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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			53	6		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	8	0

Variants in ZNF16

This is a list of pathogenic ClinVar variants found in the ZNF16 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-144930758-A-T		not specified	Uncertain significance (Jan 26, 2022)
8-144930772-A-G		not specified	Uncertain significance (Mar 01, 2023)
8-144930783-C-A		not specified	Uncertain significance (Dec 08, 2023)
8-144930814-T-C		not specified	Uncertain significance (Oct 22, 2021)
8-144930832-G-C		not specified	Uncertain significance (Mar 01, 2024)
8-144930854-T-C		not specified	Uncertain significance (Jan 25, 2023)
8-144930862-G-A		not specified	Uncertain significance (Feb 11, 2025)
8-144930866-G-A		not specified	Uncertain significance (May 13, 2024)
8-144930908-G-A		not specified	Uncertain significance (Dec 27, 2023)
8-144930961-C-T		not specified	Uncertain significance (Nov 08, 2024)
8-144930970-C-T		not specified	Uncertain significance (Mar 06, 2023)
8-144930983-T-A		not specified	Uncertain significance (Apr 20, 2024)
8-144931099-T-C		not specified	Uncertain significance (May 25, 2022)
8-144931124-T-G		not specified	Uncertain significance (Aug 23, 2021)
8-144931144-G-A		not specified	Uncertain significance (Jul 05, 2023)
8-144931145-T-A		not specified	Uncertain significance (Nov 21, 2022)
8-144931163-C-T		not specified	Uncertain significance (Jan 10, 2025)
8-144931198-G-T		not specified	Uncertain significance (Aug 10, 2021)
8-144931216-T-C		not specified	Uncertain significance (Jul 14, 2024)
8-144931223-A-T		not specified	Uncertain significance (Jun 07, 2022)
8-144931226-C-G		not specified	Uncertain significance (May 27, 2022)
8-144931229-G-A		not specified	Uncertain significance (Sep 04, 2024)
8-144931252-G-A		not specified	Uncertain significance (Feb 07, 2025)
8-144931327-T-C		not specified	Uncertain significance (Feb 10, 2022)
8-144931336-G-A		not specified	Uncertain significance (Sep 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF16	protein_coding	protein_coding	ENST00000276816	2	20531

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.65e-12	0.107	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.122	373	380	0.982	0.0000201	4569
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000572	0.000572
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000217	0.000217
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.000274	0.000273
Middle Eastern	0.000217	0.000217
South Asian	0.000229	0.000229
Other	0.000163	0.000163

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

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

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