PLEKHA6

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

Basic information

Region (hg38): 1:204218852-204377665

Links

ENSG00000143850 ∙ NCBI:22874 ∙ OMIM:607771 ∙ HGNC:17053 ∙ Uniprot:Q9Y2H5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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.

• Inborn genetic diseases (69 variants)
• not provided (1 variants)

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			68	2		70
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	68	2	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
1-204223483-G-T		not specified	Uncertain significance (Oct 26, 2021)
1-204223501-C-T		not specified	Uncertain significance (Sep 27, 2021)
1-204223531-G-A			Likely benign (Dec 01, 2022)
1-204228092-T-G		not specified	Uncertain significance (Jun 18, 2021)
1-204228125-C-T		not specified	Uncertain significance (Oct 10, 2023)
1-204228185-C-T		not specified	Uncertain significance (Jul 25, 2023)
1-204228208-A-G		not specified	Uncertain significance (Jan 18, 2023)
1-204228815-A-C		not specified	Uncertain significance (Jun 07, 2023)
1-204228815-A-G		not specified	Uncertain significance (Sep 30, 2021)
1-204228828-G-A		not specified	Uncertain significance (Sep 27, 2021)
1-204228857-G-A		not specified	Uncertain significance (Aug 28, 2023)
1-204228972-C-G		not specified	Uncertain significance (Nov 08, 2021)
1-204228992-C-T		not specified	Uncertain significance (Aug 02, 2021)
1-204228993-G-A		not specified	Uncertain significance (Dec 06, 2021)
1-204229007-C-T		not specified	Uncertain significance (Jan 17, 2024)
1-204229025-T-C		not specified	Uncertain significance (Feb 26, 2024)
1-204229029-C-T		not specified	Uncertain significance (Nov 29, 2021)
1-204229091-C-T		not specified	Uncertain significance (Mar 24, 2023)
1-204229100-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-204230429-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-204230433-G-C		not specified	Likely benign (Dec 20, 2023)
1-204230477-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-204230478-G-A		not specified	Uncertain significance (Oct 26, 2022)
1-204230511-G-A		not specified	Uncertain significance (Sep 06, 2022)
1-204241400-C-T		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHA6	protein_coding	protein_coding	ENST00000272203	20	158815

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0137	0.986	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.708	611	662	0.923	0.0000440	6750
Missense in Polyphen		183	206.64	0.88559		2082
Synonymous	1.02	233	254	0.918	0.0000155	2104
Loss of Function	4.87	14	51.9	0.270	0.00000276	571

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000187	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000100	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000728	0.0000653
Other	0.000165	0.000163

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

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

Mouse Genome Informatics

• Gene name: Plekha6