein
    6. NM_001349823.2NP_001336752.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform 8

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) encodes isoform 8.
      Source sequence(s)
      AL663070
      UniProtKB/TrEMBL
      B4DWH2
      Conserved Domains (1) summary
      pfam13347
      Location:2381
      MFS_2; MFS/sugar transport protein
    7. NM_032793.5NP_116182.2  sodium-dependent lysophosphatidylcholine symporter 1 isoform 2

      See identical proteins and their annotated locations for NP_116182.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AB073383, BP321361, DB376308
      Consensus CDS
      CCDS446.1
      UniProtKB/TrEMBL
      B4DNN7
      Related
      ENSP00000361898.6, ENST00000372811.10
      Conserved Domains (1) summary
      pfam13347
      Location:48496
      MFS_2; MFS/sugar transport protein

    RNA

    1. NR_109896.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AB073383, BP321361, DB376308
      Related
      ENST00000483824.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      39955145..39969956
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047432490.1XP_047288446.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      39824591..39839402
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339264.1XP_054195239.1  sodium-dependent lysophosphatidylcholine symporter 1 isoform X1