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    FRMD3 FERM domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 257019, updated on 10-Dec-2024

    Summary

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    Official Symbol
    FRMD3provided by HGNC
    Official Full Name
    FERM domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:24125
    See related
    Ensembl:ENSG00000172159 MIM:607619; AllianceGenome:HGNC:24125
    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
    4.1O; P410; EPB41LO; EPB41L4O
    Summary
    The protein encoded by this gene is a single pass membrane protein primarily found in ovaries. A similar protein in erythrocytes helps determine the shape of red blood cells, but the function of the encoded protein has not been determined. There is some evidence that this is a tumor suppressor gene, and there is also evidence linking defects in this gene to susceptibility to diabetic nephropathy in type 1 diabetes. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
    Expression
    Broad expression in heart (RPKM 8.0), kidney (RPKM 5.0) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FRMD3 in Genome Data Viewer
    Location:
    9q21.32
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (83242992..83585794, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (95392782..95735519, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (85857907..86153316, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987087 Neighboring gene uncharacterized LOC124902188 Neighboring gene uncharacterized LOC124902189 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:85389408-85390018 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_108276 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:85478762-85479961 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:85496837-85497338 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:85497339-85497838 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:85498304-85499130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:85500782-85501606 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:85503259-85504084 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:85504085-85504909 Neighboring gene VISTA enhancer hs618 Neighboring gene RAS and EF-hand domain containing Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:85842683-85843384 Neighboring gene RN7SK pseudogene 242 Neighboring gene FRMD3 antisense RNA 1 Neighboring gene uncharacterized LOC124902190 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_108296 Neighboring gene RNA, U4 small nuclear 29, pseudogene Neighboring gene Sharpr-MPRA regulatory region 2550 Neighboring gene Sharpr-MPRA regulatory region 10133 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28493 Neighboring gene Sharpr-MPRA regulatory region 3056 Neighboring gene Sharpr-MPRA regulatory region 13153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28495 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:86243894-86244482 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:86244483-86245069 Neighboring gene RNA, U4 small nuclear 15, pseudogene Neighboring gene IDNK gluconokinase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. FRMD3, a novel putative tumour suppressor in NSCLC. Haase D, et al. Oncogene, 2007 Jun 28. PMID 17260017
    2. From single nucleotide polymorphism to transcriptional mechanism: a model for FRMD3 in diabetic nephropathy. Martini S, et al. Diabetes, 2013 Jul. PMID 23434934, Free PMC Article
    3. Hsa-miR-3651 could serve as a novel predictor for in-breast recurrence via FRMD3. Zellinger B, et al. Breast Cancer, 2022 Mar. PMID 34865205, Free PMC Article
    4. FRMD3 inhibits the growth and metastasis of breast cancer through the ubiquitination-mediated degradation of vimentin and subsequent impairment of focal adhesion. Shao W, et al. Cell Death Dis, 2023 Jan 11. PMID 36631457, Free PMC Article
    5. Molecular cloning and characterization of the protein 4.1O gene, a novel member of the protein 4.1 family with focal expression in ovary. Ni X, et al. J Hum Genet, 2003. PMID 12601556

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FRMD3 inhibits the growth and metastasis of breast cancer through the ubiquitination-mediated degradation of vimentin and subsequent impairment of focal adhesion.
      Title: FRMD3 inhibits the growth and metastasis of breast cancer through the ubiquitination-mediated degradation of vimentin and subsequent impairment of focal adhesion.
    2. Hsa-miR-3651 could serve as a novel predictor for in-breast recurrence via FRMD3.
      Title: Hsa-miR-3651 could serve as a novel predictor for in-breast recurrence via FRMD3.
    3. The risk (G and C) and non-risk (C and T) allele frequencies of the SNPs at the rs1888747 and rs739401 loci of FRMD3 and CARS, respectively, did not differ significantly between the diabetics with (case) and without (control) nephropathy (P > 0.05).
      Title: Evaluation of associations between single nucleotide polymorphisms in the FRMD3 and CARS genes and diabetic nephropathy in a Kuwaiti population.
    4. model for FRMD3 in diabetic nephropathy proposes a possible transcriptional link through which the polymorphism in the FRMD3 promoter could influence transcriptional regulation within the bone morphogenetic protein (BMP)-signaling pathway
      Title: From single nucleotide polymorphism to transcriptional mechanism: a model for FRMD3 in diabetic nephropathy.
    5. These analyses reveal a role for FRMD3 in AA T2DN susceptibility.
      Title: Differential effects of MYH9 and APOL1 risk variants on FRMD3 Association with Diabetic ESRD in African Americans.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Replication study for the association between four Loci identified by a genome-wide association study on European American subjects with type 1 diabetes and susceptibility to diabetic nephropathy in Japanese subjects with type 2 diabetes.
    7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    8. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association scan for diabetic nephropathy susceptibility genes in type 1 diabetes.
    9. identify FRMD3 as a novel putative tumour suppressor gene suggesting an important role in the origin and progression of lung cancer.
      Title: FRMD3, a novel putative tumour suppressor in NSCLC.
    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

    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

    • MGC20553

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cytoskeletal protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in actomyosin structure organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    FERM domain-containing protein 3
    Names
    band 4.1-like protein 4
    band 4.1-like protein 4O
    ovary type protein 4.1
    protein 4.1O

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001244959.2 → NP_001231888.1  FERM domain-containing protein 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction at the 3' end of an exon and has an alternate 3' terminal exon compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK094281, AK223597, BC041376
      Consensus CDS
      CCDS59133.1
      UniProtKB/Swiss-Prot
      A2A2Y4
      Related
      ENSP00000365621.1, ENST00000376438.5
      Conserved Domains (5) summary
      smart00295
      Location:33 → 225
      B41; Band 4.1 homologues
      pfam00373
      Location:117 → 225
      FERM_M; FERM central domain
      pfam08736
      Location:323 → 357
      FA; FERM adjacent (FA)
      pfam09379
      Location:36 → 98
      FERM_N; FERM N-terminal domain
      cl17171
      Location:206 → 309
      PH-like; Pleckstrin homology-like domain

    2. NM_001244960.2 → NP_001231889.1  FERM domain-containing protein 3 isoform 3

      See identical proteins and their annotated locations for NP_001231889.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks the first exon compared to variant 1 and has an alternate, downstream first exon instead. The resulting isoform (3) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AK223597, AL137847, AY137774, BM873990
      Consensus CDS
      CCDS75852.1
      UniProtKB/Swiss-Prot
      A2A2Y4
      Related
      ENSP00000484839.1, ENST00000621208.4
      Conserved Domains (5) summary
      smart00295
      Location:7 → 181
      B41; Band 4.1 homologues
      pfam00373
      Location:73 → 181
      FERM_M; FERM central domain
      pfam08736
      Location:279 → 313
      FA; FERM adjacent (FA)
      pfam09379
      Location:7 → 54
      FERM_N; FERM N-terminal domain
      cl17171
      Location:162 → 265
      PH-like; Pleckstrin homology-like domain

    3. NM_001244961.2 → NP_001231890.1  FERM domain-containing protein 3 isoform 4

      See identical proteins and their annotated locations for NP_001231890.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks the first exon compared to variant 1 and has an alternate, downstream first exon instead. It also uses an alternate splice junction at the 3' end of an exon and has an alternate 3' terminal exon compared to variant 1. The resulting isoform (4) has shorter and distinct N and C-terminus compared to isoform 1.
      Source sequence(s)
      BC037253
      Consensus CDS
      CCDS59132.1
      UniProtKB/Swiss-Prot
      A2A2Y4
      Related
      ENSP00000365617.1, ENST00000376434.5
      Conserved Domains (2) summary
      pfam08736
      Location:129 → 163
      FA; FERM adjacent (FA)
      cl17171
      Location:12 → 115
      PH-like; Pleckstrin homology-like domain

    4. NM_001244962.2 → NP_001231891.1  FERM domain-containing protein 3 isoform 5

      See identical proteins and their annotated locations for NP_001231891.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks the first exon compared to variant 1 and has an alternate, downstream first exon instead. It also uses an alternate splice junction at the 3' end of an exon and has an alternate 3' terminal exon compared to variant 1. The resulting isoform (5) has shorter and distinct N and C-terminus compared to isoform 1.
      Source sequence(s)
      BC023560
      Consensus CDS
      CCDS59131.1
      UniProtKB/Swiss-Prot
      A2A2Y4
      Related
      ENSP00000328615.1, ENST00000328788.5

    5. NM_001375487.1 → NP_001362416.1  FERM domain-containing protein 3 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AL137847

    6. NM_174938.6 → NP_777598.3  FERM domain-containing protein 3 isoform 1

      See identical proteins and their annotated locations for NP_777598.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK223597, AL137847, BC041376, BM873990
      Consensus CDS
      CCDS43840.1
      UniProtKB/Swiss-Prot
      A2A2Y4, A8MQB0, B4DN14, Q53EP2, Q5JV59, Q5VZA1, Q86WP8, Q8IZ44, Q8N3Y5, Q8N9L2
      Related
      ENSP00000303508.3, ENST00000304195.8
      Conserved Domains (5) summary
      smart00295
      Location:33 → 225
      B41; Band 4.1 homologues
      pfam00373
      Location:117 → 225
      FERM_M; FERM central domain
      pfam08736
      Location:323 → 357
      FA; FERM adjacent (FA)
      pfam09379
      Location:36 → 98
      FERM_N; FERM N-terminal domain
      cl17171
      Location:206 → 309
      PH-like; Pleckstrin homology-like domain

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      83242992..83585794 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024447487.2 → XP_024303255.1  FERM domain-containing protein 3 isoform X2

      Conserved Domains (3) summary
      smart00295
      Location:2 → 129
      B41; Band 4.1 homologues
      pfam08736
      Location:227 → 261
      FA; FERM adjacent (FA)
      cl17171
      Location:110 → 213
      PH-like; Pleckstrin homology-like domain

    2. XM_047423155.1 → XP_047279111.1  FERM domain-containing protein 3 isoform X2

    3. XM_017014588.2 → XP_016870077.1  FERM domain-containing protein 3 isoform X1

    4. XM_024447488.2 → XP_024303256.1  FERM domain-containing protein 3 isoform X2

      Conserved Domains (3) summary
      smart00295
      Location:2 → 129
      B41; Band 4.1 homologues
      pfam08736
      Location:227 → 261
      FA; FERM adjacent (FA)
      cl17171
      Location:110 → 213
      PH-like; Pleckstrin homology-like domain

    5. XM_047423154.1 → XP_047279110.1  FERM domain-containing protein 3 isoform X2

    6. XM_047423153.1 → XP_047279109.1  FERM domain-containing protein 3 isoform X2

    7. XM_017014589.2 → XP_016870078.1  FERM domain-containing protein 3 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      95392782..95735519 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362625.1 → XP_054218600.1  FERM domain-containing protein 3 isoform X2

    2. XM_054362629.1 → XP_054218604.1  FERM domain-containing protein 3 isoform X2

    3. XM_054362623.1 → XP_054218598.1  FERM domain-containing protein 3 isoform X1

    4. XM_054362624.1 → XP_054218599.1  FERM domain-containing protein 3 isoform X2

    5. XM_054362627.1 → XP_054218602.1  FERM domain-containing protein 3 isoform X2

    6. XM_054362626.1 → XP_054218601.1  FERM domain-containing protein 3 isoform X2

    7. XM_054362628.1 → XP_054218603.1  FERM domain-containing protein 3 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2A2Y4.1 GenPept UniProtKB/Swiss-Prot:A2A2Y4

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

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