PLEKHF2

pleckstrin homology and FYVE domain containing 2, the group of Zinc fingers FYVE-type|Pleckstrin homology domain containing

Basic information

Region (hg38): 8:95115642-95156698

Links

ENSG00000175895 ∙ NCBI:79666 ∙ OMIM:615208 ∙ HGNC:20757 ∙ Uniprot:Q9H8W4 ∙ 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 PLEKHF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHF2 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in PLEKHF2

This is a list of pathogenic ClinVar variants found in the PLEKHF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-95154148-T-C		not specified	Uncertain significance (Jun 16, 2023)
8-95154193-C-T		not specified	Uncertain significance (Jul 30, 2024)
8-95154265-A-G		not specified	Uncertain significance (Feb 16, 2023)
8-95154522-C-T		not specified	Uncertain significance (Nov 18, 2022)
8-95154537-A-G		not specified	Uncertain significance (May 30, 2023)
8-95154669-G-C		not specified	Uncertain significance (Apr 29, 2024)
8-95154730-A-C		not specified	Uncertain significance (Jun 23, 2023)
8-95154754-A-G		not specified	Uncertain significance (Oct 10, 2023)
8-95154774-G-A		not specified	Uncertain significance (Sep 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHF2	protein_coding	protein_coding	ENST00000315367	1	22881

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.867	0.131	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.88	76	138	0.549	0.00000747	1659
Missense in Polyphen		21	63.929	0.32849		762
Synonymous	1.76	31	46.2	0.671	0.00000221	474
Loss of Function	2.38	0	6.60	0.00	3.80e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in early endosome fusion upstream of RAB5, hence regulating receptor trafficking and fluid-phase transport. Enhances cellular sensitivity to TNF-induced apoptosis (PubMed:18288467). {ECO:0000269|PubMed:18288467, ECO:0000269|PubMed:19995552, ECO:0000269|PubMed:22816767}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.295
• hipred: Y
• hipred_score: 0.593
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekhf2

Gene ontology

• Biological process: protein transport
• Cellular component: endoplasmic reticulum;transport vesicle;early endosome membrane
• Molecular function: protein binding;phosphatidylinositol binding;metal ion binding