ZNF16

protein-coding

zinc finger protein 16, the group of Zinc fingers C2H2-type

Gene summary

The protein encoded by this gene contains multiple tandem zinc finger motifs. The encoded protein is involved in the differentiation of erythroid and megakaryocytic cells. This gene is located in a cluster of related genes on chromosome 8 encoding zinc finger proteins. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2012]

MANE transcript

NM_006958.3

Inheritance

—

ClinVar variants

U:99B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr8:144,930,358-144,950,888

External References & Databases

Ensembl (ENSG00000170631)

Transcript & Mutation Effects

hg38 • Region Span ~20.5 kb

Loading mutation effect viewer...

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 ZNF16 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 104

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006958.3. 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			98 clinvar	8 clinvar		106
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	99	10	0	109

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006958.3	RefSeq	NP_008889.2	2	MANE Select
ENST00000394909.7	Ensembl	ENSP00000378369.2	2	MANE Select
NM_001029976.3	RefSeq	NP_001025147.2	2	Standard
NM_001413564.1	RefSeq	NP_001400493.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
cell cycle
positive regulation of cell population proliferation
positive regulation of kinase activity
negative regulation of apoptotic process

Molecular Function

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

Cellular Component

nucleus
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000276816
Coding exons: 2
Length: 20531
Individuals with no LoFs: 125690
Homozygous LoFs: 0
Heterozygous LoFs: 58
Defined: 125748
p: 0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.122	373	380	0.982	0.0000201	4569
Missense (PolyPhen)		75	97.725	0.76746		1247
Synonymous	-0.377	145	139	1.04	0.00000746	1243
Loss of Function	0.613	20	23.2	0.863	0.00000149	275

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00020	0.00017	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00027	0.00027	rare
South Asian	0.00023	0.00023	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a transcriptional activator. Promotes cell proliferation by facilitating the cell cycle phase transition from the S to G2/M phase. Involved in both the hemin- and phorbol myristate acetate (PMA)-induced erythroid and megakaryocytic differentiation, respectively. Plays also a role as an inhibitor of cell apoptosis. {ECO:0000269|PubMed:16628192, ECO:0000269|PubMed:19763908, ECO:0000269|PubMed:21874239}.;

Recessive Scores

pRec: 0.0948

Intolerance Scores

LoFtool: 0.922
RVIS EVS: 0.71
RVIS percentile EVS: 85.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.352

Gene Damage Prediction

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