PARVB

parvin beta, the group of Parvins

Basic information

Region (hg38): 22:43999211-44172939

Links

ENSG00000188677 ∙ NCBI:29780 ∙ OMIM:608121 ∙ HGNC:14653 ∙ Uniprot:Q9HBI1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PARVB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PARVB gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	3	4
missense			26		1	27
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	27	1	5

Variants in PARVB

This is a list of pathogenic ClinVar variants found in the PARVB region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-43999610-G-T		not specified	Uncertain significance (Aug 23, 2021)
22-43999619-C-T		not specified	Uncertain significance (Sep 17, 2021)
22-44093935-C-A		not specified	Uncertain significance (Jul 06, 2021)
22-44093970-C-G			Benign (Dec 31, 2019)
22-44093973-T-C		not specified	Uncertain significance (Dec 21, 2022)
22-44119048-A-G		not specified	Uncertain significance (Jan 10, 2023)
22-44119094-G-T		not specified	Uncertain significance (Dec 14, 2021)
22-44119129-A-G		not specified	Uncertain significance (Mar 16, 2022)
22-44131517-C-T		not specified	Uncertain significance (Dec 27, 2023)
22-44131534-G-A		not specified	Uncertain significance (Dec 13, 2023)
22-44131612-C-T		not specified	Uncertain significance (May 10, 2024)
22-44131621-G-A		not specified	Uncertain significance (May 17, 2023)
22-44132960-C-T		not specified	Uncertain significance (Sep 08, 2023)
22-44133004-G-A		not specified	Uncertain significance (Jun 10, 2024)
22-44136463-C-T		not specified	Uncertain significance (Sep 22, 2023)
22-44136467-A-G		not specified	Uncertain significance (Jun 18, 2024)
22-44140138-G-A		not specified	Uncertain significance (Aug 12, 2021)
22-44147874-C-G		not specified	Uncertain significance (Jan 16, 2024)
22-44147886-C-T			Benign (Feb 25, 2018)
22-44147891-A-G		not specified	Uncertain significance (Jan 31, 2023)
22-44147909-G-C		not specified	Uncertain significance (Mar 21, 2023)
22-44147921-A-G		not specified	Uncertain significance (Aug 03, 2022)
22-44151514-A-G		not specified	Uncertain significance (May 31, 2022)
22-44151515-C-G		not specified	Uncertain significance (Nov 01, 2022)
22-44151535-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PARVB	protein_coding	protein_coding	ENST00000406477	14	173739

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.38e-13	0.0668	125656	0	92	125748	0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0967	233	237	0.982	0.0000141	2581
Missense in Polyphen		66	69.781	0.94581		776
Synonymous	0.416	92	97.2	0.946	0.00000595	779
Loss of Function	0.508	21	23.7	0.887	0.00000109	277

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000877	0.000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.00104	0.00103
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000285	0.000281
Middle Eastern	0.00104	0.00103
South Asian	0.000393	0.000392
Other	0.000656	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein that plays a role in integrin signaling via ILK and in activation of the GTPases CDC42 and RAC1 by guanine exchange factors, such as ARHGEF6. Is involved in the reorganization of the actin cytoskeleton and formation of lamellipodia. Plays a role in cell adhesion, cell spreading, establishment or maintenance of cell polarity, and cell migration. {ECO:0000269|PubMed:11402068, ECO:0000269|PubMed:15005707, ECO:0000269|PubMed:15159419, ECO:0000269|PubMed:15284246, ECO:0000269|PubMed:18325335}.
• Pathway: Focal adhesion - Homo sapiens (human);Focal Adhesion;Integrin-linked kinase signaling;Regulation of cytoskeletal remodeling and cell spreading by IPP complex components;Cell-extracellular matrix interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.206

Intolerance Scores

• loftool: 0.782
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.41

Haploinsufficiency Scores

• pHI: 0.0925
• hipred: N
• hipred_score: 0.453
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.666

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Parvb
• Phenotype: homeostasis/metabolism phenotype; normal phenotype; hematopoietic system phenotype; growth/size/body region phenotype; skeleton phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: parvb
• Affected structure: trunk musculature
• Phenotype tag: abnormal
• Phenotype quality: retracted

Gene ontology

• Biological process: establishment or maintenance of cell polarity;cell projection assembly;lamellipodium assembly;actin cytoskeleton reorganization;substrate adhesion-dependent cell spreading;establishment or maintenance of cell polarity regulating cell shape
• Cellular component: cytoplasm;cytosol;plasma membrane;focal adhesion;actin cytoskeleton;Z disc;lamellipodium
• Molecular function: actin binding;protein binding