ZNF418

protein-coding

zinc finger protein 418, the group of Zinc fingers C2H2-type

Gene summary

Enables DNA-binding transcription repressor activity. Predicted to be involved in microautophagy; regulation of proteasomal ubiquitin-dependent protein catabolic process; and regulation of transcription by RNA polymerase II. Is active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_133460.3

Inheritance

—

ClinVar variants

P:1U:103B:8

Top phenotype

Moyamoya angiopathy

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr19:57,921,882-57,935,402

External References & Databases

Ensembl (ENSG00000196724)

Transcript & Mutation Effects

hg38 • Region Span ~13.5 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 ZNF418 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 107

not providedTotal: 2

Moyamoya angiopathyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_133460.3. 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 clinvar		2
missense		1 clinvar	102 clinvar	6 clinvar		109
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	103	8	0	112

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 63 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_133460.3	RefSeq	NP_597717.1	3	MANE Select
ENST00000396147.6	Ensembl	ENSP00000379451.1	3	MANE Select
NM_001317027.2	RefSeq	NP_001303956.1	3	Standard
NM_001317028.2	RefSeq	NP_001303957.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription by RNA polymerase II
negative regulation of transcription, DNA-templated

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396147
Coding exons: 3
Length: 13510
Individuals with no LoFs: 125594
Homozygous LoFs: 1
Heterozygous LoFs: 152
Defined: 125747
p: 0.000609

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.368	367	348	1.06	0.0000181	4467
Missense (PolyPhen)		127	119.6	1.0619		1519
Synonymous	-0.587	129	121	1.07	0.00000621	1218
Loss of Function	0.0659	14	14.3	0.981	7.86e-7	179

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0044	0.0042	notable
Latino/Admixed American	0.00091	0.00090	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00033	0.00033	rare
South Asian	0.00026	0.00026	rare
Other	0.0017	0.0015	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcriptional repressor. {ECO:0000269|Ref.1}.;

Intolerance Scores

LoFtool: 0.963
RVIS EVS: 0.07
RVIS percentile EVS: 59.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.724

Gene Damage Prediction

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