PLEKHA6

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

Basic information

Region (hg38): 1:204218853-204378214

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.

• not_specified (185 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. These statistics are base on transcript: NM_000014935.5. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			179	7		186
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	179	7	0

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