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FMR1 fragile X mental retardation 1 [ Homo sapiens (human) ]

Gene ID: 2332, updated on 7-Oct-2018

Summary

Official Symbol
FMR1provided by HGNC
Official Full Name
fragile X mental retardation 1provided by HGNC
Primary source
HGNC:HGNC:3775
See related
Ensembl:ENSG00000102081 MIM:309550; Vega:OTTHUMG00000022606
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
POF; FMRP; POF1; FRAXA
Summary
The protein encoded by this gene binds RNA and is associated with polysomes. The encoded protein may be involved in mRNA trafficking from the nucleus to the cytoplasm. A trinucleotide repeat (CGG) in the 5' UTR is normally found at 6-53 copies, but an expansion to 55-230 repeats is the cause of fragile X syndrome. Expansion of the trinucleotide repeat may also cause one form of premature ovarian failure (POF1). Multiple alternatively spliced transcript variants that encode different protein isoforms and which are located in different cellular locations have been described for this gene. [provided by RefSeq, May 2010]
Expression
Ubiquitous expression in thyroid (RPKM 16.8), brain (RPKM 15.9) and 25 other tissues See more
Orthologs

Genomic context

See FMR1 in Genome Data Viewer
Location:
Xq27.3
Exon count:
17
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) X NC_000023.11 (147911951..147951127)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (146993469..147032647)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373349 Neighboring gene origin of replication in 5' region of FMR1 Neighboring gene FRAXA repeat instability region Neighboring gene FMR1 antisense RNA 1 Neighboring gene FMR1 neighbor Neighboring gene RNA, 5S ribosomal pseudogene 524 Neighboring gene ferritin heavy chain 1 pseudogene 8

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Fragile X syndrome
MedGen: C0016667 OMIM: 300624 GeneReviews: FMR1-Related Disorders
Compare labs
Fragile X tremor/ataxia syndrome
MedGen: C1839780 OMIM: 300623 GeneReviews: FMR1-Related Disorders
Compare labs
Premature ovarian failure 1
MedGen: C3494522 OMIM: 311360 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-04-26)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-26)

ClinGen Genome Curation Page

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag HIV-1 Gag interacts with endogenous fragile X mental retardation protein (FMRP) in an RNase-resistant manner and the NC domain in Gag plays an important role in this interaction PubMed
capsid gag FMRP is incorporated into HIV-1 particles through association with viral RNP complex including NC, CA, and RT PubMed
nucleocapsid gag FMRP is incorporated into HIV-1 particles through association with viral RNP complex including NC, CA, and RT PubMed
gag HIV-1 Gag interacts with endogenous fragile X mental retardation protein (FMRP) in an RNase-resistant manner and the NC domain in Gag plays an important role in this interaction PubMed
reverse transcriptase gag-pol FMRP is incorporated into HIV-1 particles through association with viral RNP complex including NC, CA, and RT PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • RNA transport, organism-specific biosystem (from KEGG)
    RNA transport, organism-specific biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • RNA transport, conserved biosystem (from KEGG)
    RNA transport, conserved biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC87458

Gene Ontology Provided by GOA

Function Evidence Code Pubs
G-quadruplex RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding HDA PubMed 
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
RNA stem-loop binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA strand annealing activity IDA
Inferred from Direct Assay
more info
PubMed 
chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
dynein complex binding ISS
Inferred from Sequence or Structural Similarity
more info
 
identical protein binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ion channel binding IPI
Inferred from Physical Interaction
more info
PubMed 
mRNA 3'-UTR binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA 3'-UTR binding IDA
Inferred from Direct Assay
more info
PubMed 
mRNA 5'-UTR binding IDA
Inferred from Direct Assay
more info
PubMed 
mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
miRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
microtubule binding ISS
Inferred from Sequence or Structural Similarity
more info
 
poly(G) binding IDA
Inferred from Direct Assay
more info
PubMed 
poly(U) RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
protein homodimerization activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
ribosome binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
siRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
translation initiation factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
translation regulator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
translation repressor activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
RNA splicing IEA
Inferred from Electronic Annotation
more info
 
anterograde axonal transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to DNA damage stimulus IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to UV ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to hydroxyurea ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to virus IDA
Inferred from Direct Assay
more info
PubMed 
central nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
gene silencing by RNA IEA
Inferred from Electronic Annotation
more info
 
glutamate receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
mRNA processing IEA
Inferred from Electronic Annotation
more info
 
mRNA transport ISS
Inferred from Sequence or Structural Similarity
more info
 
modulation by host of viral RNA genome replication IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cytoplasmic translation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of long-term synaptic depression ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of synaptic vesicle exocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of translational initiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of voltage-gated calcium channel activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of dendritic spine development ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of filopodium assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of gene silencing by miRNA IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of histone phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of intracellular transport of viral material IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of proteasomal protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of protein phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of receptor internalization IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of response to DNA damage stimulus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of response to DNA damage stimulus IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of translation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of alternative mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of alternative mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
regulation of dendrite morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of dendritic spine development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of dendritic spine development IDA
Inferred from Direct Assay
more info
PubMed 
regulation of filopodium assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of filopodium assembly IDA
Inferred from Direct Assay
more info
PubMed 
regulation of gene silencing by miRNA IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of mRNA stability IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of mRNA stability ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of modification of synaptic structure IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of neuronal action potential IDA
Inferred from Direct Assay
more info
PubMed 
regulation of neurotransmitter secretion ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of translation at postsynapse, modulating synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Cajal body IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with SMN complex IDA
Inferred from Direct Assay
more info
PubMed 
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon ISS
Inferred from Sequence or Structural Similarity
more info
 
axon cytoplasm IEA
Inferred from Electronic Annotation
more info
 
axon terminus ISS
Inferred from Sequence or Structural Similarity
more info
 
cell junction IEA
Inferred from Electronic Annotation
more info
 
cell projection IDA
Inferred from Direct Assay
more info
PubMed 
chromocenter ISS
Inferred from Sequence or Structural Similarity
more info
 
chromosome ISS
Inferred from Sequence or Structural Similarity
more info
 
chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
cytoplasmic ribonucleoprotein granule IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasmic ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic stress granule IEA
Inferred from Electronic Annotation
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
dendrite ISS
Inferred from Sequence or Structural Similarity
more info
 
dendritic filopodium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendritic filopodium ISS
Inferred from Sequence or Structural Similarity
more info
 
dendritic spine IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendritic spine ISS
Inferred from Sequence or Structural Similarity
more info
 
dendritic spine neck IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extrinsic component of plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
filopodium tip ISS
Inferred from Sequence or Structural Similarity
more info
 
glial cell projection ISS
Inferred from Sequence or Structural Similarity
more info
 
growth cone IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
growth cone IDA
Inferred from Direct Assay
more info
PubMed 
growth cone filopodium ISS
Inferred from Sequence or Structural Similarity
more info
 
mRNA cap binding complex ISS
Inferred from Sequence or Structural Similarity
more info
 
membrane HDA PubMed 
messenger ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 
neuron projection IDA
Inferred from Direct Assay
more info
PubMed 
neuronal cell body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuronal ribonucleoprotein granule IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuronal ribonucleoprotein granule ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus TAS
Traceable Author Statement
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
perikaryon IDA
Inferred from Direct Assay
more info
PubMed 
perikaryon ISS
Inferred from Sequence or Structural Similarity
more info
 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with polysomal ribosome TAS
Traceable Author Statement
more info
PubMed 
polysome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
polysome IDA
Inferred from Direct Assay
more info
PubMed 
polysome ISS
Inferred from Sequence or Structural Similarity
more info
 
postsynapse ISS
Inferred from Sequence or Structural Similarity
more info
 
postsynaptic density IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
postsynaptic density ISS
Inferred from Sequence or Structural Similarity
more info
 
postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
presynapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
presynapse ISS
Inferred from Sequence or Structural Similarity
more info
 
presynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein granule IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synapse ISS
Inferred from Sequence or Structural Similarity
more info
 
viral replication complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
synaptic functional regulator FMR1
Names
fragile X mental retardation protein 1

NCBI Reference Sequences (RefSeq)

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_007529.2 RefSeqGene

    Range
    4961..44137
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_762

mRNA and Protein(s)

  1. NM_001185075.1NP_001172004.1  synaptic functional regulator FMR1 isoform ISO6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (ISO6) lacks an alternate segment and uses a different splice site in the 3' coding region which shifts the reading frame, compared to variant ISO1. The resulting protein (isoform ISO6) has a shorter and distinct C-terminus when it is compared to isoform ISO1.
    Source sequence(s)
    BC086957, BQ213316, BX498094, CK825936, L29074
    Consensus CDS
    CCDS55518.1
    UniProtKB/Swiss-Prot
    Q06787
    Related
    ENSP00000359502.3, ENST00000370471.7
    Conserved Domains (3) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    pfam00013
    Location:283325
    KH_1; KH domain
    pfam05641
    Location:63120
    Agenet; Agenet domain
  2. NM_001185076.1NP_001172005.1  synaptic functional regulator FMR1 isoform ISO7

    See identical proteins and their annotated locations for NP_001172005.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (ISO7) lacks an alternate segment, compared to variant ISO1. The resulting protein (isoform ISO7) is shorter when it is compared to isoform ISO1.
    Source sequence(s)
    BC086957, BQ213316, BQ417290, CN315330, CX871385, L29074
    Consensus CDS
    CCDS55519.1
    UniProtKB/Swiss-Prot
    Q06787
    Related
    ENSP00000218200.8, ENST00000218200.12
    Conserved Domains (5) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    pfam00013
    Location:283325
    KH_1; KH domain
    pfam05641
    Location:63120
    Agenet; Agenet domain
    pfam12235
    Location:399551
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16098
    Location:529611
    FXMR_C2; Fragile X-related mental retardation protein C-terminal region 2
  3. NM_001185081.1NP_001172010.1  synaptic functional regulator FMR1 isoform ISO12

    Status: REVIEWED

    Description
    Transcript Variant: This variant (ISO12) lacks two alternate segments and uses a different splice site which changes the reading frame, compared to variant ISO1. The resulting protein (isoform ISO12) has a shorter and distinct C-terminus when it is compared to isoform ISO1.
    Source sequence(s)
    BC086957, BQ213316, BQ287827, CK825936, L29074
    UniProtKB/Swiss-Prot
    Q06787
    Conserved Domains (3) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    pfam00013
    Location:283325
    KH_1; KH domain
    pfam05641
    Location:63120
    Agenet; Agenet domain
  4. NM_001185082.1NP_001172011.1  synaptic functional regulator FMR1 isoform ISO9

    See identical proteins and their annotated locations for NP_001172011.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (ISO9) lacks an alternate segment and uses a different splice site in the 3' coding region, compared to variant ISO1. The resulting protein (isoform ISO9) is shorter when it is compared to isoform ISO1.
    Source sequence(s)
    BC086957, L29074
    Consensus CDS
    CCDS76039.1
    UniProtKB/Swiss-Prot
    Q06787
    Related
    ENSP00000413764.3, OTTHUMP00000275550, ENST00000440235.6, OTTHUMT00000476314
    Conserved Domains (5) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    pfam00013
    Location:283325
    KH_1; KH domain
    pfam05641
    Location:63120
    Agenet; Agenet domain
    pfam12235
    Location:399526
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16098
    Location:504586
    FXMR_C2; Fragile X-related mental retardation protein C-terminal region 2
  5. NM_002024.5NP_002015.1  synaptic functional regulator FMR1 isoform ISO1

    See identical proteins and their annotated locations for NP_002015.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (ISO1) represents the longest transcript and it encodes the longest protein (isoform ISO1).
    Source sequence(s)
    BC086957, L29074, X69962
    Consensus CDS
    CCDS14682.1
    UniProtKB/Swiss-Prot
    Q06787
    Related
    ENSP00000359506.4, OTTHUMP00000024197, ENST00000370475.8, OTTHUMT00000058655
    Conserved Domains (5) summary
    smart00322
    Location:221280
    KH; K homology RNA-binding domain
    pfam00013
    Location:283325
    KH_1; KH domain
    pfam05641
    Location:63120
    Agenet; Agenet domain
    pfam12235
    Location:420572
    FXMRP1_C_core; Fragile X-related 1 protein core C terminal
    pfam16098
    Location:550632
    FXMR_C2; Fragile X-related mental retardation protein C-terminal region 2

RNA

  1. NR_033699.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (ISO4) lacks an alternate segment, compared to variant ISO1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant ISO1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC086957, BQ213316, BX498094, CK825936, L29074
  2. NR_033700.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (ISO10) lacks two alternate segments, compared to variant ISO1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant ISO1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC086957, BQ213316, CK825936, L29074

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p12 Primary Assembly

    Range
    147911951..147951127
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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