GeneBe

ZNF16

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

Basic information

Region (hg38): 8:144930358-144950888

Links

ENSG00000170631 ∙ NCBI:7564 ∙ OMIM:601262 ∙ HGNC:12947 ∙ Uniprot:P17020 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF16 gene.

  • not_specified (94 variants)
  • not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF16 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006958.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
 2
missense
86
clinvar
8
clinvar
 94
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 86 10 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ZNF16protein_codingprotein_codingENST00000276816 220531
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.65e-120.1071256900581257480.000231
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1223733800.9820.00002014569
Missense in Polyphen7597.7250.767461247
Synonymous-0.3771451391.040.000007461243
Loss of Function0.6132023.20.8630.00000149275

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005720.000572
Ashkenazi Jewish0.00009920.0000992
East Asian0.0002170.000217
Finnish0.00009290.0000924
European (Non-Finnish)0.0002740.000273
Middle Eastern0.0002170.000217
South Asian0.0002290.000229
Other0.0001630.000163

dbNSFP

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

Haploinsufficiency Scores

pHI
0.133
hipred
N
hipred_score
0.112
ghis
0.455

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.352

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

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;positive regulation of erythrocyte differentiation;positive regulation of megakaryocyte differentiation;cell division;positive regulation of cell division;cellular response to sodium dodecyl sulfate;positive regulation of cell cycle phase transition
Cellular component
nucleus;nucleolus
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding