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

Gene ID: 9758, updated on 3-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (11822439..12724523)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (11404988..12305982)
105.20220307 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. 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
  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. 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
  4. 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
  5. Preso, a novel PSD-95-interacting FERM and PDZ domain protein that regulates dendritic spine morphogenesis. Lee HW, et al. J Neurosci, 2008 Dec 31. PMID 19118189, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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_2023_10

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

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

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

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

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

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

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

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

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

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

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