PLEKHA7

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

Basic information

Region (hg38): 11:16777296-17014415

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.

• Inborn genetic diseases (62 variants)
• not provided (8 variants)
• PLEKHA7-related condition (2 variants)
• not specified (1 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.

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				2	4	6
missense		1	61	3	1	66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	1	61	5	5

Highest pathogenic variant AF is 0.00000657

Variants in PLEKHA7

This is a list of pathogenic ClinVar variants found in the PLEKHA7 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-16782878-C-T		PLEKHA7-related disorder	Likely benign (May 21, 2019)
11-16783720-G-A		PLEKHA7-related disorder	Likely benign (Apr 24, 2020)
11-16783795-G-A		PLEKHA7-related disorder	Benign (Apr 23, 2019)
11-16789094-A-C		PLEKHA7-related disorder	Likely pathogenic (Jan 03, 2024)
11-16789118-G-A		not specified	Uncertain significance (May 30, 2023)
11-16789122-G-A		not specified	Uncertain significance (Mar 06, 2023)
11-16789150-C-T		PLEKHA7-related disorder	Likely benign (Dec 27, 2021)
11-16789208-C-T		not specified	Uncertain significance (Jun 13, 2023)
11-16789234-T-G		PLEKHA7-related disorder	Likely benign (Jun 13, 2019)
11-16789237-A-G		PLEKHA7-related disorder	Likely benign (Jan 11, 2023)
11-16789264-T-G		PLEKHA7-related disorder	Likely benign (May 01, 2019)
11-16789777-G-A		not specified	Uncertain significance (Dec 21, 2022)
11-16789782-G-C		not specified	Uncertain significance (Mar 21, 2023)
11-16789782-G-T		not specified	Uncertain significance (Jan 03, 2022)
11-16789816-G-A		not specified	Uncertain significance (Sep 17, 2021)
11-16790811-C-T		PLEKHA7-related disorder	Likely benign (Sep 17, 2019)
11-16790867-C-T		not specified	Uncertain significance (Jun 07, 2023)
11-16791004-C-T		PLEKHA7-related disorder	Benign (Feb 22, 2019)
11-16791013-T-C		not specified	Uncertain significance (Jul 05, 2023)
11-16791015-G-A		not specified	Uncertain significance (Mar 23, 2023)
11-16791062-G-A		PLEKHA7-related disorder	Likely benign (Apr 01, 2019)
11-16791119-T-A		PLEKHA7-related disorder	Likely benign (Dec 20, 2023)
11-16791129-G-A		not specified	Uncertain significance (Nov 10, 2021)
11-16791166-C-T		not specified	Uncertain significance (Jan 16, 2024)
11-16794505-T-C		not specified	Uncertain significance (Dec 19, 2022)

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