ZNF106

protein-coding

zinc finger protein 106, the group of Zinc fingers C2H2-type|WD repeat domain containing

Gene summary

Enables RNA binding activity. Predicted to be involved in insulin receptor signaling pathway. Predicted to be located in nuclear speck and nucleolus. Predicted to be active in cytosol and membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZFP106

MANE transcript

NM_001366845.3

Inheritance

—

ClinVar variants

U:250B:24

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr15:42,412,823-42,491,141

External References & Databases

Ensembl (ENSG00000103994)

Transcript & Mutation Effects

hg38 • Region Span ~78.3 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 ZNF106 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 262

not providedTotal: 5

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001366845.3. 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 clinvar		4
missense			245 clinvar	21 clinvar	1 clinvar	267
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	250	23	1	274

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001366845.3	RefSeq	NP_001353774.1	21	MANE Select
ENST00000564754.7	Ensembl	ENSP00000456845.2	21	MANE Select
NM_001284306.2	RefSeq	NP_001271235.1	17	Standard
NM_001284307.4	RefSeq	NP_001271236.1	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

insulin receptor signaling pathway

Molecular Function

RNA binding
SH3 domain binding
metal ion binding

Cellular Component

nucleolus
cytosol
membrane
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000263805
Coding exons: 19
Length: 78301
Individuals with no LoFs: 125698
Homozygous LoFs: 0
Heterozygous LoFs: 49
Defined: 125747
p: 0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.11	907	1.01e+3	0.902	0.0000546	12379
Missense (PolyPhen)		277	373.94	0.74076		4407
Synonymous	0.369	358	367	0.975	0.0000192	3668
Loss of Function	6.18	25	87.3	0.286	0.00000542	969

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00033	0.00033	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00020	0.00020	rare
South Asian	0.00018	0.00016	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.105

Intolerance Scores

RVIS EVS: -0.45
RVIS percentile EVS: 24.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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