ZNF516

zinc finger protein 516, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 18:76357682-76495242

Links

ENSG00000101493 ∙ NCBI:9658 ∙ OMIM:615114 ∙ HGNC:28990 ∙ Uniprot:Q92618 ∙ 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 ZNF516 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF516 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	3	5
missense			98	8		106
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	98	10	3

Variants in ZNF516

This is a list of pathogenic ClinVar variants found in the ZNF516 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-76378900-G-T		not specified	Uncertain significance (Jun 21, 2023)
18-76379010-G-A		not specified	Uncertain significance (May 26, 2022)
18-76379020-C-T		not specified	Uncertain significance (Oct 06, 2021)
18-76379044-C-T		not specified	Uncertain significance (Jun 11, 2024)
18-76379048-G-A			Likely benign (Apr 01, 2023)
18-76379058-C-A		not specified	Uncertain significance (Sep 26, 2022)
18-76379085-A-G		not specified	Uncertain significance (Dec 27, 2023)
18-76379092-G-T		not specified	Uncertain significance (Jan 19, 2022)
18-76379115-C-T		not specified	Uncertain significance (Oct 17, 2023)
18-76379134-C-T		not specified	Uncertain significance (May 02, 2023)
18-76379201-C-T			Likely benign (Apr 01, 2023)
18-76379220-G-C		not specified	Uncertain significance (Nov 09, 2023)
18-76379241-G-A		not specified	Likely benign (May 16, 2024)
18-76379268-G-A		not specified	Uncertain significance (Feb 21, 2024)
18-76379283-G-A		not specified	Uncertain significance (May 01, 2024)
18-76379290-G-C		not specified	Uncertain significance (Nov 27, 2023)
18-76379319-G-A		not specified	Uncertain significance (Sep 01, 2021)
18-76379352-C-T		not specified	Uncertain significance (Feb 23, 2023)
18-76379369-T-G		not specified	Uncertain significance (Oct 12, 2021)
18-76379394-T-G		not specified	Uncertain significance (Oct 12, 2021)
18-76379408-C-G		not specified	Uncertain significance (Oct 11, 2021)
18-76379415-G-A		not specified	Uncertain significance (Jan 26, 2022)
18-76379453-C-G		not specified	Uncertain significance (Jun 07, 2024)
18-76379488-C-A			Likely benign (Sep 11, 2018)
18-76379491-A-G		not specified	Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF516	protein_coding	protein_coding	ENST00000443185	6	137503

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000755	2645	121702	297	124644	0.854

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.992	720	799	0.901	0.0000576	7466
Missense in Polyphen		141	255.92	0.55095		2348
Synonymous	-2.41	431	372	1.16	0.0000316	2385
Loss of Function	5.23	2	35.7	0.0559	0.00000176	387

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	2.00	1.77
Ashkenazi Jewish	1.00	0.880
East Asian	0.999	0.905
Finnish	1.00	0.798
European (Non-Finnish)	1.00	0.840
Middle Eastern	0.999	0.905
South Asian	0.997	0.936
Other	0.997	0.877

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator that binds to the promoter and activates the transcription of genes promoting brown adipose tissue (BAT) differentiation. Among brown adipose tissue-specific genes, binds the proximal region of the promoter of the UCP1 gene to activate its transcription and thereby regulate thermogenesis (By similarity). May also play a role in the cellular response to replication stress (PubMed:23446422). {ECO:0000250|UniProtKB:Q7TSH3, ECO:0000269|PubMed:23446422}.
• Pathway: Thermogenesis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.105

Haploinsufficiency Scores

• pHI: 0.191
• hipred: Y
• hipred_score: 0.554
• ghis: 0.492

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.737

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp516

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;response to cold;positive regulation of transcription, DNA-templated;brown fat cell differentiation;adipose tissue development;positive regulation of cold-induced thermogenesis
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;activating transcription factor binding;metal ion binding