ZNF862

protein-coding

zinc finger protein 862, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable protein dimerization activity and zinc ion binding activity. Predicted to be involved in DNA-templated transcription and regulation of DNA-templated transcription. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001099220.3

Inheritance

ClinVar variants

P:1U:216B:21

Top phenotype

Fibromatosis, gingival 6

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr7:149,838,375-149,867,479

External References & Databases

Ensembl (ENSG00000106479)

Transcript & Mutation Effects

hg38 • Region Span ~29.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hereditary gingival fibromatosisLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0016070

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Fibromatosis, gingival 6AD

Manifestation: Craniofacial; Dental

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 35142290

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF862 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 229

not providedTotal: 4

Fibromatosis, gingival, 6Total: 2

Long QT syndromeTotal: 1

Gingival fibromatosisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001099220.3. 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	1 clinvar	3
missense		1 clinvar	213 clinvar	18 clinvar	1 clinvar	233
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	216	19	2	238

Highest pathogenic variant AF is 0.0000030986346

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001099220.3	RefSeq	NP_001092690.1	8	MANE Select
ENST00000223210.5	Ensembl	ENSP00000223210.4	8	MANE Select
ENST00000460379.1	Ensembl	ENSP00000417450.1	1	Standard
ENST00001109324.1	Ensembl	ENSP00000779129.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated
biological_process

Molecular Function

molecular_function
nucleic acid binding
metal ion binding
protein dimerization activity

Cellular Component

cellular_component
nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000223210
Coding exons: 8
Length: 29113
Individuals with no LoFs: 124692
Homozygous LoFs: 1
Heterozygous LoFs: 105
Defined: 124798
p: 0.000425

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.327	666	690	0.965	0.0000424	7555
Missense (PolyPhen)		204	230.99	0.88316		2549
Synonymous	-0.380	305	297	1.03	0.0000198	2348
Loss of Function	2.19	24	38.7	0.620	0.00000202	472

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0016	0.0015	notable
Latino/Admixed American	0.00047	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00067	0.00067	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00026	0.00026	rare
South Asian	0.00069	0.00062	rare
Other	0.0010	0.00099	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.;

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.852
RVIS EVS: -1.27
RVIS percentile EVS: 5.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.123

Gene Damage Prediction

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