ZFAND1

protein-coding

zinc finger AN1-type containing 1, the group of Zinc fingers AN1-type

Gene summary

Enables proteasome binding activity. Involved in cellular response to arsenite ion; positive regulation of intracellular protein transport; and stress granule disassembly. Located in cytoplasmic stress granule. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024699.3

Inheritance

—

ClinVar variants

U:39B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr8:81,701,334-81,732,903

External References & Databases

Ensembl (ENSG00000104231)

Transcript & Mutation Effects

hg38 • Region Span ~31.6 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 ZFAND1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 37

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024699.3. 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				1 clinvar		1
missense			35 clinvar	1 clinvar		36
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	39	2	0	41

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024699.3	RefSeq	NP_078975.2	8	MANE Select
ENST00000220669.10	Ensembl	ENSP00000220669.5	8	MANE Select
NM_001170796.1	RefSeq	NP_001164267.1	8	Standard
NM_001170797.2	RefSeq	NP_001164268.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cellular response to oxidative stress
cellular response to heat
stress granule disassembly
cellular response to osmotic stress
positive regulation of intracellular protein transport

Molecular Function

protein binding
zinc ion binding
proteasome binding

Cellular Component

cytoplasmic stress granule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000220669
Coding exons: 8
Length: 31570
Individuals with no LoFs: 125630
Homozygous LoFs: 1
Heterozygous LoFs: 106
Defined: 125737
p: 0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.000999	132	132	1.00	0.00000611	1771
Missense (PolyPhen)		30	31.848	0.94196		405
Synonymous	-0.916	52	44.2	1.18	0.00000207	450
Loss of Function	0.766	13	16.3	0.795	9.21e-7	202

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.0011	0.0011	notable
East Asian	0.00033	0.00027	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00066	0.00066	rare
South Asian	0.00025	0.00023	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in the regulation of cytoplasmic stress granules (SGs) turnover. SGs are dynamic and transient cytoplasmic ribonucleoprotein assemblies important for cellular protein homeostasis when protein production is suspended after acute exogenous stress (PubMed:29804830). Associates with SGs and is involved in the efficient and specific arsenite-induced clearance process of SGs through the recruitment of the ubiquitin-selective ATPase VCP and the 26S proteasome (PubMed:29804830). This process requires both complexes for efficient degradation of damaged ubiquitinated SG proteins during recovery from arsenite stress, and hence avoiding aberrant cytoplasmic SGs degradation via autophagy (PubMed:29804830). {ECO:0000269|PubMed:29804830}.;

Recessive Scores

pRec: 0.0901

Intolerance Scores

LoFtool: 0.255
RVIS EVS: -0.34
RVIS percentile EVS: 30.07

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.291

Gene Damage Prediction

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