ZFYVE1

zinc finger FYVE-type containing 1, the group of Zinc fingers FYVE-type

Basic information

Region (hg38): 14:72969451-73027131

Previous symbols: [ "ZNFN2A1" ]

Links

ENSG00000165861 ∙ NCBI:53349 ∙ OMIM:605471 ∙ HGNC:13180 ∙ Uniprot:Q9HBF4 ∙ 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 ZFYVE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFYVE1 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			23			23
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	24	0	2

Variants in ZFYVE1

This is a list of pathogenic ClinVar variants found in the ZFYVE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-72971036-T-A		not specified	Uncertain significance (Jun 29, 2022)
14-72971042-C-T		not specified	Uncertain significance (May 24, 2024)
14-72974796-G-A		not specified	Uncertain significance (May 20, 2024)
14-72975586-C-T		not specified	Uncertain significance (Jan 03, 2024)
14-72975696-T-C		not specified	Uncertain significance (Feb 16, 2023)
14-72977932-G-A		not specified	Uncertain significance (Sep 26, 2023)
14-72978234-C-T		not specified	Uncertain significance (Aug 17, 2021)
14-72978907-C-T		not specified	Uncertain significance (Jun 08, 2022)
14-72981853-T-C		not specified	Uncertain significance (Aug 09, 2021)
14-72981869-C-G		not specified	Uncertain significance (May 03, 2023)
14-72981882-C-A		not specified	Uncertain significance (May 24, 2024)
14-72993301-G-A		not specified	Uncertain significance (Dec 05, 2022)
14-72993312-C-T		not specified	Uncertain significance (May 27, 2022)
14-72997817-C-T		not specified	Uncertain significance (Oct 05, 2021)
14-72997852-A-G		not specified	Uncertain significance (Jan 08, 2024)
14-72998096-C-T		not specified	Uncertain significance (Aug 02, 2022)
14-72998208-G-T			Benign (Jan 30, 2018)
14-72998319-C-A			Likely benign (Apr 07, 2018)
14-73024027-T-C		not specified	Uncertain significance (May 27, 2022)
14-73024044-G-A			Benign (Apr 07, 2018)
14-73024174-T-C		not specified	Uncertain significance (Aug 22, 2023)
14-73024261-C-G		not specified	Uncertain significance (Jan 03, 2024)
14-73024277-T-G		not specified	Uncertain significance (Jan 30, 2024)
14-73024339-T-C		not specified	Uncertain significance (Dec 06, 2023)
14-73024357-C-T		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFYVE1	protein_coding	protein_coding	ENST00000556143	11	57762

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.199	0.801	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.82	303	476	0.636	0.0000297	5105
Missense in Polyphen		55	153.64	0.35799		1620
Synonymous	-0.126	190	188	1.01	0.0000117	1525
Loss of Function	4.04	8	33.1	0.242	0.00000165	392

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000705	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Autophagy - animal - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.454
• rvis_EVS: -1.2
• rvis_percentile_EVS: 5.83

Haploinsufficiency Scores

• pHI: 0.286
• hipred: Y
• hipred_score: 0.728
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.850

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfyve1

Gene ontology

• Biological process: cellular response to starvation;negative regulation of phosphatase activity;macroautophagy
• Cellular component: phagophore assembly site;autophagosome;endoplasmic reticulum;Golgi stack;membrane;mitochondria-associated endoplasmic reticulum membrane;perinuclear region of cytoplasm;extrinsic component of omegasome membrane;omegasome
• Molecular function: protein binding;1-phosphatidylinositol binding;phosphatidylinositol-3,4,5-trisphosphate binding;zinc ion binding;phosphatidylinositol-3,4-bisphosphate binding