PLEKHA7

pleckstrin homology domain containing A7, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 11:16777297-17014415

Links

ENSG00000166689

∙ NCBI:144100 ∙ OMIM:612686 ∙ HGNC:27049 ∙ Uniprot:Q6IQ23 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLEKHA7 gene.

not_specified (197 variants)
PLEKHA7-related_disorder (43 variants)
not_provided (8 variants)
Cleft_lip_with_or_without_cleft_palate (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHA7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001329630.2. 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				23 clinvar	5 clinvar	28
missense		3 clinvar	191 clinvar	13 clinvar	4 clinvar	211
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	0	4	191	36	9

Highest pathogenic variant AF is 0.0000247823

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHA7	protein_coding	protein_coding	ENST00000355661	23	236149

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.22e-9	1.00	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.214	665	681	0.977	0.0000425	7240
Missense in Polyphen		187	216.51	0.8637		2237
Synonymous	-0.155	282	279	1.01	0.0000176	2252
Loss of Function	4.77	27	70.1	0.385	0.00000452	666

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000452	0.000450
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000189	0.000185
Middle Eastern	0.0000544	0.0000544
South Asian	0.000232	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Required for zonula adherens biogenesis and maintenance. Acts via its interaction with KIAA1543/Nezha, which anchors microtubules at their minus-ends to zonula adherens, leading to the recruitment of KIFC3 kinesin to the junctional site. {ECO:0000269|PubMed:19041755}.;
Pathway: Stabilization and expansion of the E-cadherin adherens junction (Consensus)

Recessive Scores

pRec: 0.106

Intolerance Scores

loftool: 0.771
rvis_EVS: -1.39
rvis_percentile_EVS: 4.33

Haploinsufficiency Scores

pHI: 0.513
hipred: Y
hipred_score: 0.522
ghis: 0.525

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.856

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Plekha7
Phenotype: immune 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);

Zebrafish Information Network

Gene name: plekha7a
Affected structure: atrioventricular canal
Phenotype tag: abnormal
Phenotype quality: morphology

Gene ontology

Biological process: cell-cell adhesion mediated by cadherin;zonula adherens maintenance;epithelial cell-cell adhesion
Cellular component: nucleus;centrosome;cytosol;zonula adherens;cell junction;extracellular exosome
Molecular function: protein binding;delta-catenin binding