ZFYVE21

zinc finger FYVE-type containing 21, the group of Zinc fingers FYVE-type

Basic information

Region (hg38): 14:103715730-103733668

Links

ENSG00000100711 ∙ NCBI:79038 ∙ OMIM:613504 ∙ HGNC:20760 ∙ Uniprot:Q9BQ24 ∙ 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 ZFYVE21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFYVE21 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			16	1		17
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	17	2	0

Variants in ZFYVE21

This is a list of pathogenic ClinVar variants found in the ZFYVE21 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-103715893-C-A		not specified	Uncertain significance (May 28, 2024)
14-103715922-C-G		not specified	Uncertain significance (Nov 09, 2024)
14-103715927-C-T		not specified	Uncertain significance (Jun 03, 2022)
14-103727792-G-A		not specified	Uncertain significance (Apr 07, 2022)
14-103727804-C-T		not specified	Uncertain significance (Aug 11, 2022)
14-103727866-C-T		not specified	Uncertain significance (Nov 01, 2022)
14-103727887-G-A		not specified	Uncertain significance (Jan 26, 2022)
14-103728967-C-T		not specified	Uncertain significance (Jul 16, 2021)
14-103728974-A-G		not specified	Likely benign (Aug 20, 2024)
14-103729114-G-A		not specified	Uncertain significance (Jun 21, 2023)
14-103729128-G-A		not specified	Uncertain significance (Jun 22, 2023)
14-103729807-G-A		not specified	Likely benign (May 31, 2022)
14-103732631-C-T		not specified	Uncertain significance (Feb 28, 2024)
14-103732640-G-C		not specified	Uncertain significance (Dec 09, 2024)
14-103732659-C-A		not specified	Uncertain significance (Dec 16, 2022)
14-103732671-C-T		not specified	Uncertain significance (Sep 28, 2021)
14-103732679-G-A		not specified	Uncertain significance (May 08, 2024)
14-103732695-T-TGACA		Premature coronary artery atherosclerosis	Uncertain significance (Nov 22, 2023)
14-103732712-G-A		not specified	Uncertain significance (Mar 01, 2025)
14-103732737-T-A		not specified	Uncertain significance (Nov 20, 2024)
14-103732986-G-T		not specified	Uncertain significance (Mar 03, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFYVE21	protein_coding	protein_coding	ENST00000216602	8	17939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.343	0.655	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.424	138	153	0.904	0.00000996	1626
Missense in Polyphen		35	49.397	0.70854		537
Synonymous	-0.354	65	61.5	1.06	0.00000437	482
Loss of Function	2.58	3	13.0	0.230	5.55e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000716	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in cell adhesion, and thereby in cell motility which requires repeated formation and disassembly of focal adhesions. Regulates microtubule-induced PTK2/FAK1 dephosphorylation, an event important for focal adhesion disassembly, as well as integrin beta-1/ITGB1 cell surface expression. {ECO:0000269|PubMed:20439989, ECO:0000269|PubMed:21768110}.

Intolerance Scores

• loftool: 0.414
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.110
• hipred: Y
• hipred_score: 0.654
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.506

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfyve21

Gene ontology

• Cellular component: endosome;focal adhesion
• Molecular function: protein binding;metal ion binding