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

Gene ID: 2332, updated on 20-Sep-2014
Official Symbol
FMR1provided by HGNC
Official Full Name
fragile X mental retardation 1provided by HGNC
Primary source
HGNC:HGNC:3775
See related
Ensembl:ENSG00000102081; HPRD:02398; 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]
See FMR1 in Epigenomics, MapViewer
Location:
Xq27.3
Exon count:
17
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 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 LOC101928863 Neighboring gene microRNA 514a-3 Neighboring gene SRA stem-loop interacting RNA binding protein pseudogene Neighboring gene FMR1 antisense RNA 1 Neighboring gene fragile X mental retardation 1 neighbor Neighboring gene ferritin, heavy polypeptide 1 pseudogene 8

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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: C2749126 OMIM: 311360 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

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

ISCA Genome Curation Page
Haploinsufficency

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

ISCA Genome Curation Page

NHGRI GWAS Catalog

Description
Genetically distinct subsets within ANCA-associated vasculitis.
NHGRI GWA Catalog

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

  • 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) ...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC87458

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding TAS
Traceable Author Statement
more info
PubMed 
mRNA binding TAS
Traceable Author Statement
more info
PubMed 
microtubule binding IEA
Inferred from Electronic Annotation
more info
 
poly(A) RNA binding IDA
Inferred from Direct Assay
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
central nervous system development IEA
Inferred from Electronic Annotation
more info
 
mRNA transport IEA
Inferred from Electronic Annotation
more info
 
negative regulation of translational initiation ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
 
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
cytoplasmic ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic stress granule IEA
Inferred from Electronic Annotation
more info
 
dendritic shaft IEA
Inferred from Electronic Annotation
more info
 
dendritic spine IEA
Inferred from Electronic Annotation
more info
 
mRNA cap binding complex ISS
Inferred from Sequence or Structural Similarity
more info
 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus TAS
Traceable Author Statement
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
PubMed 
colocalizes_with polysomal ribosome TAS
Traceable Author Statement
more info
PubMed 
synapse IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
fragile X mental retardation protein 1
Names
fragile X mental retardation protein 1

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_007529.1 

    Range
    4961..44139
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001185075.1NP_001172004.1  fragile X mental retardation protein 1 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/TrEMBL
    G8JLE9
    UniProtKB/Swiss-Prot
    Q06787
    Related
    ENSP00000359502, ENST00000370471
    Conserved Domains (2) summary
    cd00105
    Location:286325
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam05641
    Location:59117
    Agenet; Agenet domain
  2. NM_001185076.1NP_001172005.1  fragile X mental retardation protein 1 isoform ISO7

    See proteins identical to 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, ENST00000218200
    Conserved Domains (3) summary
    cd00105
    Location:286325
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam05641
    Location:59117
    Agenet; Agenet domain
    pfam12235
    Location:406488
    FXR1P_C; Fragile X-related 1 protein C terminal
  3. NM_001185081.1NP_001172010.1  fragile X mental retardation protein 1 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 (2) summary
    cd00105
    Location:286325
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam05641
    Location:59117
    Agenet; Agenet domain
  4. NM_001185082.1NP_001172011.1  fragile X mental retardation protein 1 isoform ISO9

    See proteins identical to 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, OTTHUMP00000275550, ENST00000440235, OTTHUMT00000476314
    Conserved Domains (3) summary
    cd00105
    Location:286325
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam05641
    Location:59117
    Agenet; Agenet domain
    pfam12235
    Location:406531
    FXR1P_C; Fragile X-related 1 protein C terminal
  5. NM_002024.5NP_002015.1  fragile X mental retardation protein 1 isoform ISO1

    See proteins identical to 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, OTTHUMP00000024197, ENST00000370475, OTTHUMT00000058655
    Conserved Domains (3) summary
    cd00105
    Location:286325
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    pfam05641
    Location:59117
    Agenet; Agenet domain
    pfam12235
    Location:427509
    FXR1P_C; Fragile X-related 1 protein C terminal

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 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000023.11 

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

Alternate HuRef

Genomic

  1. AC_000155.1 

    Range
    135963879..135993282
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018934.2 

    Range
    146904323..146943501
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)