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

Gene ID: 257019, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (83242992..83585794, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (95392782..95735519, complement)
105.20220307 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: 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. 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
  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. FRMD3, a novel putative tumour suppressor in NSCLC. Haase D, et al. Oncogene, 2007 Jun 28. PMID 17260017
  4. 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
  5. Evaluation of associations between single nucleotide polymorphisms in the FRMD3 and CARS genes and diabetic nephropathy in a Kuwaiti population. Al-waheeb S, et al. Genet Mol Res, 2016 Jan 29. PMID 26909942

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)

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

  • 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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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_2023_10

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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