ZNF343

protein-coding

zinc finger protein 343, the group of Zinc fingers C2H2-type

Gene summary

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024325.6

Inheritance

—

ClinVar variants

U:97B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr20:2,481,817-2,524,702

External References & Databases

Ensembl (ENSG00000088876)

Transcript & Mutation Effects

hg38 • Region Span ~42.9 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 ZNF343 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 96

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024325.6. 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				9 clinvar		9
missense			93 clinvar	6 clinvar		99
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	97	15	0	112

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 61 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024325.6	RefSeq	NP_077301.4	4	MANE Select
ENST00000278772.9	Ensembl	ENSP00000278772.4	4	MANE Select
NM_001282495.1	RefSeq	NP_001269424.1	4	Standard
NM_001282496.2	RefSeq	NP_001269425.1	4	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

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: ENST00000278772
Coding exons: 4
Length: 42886
Individuals with no LoFs: 125552
Homozygous LoFs: 1
Heterozygous LoFs: 178
Defined: 125731
p: 0.000712

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.135	308	315	0.979	0.0000157	3915
Missense (PolyPhen)		61	72.047	0.84668		949
Synonymous	0.181	115	117	0.979	0.00000603	1083
Loss of Function	0.774	4	6.06	0.660	2.56e-7	73

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00030	0.00030	rare
South Asian	0.0043	0.0043	notable
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Recessive Scores

pRec: 0.0771

Intolerance Scores

LoFtool: 0.970
RVIS EVS: 0.62
RVIS percentile EVS: 83.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0172

Gene Damage Prediction

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