PLEKHA6

pleckstrin homology domain containing A6, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 1:204218853-204378214

Links

ENSG00000143850NCBI:22874OMIM:607771HGNC:17053Uniprot:Q9Y2H5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLEKHA6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHA6 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
0
missense
88
clinvar
5
clinvar
93
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 88 5 0

Variants in PLEKHA6

This is a list of pathogenic ClinVar variants found in the PLEKHA6 region.

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

Position Type Phenotype Significance ClinVar
1-204223477-C-T not specified Uncertain significance (Jun 19, 2024)3307507
1-204223481-T-C not specified Uncertain significance (Mar 18, 2024)3307511
1-204223483-G-T not specified Uncertain significance (Oct 26, 2021)2218103
1-204223501-C-T not specified Uncertain significance (Sep 27, 2021)2252544
1-204223531-G-A Likely benign (Dec 01, 2022)2639826
1-204228092-T-G not specified Uncertain significance (Jun 18, 2021)2350169
1-204228125-C-T not specified Uncertain significance (Oct 10, 2023)3214811
1-204228185-C-T not specified Uncertain significance (Jul 25, 2023)2595396
1-204228208-A-G not specified Uncertain significance (Jan 18, 2023)2454673
1-204228762-C-A not specified Uncertain significance (May 24, 2024)3307517
1-204228815-A-C not specified Uncertain significance (Jun 07, 2023)2525273
1-204228815-A-G not specified Uncertain significance (Sep 30, 2021)2252953
1-204228828-G-A not specified Uncertain significance (Sep 27, 2021)2374169
1-204228857-G-A not specified Uncertain significance (Aug 28, 2023)2621722
1-204228972-C-G not specified Uncertain significance (Nov 08, 2021)2259147
1-204228992-C-T not specified Uncertain significance (Aug 02, 2021)2210199
1-204228993-G-A not specified Uncertain significance (Dec 06, 2021)2378519
1-204229007-C-T not specified Uncertain significance (Jan 17, 2024)3214810
1-204229025-T-C not specified Uncertain significance (Feb 26, 2024)3214809
1-204229029-C-T not specified Uncertain significance (Nov 29, 2021)2262365
1-204229091-C-T not specified Uncertain significance (Mar 24, 2023)2508214
1-204229100-C-T not specified Uncertain significance (Dec 21, 2023)3214808
1-204230429-C-T not specified Uncertain significance (Jul 06, 2021)2226817
1-204230433-G-C not specified Likely benign (Dec 20, 2023)3214807
1-204230477-C-T not specified Uncertain significance (Mar 29, 2022)2352534

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PLEKHA6protein_codingprotein_codingENST00000272203 20158815
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01370.9861257270211257480.0000835
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7086116620.9230.00004406750
Missense in Polyphen183206.640.885592082
Synonymous1.022332540.9180.00001552104
Loss of Function4.871451.90.2700.00000276571

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001870.000185
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00009250.0000924
European (Non-Finnish)0.0001000.0000967
Middle Eastern0.00005440.0000544
South Asian0.00007280.0000653
Other0.0001650.000163

dbNSFP

Source: dbNSFP

Pathway
Metabolism of lipids;Metabolism;EGFR1;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

pRec
0.118

Intolerance Scores

loftool
0.481
rvis_EVS
-1.21
rvis_percentile_EVS
5.73

Haploinsufficiency Scores

pHI
0.219
hipred
N
hipred_score
0.414
ghis
0.544

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.896

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Plekha6
Phenotype