ZNF410

protein-coding

zinc finger protein 410, the group of Zinc fingers C2H2-type

Gene summary

Enables DNA-binding transcription factor activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of gene expression and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_021188.3

Inheritance

—

ClinVar variants

U:57B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr14:73,886,617-73,932,521

External References & Databases

Ensembl (ENSG00000119725)

Transcript & Mutation Effects

hg38 • Region Span ~45.9 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 ZNF410 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 49

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021188.3. 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				2 clinvar		2
missense			50 clinvar			50
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	57	2	0	59

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 111 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021188.3	RefSeq	NP_067011.1	11	MANE Select
ENST00000555044.6	Ensembl	ENSP00000451763.2	11	MANE Select
NM_001242924.2	RefSeq	NP_001229853.1	12	Standard
NM_001242926.2	RefSeq	NP_001229855.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II

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: ENST00000442160
Coding exons: 12
Length: 45895
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125744
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.36	164	274	0.598	0.0000141	3353
Missense (PolyPhen)		57	99.87	0.57074		1189
Synonymous	0.299	97	101	0.962	0.00000495	1016
Loss of Function	3.68	6	26.4	0.227	0.00000127	329

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription factor that activates transcription of matrix-remodeling genes such as MMP1 during fibroblast senescence. {ECO:0000269|PubMed:12370286}.;

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.638
RVIS EVS: -0.47
RVIS percentile EVS: 23.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.841

Gene Damage Prediction

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