ZFYVE28

zinc finger FYVE-type containing 28, the group of Zinc fingers FYVE-type

Basic information

Region (hg38): 4:2269581-2418651

Links

ENSG00000159733 ∙ NCBI:57732 ∙ OMIM:614176 ∙ HGNC:29334 ∙ Uniprot:Q9HCC9 ∙ 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 ZFYVE28 gene.

• Inborn genetic diseases (48 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFYVE28 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			42	6	2	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	42	7	4

Variants in ZFYVE28

This is a list of pathogenic ClinVar variants found in the ZFYVE28 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-2270795-G-A		not specified	Uncertain significance (Jun 27, 2023)
4-2270834-G-A		not specified	Uncertain significance (Feb 05, 2024)
4-2270851-G-C		not specified	Uncertain significance (Apr 28, 2022)
4-2271372-G-A		not specified	Likely benign (Aug 30, 2022)
4-2271411-G-C		not specified	Uncertain significance (Jan 16, 2024)
4-2273268-G-A		not specified	Uncertain significance (Jan 29, 2024)
4-2274074-C-T		not specified	Uncertain significance (Mar 29, 2022)
4-2274104-C-T		not specified	Uncertain significance (Dec 21, 2023)
4-2274119-G-A		not specified	Uncertain significance (Aug 21, 2023)
4-2274133-G-A		not specified	Uncertain significance (Dec 17, 2023)
4-2274169-G-A		not specified	Likely benign (Jan 03, 2022)
4-2304317-C-T		not specified	Uncertain significance (Dec 28, 2023)
4-2304318-G-A			Benign (Jul 10, 2018)
4-2304320-G-C		not specified	Uncertain significance (Feb 10, 2023)
4-2304322-G-A		not specified	Uncertain significance (Nov 14, 2023)
4-2304329-G-A		not specified	Uncertain significance (Apr 06, 2022)
4-2304330-G-T		not specified	Uncertain significance (Apr 08, 2022)
4-2304403-G-A		not specified	Uncertain significance (Dec 23, 2022)
4-2304437-G-C		not specified	Uncertain significance (Dec 13, 2022)
4-2304502-G-A		not specified	Uncertain significance (Oct 31, 2023)
4-2304523-G-A		not specified	Uncertain significance (Jul 12, 2023)
4-2304548-C-A		not specified	Uncertain significance (Dec 27, 2022)
4-2304550-G-A		not specified	Likely benign (Mar 22, 2023)
4-2304559-G-A		not specified	Uncertain significance (Jul 20, 2021)
4-2304568-A-G		not specified	Uncertain significance (Nov 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFYVE28	protein_coding	protein_coding	ENST00000290974	13	149082

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0723	0.928	125723	0	19	125742	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.250	608	591	1.03	0.0000408	5729
Missense in Polyphen		176	236.11	0.74543		2296
Synonymous	-1.57	309	276	1.12	0.0000221	1820
Loss of Function	4.01	9	34.4	0.262	0.00000156	409

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000126	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negative regulator of epidermal growth factor receptor (EGFR) signaling. Acts by promoting EGFR degradation in endosomes when not monoubiquitinated. {ECO:0000269|PubMed:19460345}.
• Pathway: Internalization of ErbB1 (Consensus)

Intolerance Scores

• loftool: 0.168
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.04

Haploinsufficiency Scores

• pHI: 0.207
• hipred: Y
• hipred_score: 0.775
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.152

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfyve28
• Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); skeleton phenotype

Gene ontology

• Biological process: negative regulation of epidermal growth factor-activated receptor activity;negative regulation of epidermal growth factor receptor signaling pathway
• Cellular component: cytosol;early endosome membrane
• Molecular function: protein binding;phosphatidylinositol-3-phosphate binding;metal ion binding