PARVA
parvin alpha, the group of Parvins
Basic information
Region (hg38): 11:12377563-12535356
Previous symbols: [ "MXRA2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (41 variants)
- not_provided (1 variants)
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. These statistics are base on transcript: NM_000018222.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 40 | 40 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 40 | 1 | 0 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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
- essential_gene_gene_trap
- 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