ZFYVE9

zinc finger FYVE-type containing 9, the group of Zinc fingers FYVE-type

Basic information

Region (hg38): 1:52142088-52348671

Previous symbols: [ "MADHIP" ]

Links

ENSG00000157077 ∙ NCBI:9372 ∙ OMIM:603755 ∙ HGNC:6775 ∙ Uniprot:O95405 ∙ 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 ZFYVE9 gene.

• Inborn genetic diseases (54 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFYVE9 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			50	4		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	4	0

Variants in ZFYVE9

This is a list of pathogenic ClinVar variants found in the ZFYVE9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-52233247-A-G		not specified	Uncertain significance (Mar 14, 2023)
1-52237550-C-T		not specified	Uncertain significance (Mar 07, 2023)
1-52237554-G-A		not specified	Uncertain significance (Jan 17, 2024)
1-52237674-A-G		not specified	Uncertain significance (Nov 03, 2022)
1-52237772-A-C		not specified	Uncertain significance (Mar 07, 2023)
1-52237800-C-T		not specified	Uncertain significance (Oct 04, 2022)
1-52237910-G-A		not specified	Uncertain significance (Dec 13, 2022)
1-52237940-C-G		not specified	Uncertain significance (Aug 02, 2021)
1-52237955-G-A		not specified	Uncertain significance (Dec 21, 2022)
1-52237995-A-G		not specified	Uncertain significance (Apr 28, 2022)
1-52238083-G-C		not specified	Uncertain significance (Jan 26, 2023)
1-52238103-T-C		not specified	Uncertain significance (Dec 13, 2023)
1-52238118-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-52238160-A-G		not specified	Uncertain significance (Jan 26, 2022)
1-52238166-G-A		not specified	Likely benign (May 15, 2023)
1-52238211-C-T		not specified	Uncertain significance (Apr 07, 2022)
1-52238225-A-G		not specified	Uncertain significance (Oct 16, 2023)
1-52238310-G-C		not specified	Uncertain significance (Aug 09, 2021)
1-52238358-G-T		not specified	Uncertain significance (May 16, 2022)
1-52238418-G-T		not specified	Uncertain significance (Apr 13, 2022)
1-52238448-A-T		not specified	Uncertain significance (Dec 19, 2022)
1-52238487-G-A		not specified	Likely benign (Aug 21, 2023)
1-52238511-A-G		not specified	Likely benign (Jan 05, 2022)
1-52238570-G-C		not specified	Uncertain significance (Jul 13, 2021)
1-52238582-A-G		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFYVE9	protein_coding	protein_coding	ENST00000287727	17	204313

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.902	0.0976	125732	0	14	125746	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	604	742	0.814	0.0000358	9455
Missense in Polyphen		162	295.91	0.54746		3833
Synonymous	0.850	254	272	0.934	0.0000140	2688
Loss of Function	5.57	11	56.0	0.196	0.00000266	746

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000918	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000713	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000986	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Early endosomal protein that functions to recruit SMAD2/SMAD3 to intracellular membranes and to the TGF-beta receptor. Plays a significant role in TGF-mediated signaling by regulating the subcellular location of SMAD2 and SMAD3 and modulating the transcriptional activity of the SMAD3/SMAD4 complex. Possibly associated with TGF-beta receptor internalization. {ECO:0000269|PubMed:15356634, ECO:0000269|PubMed:9865696}.
• Pathway: TGF-beta signaling pathway - Homo sapiens (human);Endocytosis - Homo sapiens (human);TGF-Ncore;TGF-beta Signaling Pathway;TGF-beta Receptor Signaling;Disease;Signal Transduction;TGF_beta_Receptor;SMAD2/3 Phosphorylation Motif Mutants in Cancer;SMAD2/3 MH2 Domain Mutants in Cancer;Loss of Function of SMAD2/3 in Cancer;Signaling by TGF-beta Receptor Complex in Cancer;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Downregulation of TGF-beta receptor signaling;TGF-beta receptor signaling activates SMADs;Diseases of signal transduction;TGF-beta receptor signaling (Consensus)

Intolerance Scores

• loftool: 0.532
• rvis_EVS: 0.14
• rvis_percentile_EVS: 63.65

Haploinsufficiency Scores

• pHI: 0.562
• hipred: N
• hipred_score: 0.493
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.962

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfyve9

Zebrafish Information Network

• Gene name: zfyve9a
• Affected structure: spinal cord
• Phenotype tag: abnormal
• Phenotype quality: process quality

Gene ontology

• Biological process: proteolysis;endocytosis;transforming growth factor beta receptor signaling pathway;endosomal transport
• Cellular component: early endosome;cytosol;early endosome membrane;protein-containing complex;intracellular membrane-bounded organelle
• Molecular function: protein binding;1-phosphatidylinositol binding;serine-type peptidase activity;protein domain specific binding;metal ion binding