ZNF684

zinc finger protein 684, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 1:40531573-40548167

Links

ENSG00000117010 ∙ NCBI:127396 ∙ ∙ HGNC:28418 ∙ Uniprot:Q5T5D7 ∙ 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 ZNF684 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF684 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			28	2		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	0

Variants in ZNF684

This is a list of pathogenic ClinVar variants found in the ZNF684 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-40540587-A-G		not specified	Likely benign (Nov 15, 2021)
1-40540644-T-C		not specified	Uncertain significance (Dec 20, 2022)
1-40540703-A-G		not specified	Uncertain significance (Jun 06, 2023)
1-40540707-C-T		not specified	Uncertain significance (Sep 27, 2024)
1-40541650-G-A		not specified	Uncertain significance (Oct 01, 2024)
1-40541683-G-A		not specified	Uncertain significance (Nov 27, 2023)
1-40546588-C-T		not specified	Likely benign (Nov 15, 2021)
1-40546589-C-T		not specified	Uncertain significance (Sep 25, 2024)
1-40546600-C-T		not specified	Uncertain significance (Sep 08, 2024)
1-40546792-A-G		not specified	Uncertain significance (Jul 09, 2024)
1-40546815-C-T			Likely benign (Jan 01, 2023)
1-40546816-G-A		not specified	Uncertain significance (Nov 06, 2024)
1-40546823-C-G		not specified	Uncertain significance (Dec 11, 2023)
1-40546861-A-C		not specified	Uncertain significance (Jan 09, 2024)
1-40546878-A-C		not specified	Uncertain significance (Mar 04, 2025)
1-40546906-G-A		not specified	Uncertain significance (Dec 14, 2021)
1-40546909-T-G		not specified	Uncertain significance (Feb 20, 2025)
1-40546910-A-G		not specified	Uncertain significance (Nov 26, 2024)
1-40546924-C-T		not specified	Uncertain significance (Jan 12, 2024)
1-40546963-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-40546964-C-G		not specified	Uncertain significance (Mar 07, 2024)
1-40547011-C-A		not specified	Uncertain significance (Nov 13, 2023)
1-40547047-C-A		not specified	Uncertain significance (Oct 20, 2021)
1-40547080-A-C		not specified	Uncertain significance (Apr 05, 2023)
1-40547095-T-C		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF684	protein_coding	protein_coding	ENST00000372699	4	16609

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.74e-8	0.198	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.653	169	195	0.868	0.00000905	2531
Missense in Polyphen		14	27.282	0.51316		370
Synonymous	1.27	58	71.7	0.809	0.00000391	643
Loss of Function	0.274	12	13.1	0.918	5.42e-7	207

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000731	0.000664
Ashkenazi Jewish	0.00	0.00
East Asian	0.000446	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.000446	0.000435
South Asian	0.0000327	0.0000327
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: 0.603
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• pHI: 0.178
• hipred: N
• hipred_score: 0.123
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.510

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