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    FRMPD4 FERM and PDZ domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 9758, updated on 9-Dec-2024

    Summary

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    Official Symbol
    FRMPD4provided by HGNC
    Official Full Name
    FERM and PDZ domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:29007
    See related
    Ensembl:ENSG00000169933 MIM:300838; AllianceGenome:HGNC:29007
    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
    MRX104; PDZD10; PDZK10; XLID104
    Summary
    This gene encodes a multi-domain (WW, PDZ, FERM) containing protein. Through its interaction with other proteins (such as PSD-95), it functions as a positive regulator of dendritic spine morphogenesis and density, and is required for the maintenance of excitatory synaptic transmission. [provided by RefSeq, Jan 2010]
    Expression
    Biased expression in brain (RPKM 3.1) and heart (RPKM 0.2) See more
    Orthologs
    mouse all
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    Genomic context

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    See FRMPD4 in Genome Data Viewer
    Location:
    Xp22.2
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (11822439..12724523)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (11404988..12305982)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (11840558..12742642)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20661 Neighboring gene Sharpr-MPRA regulatory region 2065 Neighboring gene MSL3 divergent transcript Neighboring gene MSL complex subunit 3 Neighboring gene MPRA-validated peak7357 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:12327767-12328270 Neighboring gene FRMPD4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29411 Neighboring gene ribosomal protein L17 pseudogene 49 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:12597924-12599123 Neighboring gene RN7SK pseudogene 290 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20663 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:12837926-12839125 Neighboring gene proteasome subunit alpha 6 pseudogene 2 Neighboring gene phosphoribosyl pyrophosphate synthetase 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Investigation of FRMPD4 variants associated with X-linked epilepsy. Li RK, et al. Seizure, 2024 Mar. PMID 37330374
    2. Possibility of a sex-specific role for a genetic variant in FRMPD4 in schizophrenia, but not cognitive function. Matosin N, et al. Neuroreport, 2016 Jan 6. PMID 26555035
    3. Structure of the FERM domain of a neural scaffold protein FRMPD4 implicated in X-linked intellectual disability. Wang M, et al. Biochem J, 2020 Dec 11. PMID 33216857
    4. Structural basis for the recognition of the scaffold protein Frmpd4/Preso1 by the TPR domain of the adaptor protein LGN. Takayanagi H, et al. Acta Crystallogr F Struct Biol Commun, 2015 Feb. PMID 25664792, Free PMC Article
    5. FRMPD4 mutations cause X-linked intellectual disability and disrupt dendritic spine morphogenesis. Piard J, et al. Hum Mol Genet, 2018 Feb 15. PMID 29267967, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Investigation of FRMPD4 variants associated with X-linked epilepsy.
      Title: Investigation of FRMPD4 variants associated with X-linked epilepsy.
    2. Structure of the FERM domain of a neural scaffold protein FRMPD4 implicated in X-linked intellectual disability.
      Title: Structure of the FERM domain of a neural scaffold protein FRMPD4 implicated in X-linked intellectual disability.
    3. The findings point to an important role of FRMPD4 in normal cognitive development and function in humans and mice, and support the hypothesis that FRMPD4 mutations cause ID by disrupting dendritic spine morphogenesis in glutamatergic neurons.
      Title: FRMPD4 mutations cause X-linked intellectual disability and disrupt dendritic spine morphogenesis.
    4. Study suggests that the variant rs5979717 in FRMPD4 may play a role in schizophrenia etiology in females
      Title: Possibility of a sex-specific role for a genetic variant in FRMPD4 in schizophrenia, but not cognitive function.
    5. A crystal structure of Frmpd4-bound LGN in an oxidized form is also reported, although oxidation does not appear to strongly affect the interaction with Frmpd4.
      Title: Structural basis for the recognition of the scaffold protein Frmpd4/Preso1 by the TPR domain of the adaptor protein LGN.
    6. Preso positively regulates spine density through its interaction with the synaptic plasma membrane, actin filaments, PSD-95, and the betaPix-based Rac1 signaling pathway.
      Title: Preso, a novel PSD-95-interacting FERM and PDZ domain protein that regulates dendritic spine morphogenesis.
    7. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Intellectual disability, X-linked 104
    MedGen: C4310817 OMIM: 300983 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0316, MGC142260, MGC142262

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol-4,5-bisphosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-4,5-bisphosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of synapse structural plasticity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in dendritic spine IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in dendritic spine IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    FERM and PDZ domain-containing protein 4
    Names
    PDZ domain-containing protein 10
    PSD-95-interacting FERM and PDZ domain protein
    PSD-95-interacting regulator of spine morphogenesis
    Preso

    NCBI Reference Sequences (RefSeq)

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    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_016419.3 RefSeqGene

      Range
      321013..907063
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001368395.3 → NP_001355324.1  FERM and PDZ domain-containing protein 4 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest isoform (a).
      Source sequence(s)
      AC004554, AC073613, AC112499, AC112655, AC119619
      UniProtKB/TrEMBL
      A0A590UJL7
      Related
      ENSP00000499481.1, ENST00000656302.1

    2. NM_001368396.3 → NP_001355325.1  FERM and PDZ domain-containing protein 4 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC002981, AC112499, AC112655, AC119619
      UniProtKB/TrEMBL
      A0A590UJL7

    3. NM_001368397.1 → NP_001355326.1  FERM and PDZ domain-containing protein 4 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC002981, AC112499, AC112655, AC119619
      Consensus CDS
      CCDS94551.1
      UniProtKB/TrEMBL
      A0A590UJL7, A0A6Q8PH73
      Related
      ENSP00000502607.1, ENST00000675598.1

    4. NM_001368398.3 → NP_001355327.1  FERM and PDZ domain-containing protein 4 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC004554, AC073613, AC112499, AC112655, AC119619
      UniProtKB/TrEMBL
      A0A1W2PQW0
      Related
      ENSP00000492353.2, ENST00000640291.2

    5. NM_001368399.3 → NP_001355328.1  FERM and PDZ domain-containing protein 4 isoform f

      Status: REVIEWED

      Source sequence(s)
      AC002981, AC112499, AC112655, AC119619
      Consensus CDS
      CCDS94550.1
      UniProtKB/TrEMBL
      A0A1W2PQW0, A0A5F9ZH12
      Related
      ENSP00000499962.1, ENST00000672010.1

    6. NM_001368400.3 → NP_001355329.1  FERM and PDZ domain-containing protein 4 isoform g

      Status: REVIEWED

      Source sequence(s)
      AC073524, AC112499, AC112655, AC119619
      Consensus CDS
      CCDS94552.1
      UniProtKB/TrEMBL
      A0A087WYX8, A0A1W2PQW0
      Related
      ENSP00000482182.2, ENST00000616992.2

    7. NM_001368401.1 → NP_001355330.1  FERM and PDZ domain-containing protein 4 isoform h

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8), as well as variant 9, encodes isoform h.
      Source sequence(s)
      AC002981, AC112499, AC112655, AC112657, AC119619
      UniProtKB/TrEMBL
      A0A1W2PQW0, B7ZLE1

    8. NM_001368402.3 → NP_001355331.1  FERM and PDZ domain-containing protein 4 isoform h

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9), as well as variant 8, encodes isoform h.
      Source sequence(s)
      AC073524, AC112499, AC112655, AC112657, AC119619
      UniProtKB/TrEMBL
      A0A1W2PQW0, B7ZLE1

    9. NM_014728.3 → NP_055543.2  FERM and PDZ domain-containing protein 4 isoform e

      See identical proteins and their annotated locations for NP_055543.2

      Status: REVIEWED

      Source sequence(s)
      AB002314, AC112655, AK289694, BX089361
      Consensus CDS
      CCDS35201.1
      UniProtKB/Swiss-Prot
      A8K0X9, O15032, Q14CM0
      UniProtKB/TrEMBL
      A0A1W2PQW0
      Related
      ENSP00000370057.1, ENST00000380682.5
      Conserved Domains (4) summary
      smart00295
      Location:205 → 424
      B41; Band 4.1 homologues
      cd00201
      Location:36 → 66
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      cd00992
      Location:76 → 152
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd13183
      Location:420 → 524
      FERM_C_FRMPD1_FRMPD3_FRMPD4; FERM domain C-lobe of FERM and PDZ domain containing proteins 1, 3, and 4 (FRMPD1, 3, 4)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      11822439..12724523
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017029983.2 → XP_016885472.1  FERM and PDZ domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      A0A590UJL7

    2. XM_047442680.1 → XP_047298636.1  FERM and PDZ domain-containing protein 4 isoform X2

      UniProtKB/TrEMBL
      A0A1W2PQW0

    3. XM_017029985.2 → XP_016885474.2  FERM and PDZ domain-containing protein 4 isoform X5

      UniProtKB/TrEMBL
      A0A1W2PQW0

    4. XM_005274632.4 → XP_005274689.3  FERM and PDZ domain-containing protein 4 isoform X3

      UniProtKB/TrEMBL
      A0A590UJL7

    5. XM_017029984.2 → XP_016885473.2  FERM and PDZ domain-containing protein 4 isoform X4

      UniProtKB/TrEMBL
      A0A590UJL7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      11404988..12305982
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328187.1 → XP_054184162.1  FERM and PDZ domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      A0A590UJL7

    2. XM_054328190.1 → XP_054184165.1  FERM and PDZ domain-containing protein 4 isoform X2

      UniProtKB/TrEMBL
      A0A1W2PQW0

    3. XM_054328188.1 → XP_054184163.1  FERM and PDZ domain-containing protein 4 isoform X7

      UniProtKB/TrEMBL
      A0A590UJL7

    4. XM_054328186.1 → XP_054184161.1  FERM and PDZ domain-containing protein 4 isoform X6

      UniProtKB/TrEMBL
      A0A590UJL7

    5. XM_054328189.1 → XP_054184164.1  FERM and PDZ domain-containing protein 4 isoform X8

      UniProtKB/TrEMBL
      A0A1W2PQW0
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14CM0.1 GenPept UniProtKB/Swiss-Prot:Q14CM0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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