PLEKHA1
Basic information
Region (hg38): 10:122374696-122432354
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (47 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHA1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001001974.4. 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 | 43 | 46 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 43 | 4 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PLEKHA1 | protein_coding | protein_coding | ENST00000368990 | 11 | 57656 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000235 | 0.996 | 125658 | 0 | 90 | 125748 | 0.000358 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.656 | 207 | 235 | 0.880 | 0.0000133 | 2663 |
Missense in Polyphen | 81 | 105.66 | 0.76662 | 1261 | ||
Synonymous | 0.0292 | 82 | 82.3 | 0.996 | 0.00000504 | 750 |
Loss of Function | 2.55 | 10 | 23.3 | 0.429 | 0.00000120 | 271 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000333 | 0.000333 |
Ashkenazi Jewish | 0.00109 | 0.00109 |
East Asian | 0.000218 | 0.000217 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.000396 | 0.000396 |
Middle Eastern | 0.000218 | 0.000217 |
South Asian | 0.000622 | 0.000621 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Binds specifically to phosphatidylinositol 3,4- diphosphate (PtdIns3,4P2), but not to other phosphoinositides. May recruit other proteins to the plasma membrane. {ECO:0000269|PubMed:11001876, ECO:0000269|PubMed:11513726, ECO:0000269|PubMed:14516276}.;
- Pathway
- Metabolism of lipids;Metabolism;BCR;Synthesis of PIPs at the plasma membrane;Class I PI3K signaling events;PI Metabolism;Phospholipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.165
Intolerance Scores
- loftool
- 0.845
- rvis_EVS
- -0.47
- rvis_percentile_EVS
- 23.43
Haploinsufficiency Scores
- pHI
- 0.319
- hipred
- Y
- hipred_score
- 0.589
- ghis
- 0.550
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.719
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Plekha1
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; muscle phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; skeleton phenotype; reproductive 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); normal phenotype; 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); digestive/alimentary phenotype;
Gene ontology
- Biological process
- luteinization;phosphatidylinositol biosynthetic process;spermatogenesis;androgen metabolic process;estrogen metabolic process;post-embryonic development;phosphatidylinositol 3-kinase signaling;ruffle organization;Leydig cell differentiation;multicellular organism growth;establishment of protein localization;platelet-derived growth factor receptor signaling pathway;skeletal system morphogenesis;B cell receptor signaling pathway;negative regulation of protein kinase B signaling;roof of mouth development;face morphogenesis;cellular response to hydrogen peroxide
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;membrane;ruffle membrane;extracellular exosome
- Molecular function
- protein binding;PDZ domain binding;phosphatidylinositol-3,4-bisphosphate binding