PARVA

parvin alpha, the group of Parvins

Basic information

Region (hg38): 11:12377563-12535356

Previous symbols: [ "MXRA2" ]

Links

ENSG00000197702 ∙ NCBI:55742 ∙ OMIM:608120 ∙ HGNC:14652 ∙ Uniprot:Q9NVD7 ∙ 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 PARVA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PARVA 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		1
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	19	1	0

Variants in PARVA

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

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

Position	Type	Phenotype	Significance	ClinVar
11-12377583-G-A		not specified	Uncertain significance (May 31, 2023)
11-12377601-G-C		not specified	Uncertain significance (Mar 28, 2024)
11-12377610-C-T		not specified	Uncertain significance (Oct 08, 2024)
11-12377732-T-C		not specified	Uncertain significance (Jan 04, 2022)
11-12377744-C-G		not specified	Uncertain significance (Dec 03, 2021)
11-12473771-A-C		not specified	Uncertain significance (Sep 01, 2024)
11-12473799-T-C		not specified	Uncertain significance (Jan 02, 2024)
11-12473826-C-T		not specified	Uncertain significance (Jun 22, 2022)
11-12473958-A-T		not specified	Uncertain significance (Apr 08, 2024)
11-12473959-C-A		not specified	Uncertain significance (Jul 27, 2022)
11-12477896-T-C		not specified	Uncertain significance (Jan 02, 2024)
11-12477916-T-A		not specified	Uncertain significance (Sep 30, 2024)
11-12496553-G-C		not specified	Uncertain significance (Jan 23, 2023)
11-12504355-G-A		not specified	Uncertain significance (Nov 09, 2021)
11-12504395-C-A		not specified	Uncertain significance (Dec 07, 2024)
11-12504399-C-A		not specified	Uncertain significance (Jan 30, 2024)
11-12508588-G-T		not specified	Uncertain significance (Feb 10, 2023)
11-12508593-G-A		not specified	Uncertain significance (Feb 28, 2023)
11-12508628-A-G		not specified	Uncertain significance (Aug 17, 2022)
11-12508639-C-T		not specified	Uncertain significance (Sep 29, 2023)
11-12511518-C-G		not specified	Uncertain significance (May 31, 2023)
11-12511524-G-A		not specified	Uncertain significance (Nov 27, 2024)
11-12517633-G-A			Likely benign (Mar 01, 2023)
11-12517665-T-C		not specified	Uncertain significance (Oct 19, 2024)
11-12517692-C-T		not specified	Uncertain significance (Dec 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PARVA	protein_coding	protein_coding	ENST00000334956	13	153617

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.409	0.591	125025	0	13	125038	0.0000520

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.998	176	217	0.809	0.0000117	2635
Missense in Polyphen		44	68.511	0.64223		851
Synonymous	-0.718	98	89.4	1.10	0.00000473	829
Loss of Function	3.43	5	22.6	0.221	0.00000118	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000194	0.000188
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000820	0.0000794
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in sarcomere organization and in smooth muscle cell contraction. Required for normal development of the embryonic cardiovascular system, and for normal septation of the heart outflow tract. Plays a role in sprouting angiogenesis and is required for normal adhesion of vascular smooth muscle cells to endothelial cells during blood vessel development (By similarity). Plays a role in the reorganization of the actin cytoskeleton, formation of lamellipodia and ciliogenesis. Plays a role in the establishement of cell polarity, cell adhesion, cell spreading, and directed cell migration. {ECO:0000250, ECO:0000269|PubMed:11134073, ECO:0000269|PubMed:11331308, ECO:0000269|PubMed:15284246, ECO:0000269|PubMed:20393563}.
• Pathway: Focal adhesion - Homo sapiens (human);Primary Focal Segmental Glomerulosclerosis FSGS;Focal Adhesion;Integrin-linked kinase signaling;Localization of the PINCH-ILK-PARVIN complex to focal adhesions;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: 0.171

Intolerance Scores

• loftool: 0.621
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.241
• hipred: Y
• hipred_score: 0.774
• ghis: 0.637

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.640

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Parva
• Phenotype: homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype; embryo phenotype; renal/urinary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: parvaa
• Affected structure: caudal fin lower lobe
• Phenotype tag: abnormal
• Phenotype quality: rough

Gene ontology

• Biological process: sprouting angiogenesis;outflow tract septum morphogenesis;establishment or maintenance of cell polarity;regulation of cell shape;cell projection assembly;actin cytoskeleton reorganization;heterotypic cell-cell adhesion;substrate adhesion-dependent cell spreading;cilium assembly;actin-mediated cell contraction;smooth muscle cell chemotaxis
• Cellular component: cytoplasm;cytosol;plasma membrane;focal adhesion;actin cytoskeleton;Z disc
• Molecular function: actin binding;protein binding;cadherin binding