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BEAN1 brain expressed associated with NEDD4 1 [ Homo sapiens (human) ]

Gene ID: 146227, updated on 5-Mar-2024

Summary

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Official Symbol
BEAN1provided by HGNC
Official Full Name
brain expressed associated with NEDD4 1provided by HGNC
Primary source
HGNC:HGNC:24160
See related
Ensembl:ENSG00000166546 MIM:612051; AllianceGenome:HGNC:24160
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
BEAN; SCA31
Summary
The protein encoded by this gene is one of several proteins that interact with NEDD4, a member of a family of ubiquitin-protein ligases. These proteins have PY motifs in common that bind to the WW domains of NEDD4. NEDD4 is developmentally regulated, and is highly expressed in embryonic tissues. Mutations in this gene (i.e., intronic insertions of >100 copies of pentanucleotide repeats including a (TGGAA)n sequence) are associated with spinocerebellar ataxia type 31. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
16q21
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (66427295..66495288)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (72221512..72289583)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (66461198..66529191)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66400487-66401036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66401847-66402553 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66404897-66405398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66406597-66407126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66407769-66408342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66413378-66414004 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66417102-66417626 Neighboring gene cadherin 5 Neighboring gene Sharpr-MPRA regulatory region 12004 Neighboring gene long intergenic non-protein coding RNA 920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66462026-66462626 Neighboring gene nuclear envelope phosphatase-regulatory subunit 1-like Neighboring gene uncharacterized LOC124903698 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7558 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66510981-66511522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66512063-66512603 Neighboring gene BEAN1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66513685-66514224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66518060-66519040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66521703-66522203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66543229-66544204 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66545181-66546156 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66546157-66547132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66553931-66554431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10940 Neighboring gene thymidine kinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10941 Neighboring gene CKLF-CMTM1 readthrough Neighboring gene chemokine like factor

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. O-GlcNAc regulates NEDD4-1 stability via caspase-mediated pathway. Jiang K, et al. Biochem Biophys Res Commun, 2016 Mar 18. PMID 26876577
  2. Abnormal RNA structures (RNA foci) containing a penta-nucleotide repeat (UGGAA)n in the Purkinje cell nucleus is associated with spinocerebellar ataxia type 31 pathogenesis. Niimi Y, et al. Neuropathology, 2013 Dec. PMID 23607545
  3. Pentanucleotide repeats at the spinocerebellar ataxia type 31 (SCA31) locus in Caucasians. Ishikawa K, et al. Neurology, 2011 Nov 15. PMID 22049201
  4. [Spinocerebellar ataxia type 31]. Ishikawa K, et al. Rinsho Shinkeigaku, 2010 Nov. PMID 21921537
  5. SCA31 is rare in the Chinese population on Taiwan. Lee YC, et al. Neurobiol Aging, 2012 Feb. PMID 21163552

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. this study reveals a regulation mechanism of NEDD4-1 stability by O-GlcNAcylation.
    Title: O-GlcNAc regulates NEDD4-1 stability via caspase-mediated pathway.
  2. Our data indicate that SCA31 is absent or rare in the Chinese population on Taiwan.
    Title: SCA31 is rare in the Chinese population on Taiwan.
  3. This study describes the structure of SCA31 pentanucleotide repeat sequences in a cohort of Caucasian patients with spinocerebellar ataxia.
    Title: Pentanucleotide repeats at the spinocerebellar ataxia type 31 (SCA31) locus in Caucasians.
  4. SCA31 is associated with "inserted" pentanucleotide repeats containing (TGGAA)n.
    Title: Spinocerebellar ataxia type 31 is associated with "inserted" penta-nucleotide repeats containing (TGGAA)n.
  5. we conclude that the RNA foci containing BEAN1-direction transcript (UGGAA)n are associated with Purkinje cell degeneration in Spinocerebellar ataxia type 31
    Title: Abnormal RNA structures (RNA foci) containing a penta-nucleotide repeat (UGGAA)n in the Purkinje cell nucleus is associated with spinocerebellar ataxia type 31 pathogenesis.
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
Spinocerebellar ataxia type 31
MedGen: C1861736 OMIM: 117210 GeneReviews: Hereditary Ataxia Overview
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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

  • FLJ27243

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protein BEAN1
Names
brain-expressed protein associating with Nedd4 homolog

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_021403.2 RefSeqGene

    Range
    5383..60921
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001136106.5 → NP_001129578.1  protein BEAN1 isoform 2

    See identical proteins and their annotated locations for NP_001129578.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AB472391, AB472395, AC132186, BC105723, BM666201
    Consensus CDS
    CCDS58469.1
    UniProtKB/Swiss-Prot
    Q3B7T3
    Related
    ENSP00000299694.8, ENST00000299694.12

  2. NM_001178020.3 → NP_001171491.1  protein BEAN1 isoform 1

    See identical proteins and their annotated locations for NP_001171491.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB472390, AB472395, AC132186, BC105723, BM666201
    Consensus CDS
    CCDS54015.1
    UniProtKB/Swiss-Prot
    B3KPC0, H3BP97, Q3B7T3
    Related
    ENSP00000442793.2, ENST00000536005.7
    Conserved Domains (1) summary
    pfam15293
    Location:113 → 207
    NUFIP2; Nuclear fragile X mental retardation-interacting protein 2

  3. NM_001197224.4 → NP_001184153.1  protein BEAN1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream in-frame start codon, and contains alternate 3' exon structure and thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (4) is shorter at the N-terminus and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AB472392, AB472395, AC010542, AC132186

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    66427295..66495288
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522884.2 → XP_011521186.1  protein BEAN1 isoform X1

    See identical proteins and their annotated locations for XP_011521186.1

    UniProtKB/Swiss-Prot
    B3KPC0, H3BP97, Q3B7T3
    Conserved Domains (1) summary
    pfam15293
    Location:113 → 207
    NUFIP2; Nuclear fragile X mental retardation-interacting protein 2

  2. XM_011522883.2 → XP_011521185.1  protein BEAN1 isoform X1

    See identical proteins and their annotated locations for XP_011521185.1

    UniProtKB/Swiss-Prot
    B3KPC0, H3BP97, Q3B7T3
    Conserved Domains (1) summary
    pfam15293
    Location:113 → 207
    NUFIP2; Nuclear fragile X mental retardation-interacting protein 2

  3. XM_011522894.2 → XP_011521196.1  protein BEAN1 isoform X3

  4. XM_011522885.4 → XP_011521187.1  protein BEAN1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    72221512..72289583
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054379658.1 → XP_054235633.1  protein BEAN1 isoform X1

  2. XM_054379657.1 → XP_054235632.1  protein BEAN1 isoform X1

  3. XM_054379660.1 → XP_054235635.1  protein BEAN1 isoform X3

  4. XM_054379659.1 → XP_054235634.1  protein BEAN1 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001197225.4: Suppressed sequence

    Description
    NM_001197225.4: This RefSeq was removed because currently there is insufficient support for the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q3B7T3.2 GenPept UniProtKB/Swiss-Prot:Q3B7T3

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