PARVB parvin beta [Homo sapiens (human)] - Gene

Summary

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

Location:: 22q13.31

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (43999211..44172939)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (44483004..44656061)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (44395091..44568819)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed
Genetic variant predicts bevacizumab-induced hypertension in ECOG-5103 and ECOG-2100. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of hematological and biochemical traits in a Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of the rate of cognitive decline in Alzheimer's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
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 EBI GWAS CatalogPubMed
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G65608 (e-PCR)
- UniSTS:225544

SHGC-132330 (e-PCR)
- UniSTS:183570

D22S1241 (e-PCR)
- UniSTS:51733

D22S1171 (e-PCR), detects polymorphism
- UniSTS:42559

G65730 (e-PCR)
- UniSTS:166997

G65736 (e-PCR)
- UniSTS:166998

SHGC-132012 (e-PCR)
- UniSTS:170603

RH75363 (e-PCR)
- UniSTS:89748

stbK70A10TV (e-PCR)
- UniSTS:181696

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	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

NG_029743.3 RefSeqGene

Range

30093..178730

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000022.11 Reference GRCh38.p14 Primary Assembly

Range

43999211..44172939

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (1) summary

pfam00307
Location:120 → 228

CH; Calponin homology (CH) domain
XM_017028792.3 → XP_016884281.1 beta-parvin isoform X3
XM_024452235.2 → XP_024308003.1 beta-parvin isoform X1

Conserved Domains (1) summary

pfam00307
Location:105 → 213

CH; Calponin homology (CH) domain
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
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
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
XM_047441351.1 → XP_047297307.1 beta-parvin isoform X7