ZNF689

zinc finger protein 689, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 16:30602558-30624012

Links

ENSG00000156853 ∙ NCBI:115509 ∙ OMIM:618033 ∙ HGNC:25173 ∙ Uniprot:C0HLU2, Q96CS4 ∙ 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 ZNF689 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF689 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			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in ZNF689

This is a list of pathogenic ClinVar variants found in the ZNF689 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30604299-T-C		not specified	Uncertain significance (Mar 22, 2023)
16-30604320-T-C		not specified	Uncertain significance (May 26, 2024)
16-30604412-G-T		not specified	Uncertain significance (Aug 13, 2021)
16-30604444-C-G		not specified	Uncertain significance (Dec 03, 2021)
16-30604503-C-T		not specified	Uncertain significance (Jan 16, 2024)
16-30604508-C-T		not specified	Uncertain significance (Jun 17, 2024)
16-30604530-G-C		not specified	Uncertain significance (Apr 20, 2023)
16-30604628-C-T		not specified	Uncertain significance (Dec 05, 2022)
16-30604661-C-A		not specified	Uncertain significance (Jun 29, 2023)
16-30604736-G-C		not specified	Uncertain significance (Apr 30, 2024)
16-30604800-C-G		not specified	Uncertain significance (Jul 19, 2022)
16-30605001-T-C		not specified	Uncertain significance (Jul 19, 2023)
16-30605130-G-A		not specified	Uncertain significance (Oct 24, 2023)
16-30605228-G-A		not specified	Uncertain significance (Feb 15, 2023)
16-30605266-G-T		not specified	Uncertain significance (Apr 08, 2024)
16-30605304-C-T		not specified	Uncertain significance (Dec 03, 2021)
16-30605343-G-A		not specified	Uncertain significance (Jul 05, 2023)
16-30605394-C-T		not specified	Uncertain significance (Oct 20, 2023)
16-30605411-A-C		not specified	Uncertain significance (Dec 20, 2021)
16-30609561-G-A		not specified	Uncertain significance (Aug 30, 2021)
16-30609575-G-A		not specified	Uncertain significance (Jul 14, 2023)
16-30609932-T-A		not specified	Uncertain significance (May 17, 2023)
16-30609943-G-T		not specified	Uncertain significance (Jun 16, 2023)
16-30609987-T-C		not specified	Likely benign (Feb 03, 2022)
16-30610017-G-A		not specified	Likely benign (Jun 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF689	protein_coding	protein_coding	ENST00000287461	3	21455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.418	0.582	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.52	218	351	0.621	0.0000245	3203
Missense in Polyphen		81	152.12	0.53249		1346
Synonymous	0.973	125	140	0.895	0.00000877	1046
Loss of Function	3.10	4	18.3	0.219	0.00000105	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000123
Ashkenazi Jewish	0.000109	0.0000992
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000382	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.000107	0.0000980
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: 0.111

Intolerance Scores

• loftool: 0.333
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.36

Haploinsufficiency Scores

• pHI: 0.199
• hipred: Y
• hipred_score: 0.572
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.878

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp689
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;skeletal muscle cell differentiation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding