ZNF682

zinc finger protein 682, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:19997058-20039505

Links

ENSG00000197124 ∙ NCBI:91120 ∙ ∙ HGNC:28857 ∙ Uniprot:O95780 ∙ 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 ZNF682 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF682 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						0
missense			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in ZNF682

This is a list of pathogenic ClinVar variants found in the ZNF682 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-20006013-T-G		not specified	Uncertain significance (Oct 06, 2022)
19-20006094-C-G		not specified	Uncertain significance (Sep 13, 2023)
19-20006097-T-C		not specified	Uncertain significance (Oct 06, 2021)
19-20006112-G-A		not specified	Uncertain significance (Nov 10, 2024)
19-20006129-C-T		not specified	Uncertain significance (Oct 06, 2023)
19-20006132-T-C		not specified	Uncertain significance (May 06, 2024)
19-20006148-G-A		not specified	Uncertain significance (Feb 22, 2024)
19-20006178-T-C		not specified	Uncertain significance (May 24, 2023)
19-20006240-C-A		not specified	Uncertain significance (Mar 07, 2023)
19-20006271-T-C		not specified	Uncertain significance (Jun 29, 2023)
19-20006334-T-C		not specified	Uncertain significance (Jan 20, 2023)
19-20006341-G-T		not specified	Uncertain significance (Aug 23, 2021)
19-20006409-C-T		not specified	Uncertain significance (Aug 02, 2023)
19-20006475-A-G		not specified	Uncertain significance (Jun 03, 2024)
19-20006501-G-A		not specified	Uncertain significance (Jul 27, 2024)
19-20006516-G-A		not specified	Uncertain significance (Jul 10, 2024)
19-20006525-G-A		not specified	Uncertain significance (Sep 03, 2024)
19-20006526-A-G		not specified	Uncertain significance (Mar 07, 2024)
19-20006535-T-C		not specified	Uncertain significance (May 30, 2023)
19-20006645-G-A		not specified	Uncertain significance (Apr 09, 2024)
19-20006814-T-G		not specified	Uncertain significance (Sep 09, 2024)
19-20006829-C-T		not specified	Uncertain significance (Nov 14, 2024)
19-20006856-G-C		not specified	Uncertain significance (May 27, 2022)
19-20006918-T-C		not specified	Uncertain significance (Sep 16, 2021)
19-20006953-T-G		not specified	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF682	protein_coding	protein_coding	ENST00000397165	4	42449

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0185	0.744	125442	0	10	125452	0.0000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0279	257	256	1.00	0.0000122	3289
Missense in Polyphen		73	73.55	0.99253		985
Synonymous	-0.484	95	89.2	1.07	0.00000430	854
Loss of Function	0.795	3	4.90	0.612	2.08e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000635	0.0000630
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.000229	0.000229
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)

Recessive Scores

• pRec: 0.0906

Intolerance Scores

• loftool: 0.665
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.112
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.375

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