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PARVB parvin beta [ Homo sapiens (human) ]

Gene ID: 29780, updated on 3-Nov-2024

Summary

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Official Symbol
PARVBprovided by HGNC
Official Full Name
parvin betaprovided by HGNC
Primary source
HGNC:HGNC:14653
See related
Ensembl:ENSG00000188677 MIM:608121; AllianceGenome:HGNC:14653
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
CGI-56
Summary
This gene encodes a member of the parvin family of actin-binding proteins, which play a role in cytoskeleton organization and cell adhesion. These proteins are associated with focal contacts and contain calponin homology domains that bind to actin filaments. This family member binds to alphaPIX and alpha-actinin, and it can inhibit the activity of integrin-linked kinase. This protein also functions in tumor suppression. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]
Expression
Ubiquitous expression in fat (RPKM 14.3), heart (RPKM 12.4) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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See PARVB in Genome Data Viewer
Location:
22q13.31
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (43999211..44172939)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (44483004..44656061)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (44395091..44568819)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:44319500-44320244 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44320245-44320987 Neighboring gene Sharpr-MPRA regulatory region 5125 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:44347552-44347721 Neighboring gene H3K27ac hESC enhancers GRCh37_chr22:44350547-44351299 and GRCh37_chr22:44351300-44352051 Neighboring gene patatin like phospholipase domain containing 3 Neighboring gene ribosomal protein L35a pseudogene 36 Neighboring gene SAMM50 sorting and assembly machinery component Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19196 Neighboring gene uncharacterized LOC124905131 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13861 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19198 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19199 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44433869-44434401 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44441960-44442509 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44444424-44445372 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:44447510-44448390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44451418-44451918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44459805-44460304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44463139-44463704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44463705-44464268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19206 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44464833-44465396 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:44501635-44502135 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr22:44502229-44503124 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44503125-44504019 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44504020-44504914 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44541321-44541950 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44541951-44542580 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44543839-44544468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44550653-44551476 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44551477-44552300 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44553755-44554288 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44554289-44554822 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:44556425-44556958 Neighboring gene tRNA-SeC (anticodon TCA) 2-1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44563307-44564086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44565977-44566498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19207 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44570650-44571382 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13864 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44576792-44577522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44577523-44578252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44578253-44578982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44588052-44588637 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44588638-44589222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44596327-44597136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44597948-44598757 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44600018-44600518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44600519-44601019 Neighboring gene parvin gamma Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44616903-44617455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44658947-44659462 Neighboring gene shisa like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44676595-44677095 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44678007-44678506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:44685764-44686707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44688595-44689536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44694997-44695529 Neighboring gene uncharacterized LOC101927499

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 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Targeted-bisulfite sequence analysis of the methylation of CpG islands in genes encoding PNPLA3, SAMM50, and PARVB of patients with non-alcoholic fatty liver disease.
    Title: Targeted-bisulfite sequence analysis of the methylation of CpG islands in genes encoding PNPLA3, SAMM50, and PARVB of patients with non-alcoholic fatty liver disease.
  2. Protein expression of beta-Parvin increases with colorectal cancer progression.
    Title: Focal Adhesion Proteins α- and β-Parvin are Overexpressed in Human Colorectal Cancer and Correlate with Tumor Progression.
  3. Taken together, our results indicate that 24-MCF treatment increases parvin-beta expression, which may inhibit ILK downstream signaling.
    Title: 24-Methylenecycloartanyl ferulate, a major compound of γ-oryzanol, promotes parvin-beta expression through an interaction with peroxisome proliferator-activated receptor-gamma 2 in human breast cancer cells.
  4. study found polymorphisms of rs5764455 and rs6006473 in PARVB gene in the Han Chinese population, and these polymorphisms were associated with the occurrence and progression of NAFLD.
    Title: Association of rs5764455 and rs6006473 polymorphisms in PARVB with liver damage of nonalcoholic fatty liver disease in Han Chinese population.
  5. Our results suggested that variations, including insertion/deletions, in PARVB, as well as those in PNPLA3, are important in the progression of NAFLD.
    Title: Targeted next-generation sequencing and fine linkage disequilibrium mapping reveals association of PNPLA3 and PARVB with the severity of nonalcoholic fatty liver disease.
  6. PARVB overexpression is a candidate biomarker for endophytic tumours and metastasis.
    Title: PARVB overexpression increases cell migration capability and defines high risk for endophytic growth and metastasis in tongue squamous cell carcinoma.
  7. PARVB plays a potential role in the pathogenesis of coronary restenosis.
    Title: Pathway analysis using genome-wide association study data for coronary restenosis--a potential role for the PARVB gene.
  8. Polymorphisms in the SAMM50 and PARVB genes in addition to those in the PNPLA3 gene were observed to be associated with the development and progression of NAFLD.
    Title: Genome-wide scan revealed that polymorphisms in the PNPLA3, SAMM50, and PARVB genes are associated with development and progression of nonalcoholic fatty liver disease in Japan.
  9. alpha-parvin, beta-parvin and migfilin were expressed in tumor cells in 53%, 2%, 28% and 53% of effusions and 57%, 20%, 83% and 25% of solid lesions, respectively.
    Title: Migfilin, α-parvin and β-parvin are differentially expressed in ovarian serous carcinoma effusions, primary tumors and solid metastases.
  10. proper localization of beta-parvin to focal adhesions requires both the paxillin and integrin-linked kinase binding sites and that paxillin is important for early targeting of beta-parvin.
    Title: Structural basis for paxillin binding and focal adhesion targeting of β-parvin.
Submit: New GeneRIF Correction See all GeneRIFs (23)

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

EBI GWAS Catalog

Description
Genetic polymorphisms of the human PNPLA3 gene are strongly associated with severity of non-alcoholic fatty liver disease in Japanese.
EBI GWAS Catalog
Genetic variant predicts bevacizumab-induced hypertension in ECOG-5103 and ECOG-2100.
EBI GWAS Catalog
Genome-wide association study of hematological and biochemical traits in a Japanese population.
EBI GWAS Catalog
Genome-wide association study of the rate of cognitive decline in Alzheimer's disease.
EBI GWAS Catalog
Genome-wide scan revealed that polymorphisms in the PNPLA3, SAMM50, and PARVB genes are associated with development and progression of nonalcoholic fatty liver disease in Japan.
EBI GWAS Catalog
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of parvin, beta (PARVB) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ17029

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in actin cytoskeleton organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cell projection assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in establishment or maintenance of cell polarity regulating cell shape IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in establishment or maintenance of cell polarity regulating cell shape IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in lamellipodium assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in lamellipodium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in substrate adhesion-dependent cell spreading IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in Z disc IEA
Inferred from Electronic Annotation
more info
  
is_active_in actin cytoskeleton IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in actin cytoskeleton IDA
Inferred from Direct Assay
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in focal adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in focal adhesion IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in lamellipodium IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in lamellipodium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
beta-parvin
Names
affixin

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_029743.3 RefSeqGene

    Range
    30093..178730
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001003828.3 → NP_001003828.1  beta-parvin isoform a

    See identical proteins and their annotated locations for NP_001003828.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, also known as CLINT or ParvB3) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AF237769, AF303887, AL031595, AL035398, CA308417
    Consensus CDS
    CCDS46724.1
    UniProtKB/Swiss-Prot
    Q9HBI1
    Related
    ENSP00000384515.3, ENST00000406477.7
    Conserved Domains (1) summary
    pfam00307
    Location:121 → 222
    CH; Calponin homology (CH) domain

  2. NM_001243385.2 → NP_001230314.1  beta-parvin isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream alternate start codon, compared to variant 1. The resulting isoform (c) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AL031595, AL033543, BC039811, CA308417, Z82174
    Consensus CDS
    CCDS58808.1
    UniProtKB/Swiss-Prot
    Q9HBI1
    Related
    ENSP00000384353.1, ENST00000404989.1
    Conserved Domains (2) summary
    cd21336
    Location:51 → 156
    CH_PARVB_rpt1; first calponin homology (CH) domain found in beta-parvin
    cd21338
    Location:198 → 327
    CH_PARVB_rpt2; second calponin homology (CH) domain found in beta-parvin

  3. NM_001243386.2 → NP_001230315.1  beta-parvin isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream alternate start codon, and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (d) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AF237769, AK308443, AL031595, AL033543, CA308417
    Consensus CDS
    CCDS74874.1
    UniProtKB/TrEMBL
    A0A087WZB5
    Related
    ENSP00000482511.1, ENST00000619710.4
    Conserved Domains (1) summary
    pfam00307
    Location:36 → 137
    CH; Calponin homology (CH) domain

  4. NM_013327.5 → NP_037459.2  beta-parvin isoform b

    See identical proteins and their annotated locations for NP_037459.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as ParvB2) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The resulting isoform (b) has a distinct and shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AF237769, AL031595, BP339885, CA308417
    Consensus CDS
    CCDS14056.1
    UniProtKB/Swiss-Prot
    B0QYM8, B0QYN1, B2R9X6, Q5TGJ5, Q86X93, Q96PN1, Q9HBI1, Q9NSP7, Q9UGT3, Q9Y368, Q9Y3L6, Q9Y3L7
    Related
    ENSP00000342492.6, ENST00000338758.12
    Conserved Domains (1) summary
    pfam00307
    Location:88 → 189
    CH; Calponin homology (CH) 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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    43999211..44172939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024452236.2 → XP_024308004.1  beta-parvin isoform X2

    Conserved Domains (1) summary
    pfam00307
    Location:120 → 228
    CH; Calponin homology (CH) domain

  2. XM_017028792.3 → XP_016884281.1  beta-parvin isoform X3

  3. XM_024452235.2 → XP_024308003.1  beta-parvin isoform X1

    Conserved Domains (1) summary
    pfam00307
    Location:105 → 213
    CH; Calponin homology (CH) domain

  4. XM_047441349.1 → XP_047297305.1  beta-parvin isoform X4

    Conserved Domains (2) summary
    cd21336
    Location:51 → 156
    CH_PARVB_rpt1; first calponin homology (CH) domain found in beta-parvin
    cd21338
    Location:198 → 327
    CH_PARVB_rpt2; second calponin homology (CH) domain found in beta-parvin

  5. XM_047441350.1 → XP_047297306.1  beta-parvin isoform X6

    Conserved Domains (2) summary
    cd21336
    Location:51 → 156
    CH_PARVB_rpt1; first calponin homology (CH) domain found in beta-parvin
    cd21338
    Location:198 → 327
    CH_PARVB_rpt2; second calponin homology (CH) domain found in beta-parvin

  6. XM_024452237.2 → XP_024308005.1  beta-parvin isoform X5

    Conserved Domains (2) summary
    cd21336
    Location:51 → 156
    CH_PARVB_rpt1; first calponin homology (CH) domain found in beta-parvin
    cd21338
    Location:198 → 327
    CH_PARVB_rpt2; second calponin homology (CH) domain found in beta-parvin

  7. XM_047441351.1 → XP_047297307.1  beta-parvin isoform X7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    44483004..44656061
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054325581.1 → XP_054181556.1  beta-parvin isoform X2

  2. XM_054325582.1 → XP_054181557.1  beta-parvin isoform X3

  3. XM_054325587.1 → XP_054181562.1  beta-parvin isoform X7

  4. XM_054325580.1 → XP_054181555.1  beta-parvin isoform X1

  5. XM_054325583.1 → XP_054181558.1  beta-parvin isoform X4

  6. XM_054325584.1 → XP_054181559.1  beta-parvin isoform X5

  7. XM_054325585.1 → XP_054181560.1  beta-parvin isoform X6

  8. XM_054325586.1 → XP_054181561.1  beta-parvin isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9HBI1.1 GenPept UniProtKB/Swiss-Prot:Q9HBI1

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