PLEKHH2

pleckstrin homology, MyTH4 and FERM domain containing H2, the group of Pleckstrin homology domain containing|FERM domain containing

Basic information

Region (hg38): 2:43637260-43767987

Links

ENSG00000152527 ∙ NCBI:130271 ∙ OMIM:612723 ∙ HGNC:30506 ∙ Uniprot:Q8IVE3 ∙ 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 PLEKHH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHH2 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		2
missense			70	4		74
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			25		1	26
Total	0	0	95	6	1

Variants in PLEKHH2

This is a list of pathogenic ClinVar variants found in the PLEKHH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-43644747-T-A		not specified	Uncertain significance (May 25, 2022)
2-43644779-G-C		not specified	Uncertain significance (Jun 05, 2024)
2-43675415-G-A		not specified	Uncertain significance (Jan 22, 2024)
2-43675449-G-A		not specified	Uncertain significance (Feb 10, 2022)
2-43675458-C-G		not specified	Uncertain significance (Jan 17, 2024)
2-43675575-G-T		not specified	Uncertain significance (Jun 23, 2021)
2-43675578-C-T		not specified	Uncertain significance (Feb 03, 2022)
2-43675584-G-T		not specified	Uncertain significance (May 04, 2022)
2-43675590-T-C		not specified	Uncertain significance (Dec 19, 2022)
2-43675769-A-G		not specified	Uncertain significance (Apr 16, 2024)
2-43675788-C-T		not specified	Uncertain significance (Jan 05, 2022)
2-43675794-C-T		not specified	Uncertain significance (Sep 23, 2023)
2-43675827-A-G		not specified	Uncertain significance (Jun 10, 2024)
2-43675871-T-C		not specified	Uncertain significance (Mar 07, 2024)
2-43675877-A-G		not specified	Uncertain significance (Dec 16, 2022)
2-43675887-A-T		not specified	Uncertain significance (Dec 14, 2021)
2-43675898-A-C		not specified	Uncertain significance (Feb 27, 2024)
2-43675905-G-A		not specified	Uncertain significance (Nov 07, 2023)
2-43675924-G-T		not specified	Uncertain significance (Jun 07, 2024)
2-43675952-T-G		not specified	Uncertain significance (Jun 24, 2022)
2-43675966-C-G		not specified	Uncertain significance (Dec 15, 2023)
2-43675975-C-G		not specified	Uncertain significance (May 31, 2022)
2-43675997-A-G		not specified	Uncertain significance (Mar 30, 2024)
2-43676000-A-G		not specified	Uncertain significance (Jan 02, 2024)
2-43676045-T-C		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHH2	protein_coding	protein_coding	ENST00000282406	29	130715

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.82e-34	0.0395	125603	0	145	125748	0.000577

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.72	893	759	1.18	0.0000382	9754
Missense in Polyphen		147	140.76	1.0443		1801
Synonymous	-1.87	308	269	1.15	0.0000136	2802
Loss of Function	2.02	63	82.9	0.760	0.00000443	1019

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00117	0.00115
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000953	0.000925
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000615	0.000607
Middle Eastern	0.000953	0.000925
South Asian	0.000880	0.000850
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In the kidney glomerulus may play a role in linking podocyte foot processes to the glomerular basement membrane. May be involved in stabilization of F-actin by attenuating its depolymerization. Can recruit TGFB1I1 from focal adhesions to podocyte lamellipodia.

Recessive Scores

• pRec: 0.0910

Intolerance Scores

• loftool: 0.614
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.289
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.310

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekhh2

Gene ontology

• Biological process: negative regulation of actin filament depolymerization
• Cellular component: nucleoplasm;cytoplasm;cytosol;plasma membrane;nuclear body;lamellipodium;cortical actin cytoskeleton
• Molecular function: actin binding;protein binding;identical protein binding