ZFYVE21

protein-coding

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

Gene summary

Predicted to enable zinc ion binding activity. Predicted to be located in endosome and focal adhesion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024071.4

Inheritance

—

ClinVar variants

U:33B:1

Top phenotype

Premature coronary artery atherosclerosis

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr14:103,715,730-103,733,668

External References & Databases

Ensembl (ENSG00000100711)

Transcript & Mutation Effects

hg38 • Region Span ~17.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZFYVE21 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 32

Premature coronary artery atherosclerosisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024071.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			30 clinvar	1 clinvar		31
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	33	1	0	34

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024071.4	RefSeq	NP_076976.1	7	MANE Select
ENST00000311141.7	Ensembl	ENSP00000310543.2	7	MANE Select
NM_001198953.2	RefSeq	NP_001185882.1	8	Standard
ENST00000216602.10	Ensembl	ENSP00000216602.6	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
metal ion binding

Cellular Component

endosome
focal adhesion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000216602
Coding exons: 8
Length: 17939
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125748
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.424	138	153	0.904	0.00000996	1626
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000072	0.000070	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.506

Gene Damage Prediction

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