ZNF616

zinc finger protein 616, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:52113091-52139938

Links

ENSG00000204611 ∙ NCBI:90317 ∙ ∙ HGNC:28062 ∙ Uniprot:Q08AN1 ∙ 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 ZNF616 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF616 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				1		1
missense			79	6		85
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	79	7	0

Variants in ZNF616

This is a list of pathogenic ClinVar variants found in the ZNF616 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-52114832-C-T		not specified	Uncertain significance (Jun 07, 2024)
19-52114873-C-T		not specified	Likely benign (Apr 12, 2022)
19-52114874-G-C		not specified	Uncertain significance (Dec 13, 2022)
19-52114878-T-G		not specified	Uncertain significance (Feb 28, 2023)
19-52114897-C-T		not specified	Uncertain significance (Jan 24, 2025)
19-52114909-T-C		not specified	Uncertain significance (Aug 16, 2021)
19-52114931-A-G		not specified	Uncertain significance (Nov 24, 2024)
19-52114967-T-C		not specified	Uncertain significance (Dec 11, 2024)
19-52115032-T-C		not specified	Uncertain significance (Jan 18, 2023)
19-52115035-A-T		not specified	Uncertain significance (May 21, 2024)
19-52115054-G-T		not specified	Uncertain significance (Jan 24, 2023)
19-52115150-G-A		not specified	Uncertain significance (Feb 08, 2025)
19-52115161-T-G		not specified	Uncertain significance (Aug 12, 2024)
19-52115173-T-C		not specified	Uncertain significance (Sep 07, 2022)
19-52115185-G-A		not specified	Uncertain significance (Sep 27, 2022)
19-52115188-C-T		not specified	Likely benign (Mar 22, 2023)
19-52115191-T-C		not specified	Uncertain significance (Feb 28, 2023)
19-52115192-C-T		not specified	Uncertain significance (Jul 20, 2022)
19-52115231-G-A		not specified	Uncertain significance (Apr 20, 2024)
19-52115236-C-T		not specified	Uncertain significance (Dec 31, 2024)
19-52115296-T-C		not specified	Uncertain significance (Jun 17, 2022)
19-52115365-G-A		not specified	Uncertain significance (Aug 17, 2022)
19-52115372-C-T		not specified	Likely benign (Nov 20, 2024)
19-52115425-T-C		not specified	Uncertain significance (Oct 06, 2024)
19-52115449-C-A		not specified	Uncertain significance (Oct 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF616	protein_coding	protein_coding	ENST00000600228	3	26832

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00801	0.574	125556	0	9	125565	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.638	453	416	1.09	0.0000224	5198
Missense in Polyphen		138	142.21	0.97039		1903
Synonymous	-0.176	145	142	1.02	0.00000693	1411
Loss of Function	0.181	3	3.36	0.894	1.43e-7	38

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000741	0.0000704
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.825
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.61

Haploinsufficiency Scores

• pHI: 0.297
• hipred: N
• hipred_score: 0.112
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.124

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
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding