ZFYVE16

zinc finger FYVE-type containing 16, the group of Protein phosphatase 1 regulatory subunits|Zinc fingers FYVE-type

Basic information

Region (hg38): 5:80408012-80483379

Links

ENSG00000039319 ∙ NCBI:9765 ∙ OMIM:608880 ∙ HGNC:20756 ∙ Uniprot:Q7Z3T8 ∙ 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 ZFYVE16 gene.

• Inborn genetic diseases (45 variants)
• not provided (5 variants)
• Cerebral arteriovenous malformation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFYVE16 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				1	1	2
missense		1	42	3	3	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	42	4	4

Variants in ZFYVE16

This is a list of pathogenic ClinVar variants found in the ZFYVE16 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-80436812-G-A			Benign (Jun 10, 2018)
5-80436840-G-A		not specified	Uncertain significance (Nov 07, 2023)
5-80436872-G-A		not specified	Likely benign (Apr 27, 2022)
5-80436882-G-T		not specified	Uncertain significance (Nov 17, 2022)
5-80436903-A-G		not specified	Likely benign (May 05, 2023)
5-80436935-A-G		not specified	Uncertain significance (Jun 23, 2023)
5-80437047-G-A		not specified	Uncertain significance (Nov 17, 2023)
5-80437140-A-G		not specified	Uncertain significance (Dec 28, 2022)
5-80437187-T-C		not specified	Uncertain significance (Aug 09, 2021)
5-80437341-A-G		not specified	Likely benign (Sep 19, 2023)
5-80437434-G-A			Benign (Jun 10, 2018)
5-80437449-T-C		not specified	Uncertain significance (Jul 19, 2022)
5-80437491-G-A		not specified	Uncertain significance (Feb 27, 2024)
5-80437543-C-T			Likely benign (Jun 01, 2023)
5-80437553-G-A		not specified	Likely benign (Nov 22, 2022)
5-80437574-G-A		not specified	Uncertain significance (Jan 04, 2024)
5-80437605-C-T		not specified	Uncertain significance (Jul 21, 2021)
5-80437607-A-G		not specified	Uncertain significance (Jul 21, 2021)
5-80437657-C-A		not specified	Uncertain significance (Dec 03, 2021)
5-80437718-G-T		not specified	Uncertain significance (Jan 12, 2024)
5-80437743-A-G		not specified	Uncertain significance (May 25, 2022)
5-80437745-A-G		not specified	Uncertain significance (Nov 17, 2022)
5-80437764-C-G		not specified	Uncertain significance (Nov 15, 2021)
5-80437865-C-T		not specified	Uncertain significance (Oct 20, 2023)
5-80437866-G-A			Benign (Jun 10, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFYVE16	protein_coding	protein_coding	ENST00000338008	17	71338

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.56e-13	1.00	125677	0	64	125741	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.144	757	768	0.985	0.0000357	10179
Missense in Polyphen		166	230.28	0.72086		3087
Synonymous	0.841	259	277	0.936	0.0000134	2884
Loss of Function	3.53	31	60.7	0.511	0.00000314	823

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000364	0.000363
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000509	0.000508
European (Non-Finnish)	0.000232	0.000229
Middle Eastern	0.000109	0.000109
South Asian	0.000478	0.000425
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in regulating membrane trafficking in the endosomal pathway. Overexpression induces endosome aggregation. Required to target TOM1 to endosomes. {ECO:0000269|PubMed:11546807, ECO:0000269|PubMed:14613930}.
• Pathway: TGF-beta signaling pathway - Homo sapiens (human);Endocytosis - Homo sapiens (human);TGF-beta Signaling Pathway;Signal Transduction;TGF_beta_Receptor;BMP receptor signaling;EGFR1;BMP Signalling Pathway;Signaling by BMP;Signaling by TGF-beta family members;TGF-beta receptor signaling (Consensus)

Recessive Scores

• pRec: 0.0976

Intolerance Scores

• loftool: 0.932
• rvis_EVS: 1.21
• rvis_percentile_EVS: 93.08

Haploinsufficiency Scores

• pHI: 0.573
• hipred: N
• hipred_score: 0.332
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.503

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfyve16

Gene ontology

• Biological process: protein targeting to lysosome;signal transduction;vesicle organization;endosomal transport;regulation of endocytosis;BMP signaling pathway
• Cellular component: early endosome;cytosol;early endosome membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding;1-phosphatidylinositol binding;phosphatidylinositol-3,4,5-trisphosphate binding;protein transporter activity;metal ion binding