ZNF789

zinc finger protein 789, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 7:99472890-99503650

Links

ENSG00000198556 ∙ NCBI:285989 ∙ ∙ HGNC:27801 ∙ Uniprot:Q5FWF6 ∙ 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 ZNF789 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF789 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in ZNF789

This is a list of pathogenic ClinVar variants found in the ZNF789 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-99476476-G-A		not specified	Uncertain significance (Dec 02, 2022)
7-99479689-T-C		not specified	Uncertain significance (Dec 19, 2022)
7-99479701-G-T		not specified	Uncertain significance (Jun 29, 2022)
7-99484102-C-T		not specified	Uncertain significance (May 24, 2023)
7-99486569-A-C		not specified	Uncertain significance (Oct 05, 2021)
7-99486598-C-G		not specified	Uncertain significance (Aug 22, 2023)
7-99486599-A-G		not specified	Uncertain significance (Sep 17, 2021)
7-99486647-G-C		not specified	Uncertain significance (Dec 19, 2022)
7-99486666-G-C		not specified	Uncertain significance (Oct 10, 2023)
7-99486748-A-G		not specified	Uncertain significance (Jul 25, 2023)
7-99486872-G-T		not specified	Uncertain significance (Jan 23, 2023)
7-99486880-T-C		not specified	Uncertain significance (Dec 06, 2021)
7-99486913-G-A		not specified	Uncertain significance (Sep 06, 2022)
7-99486991-G-A		not specified	Uncertain significance (Sep 20, 2023)
7-99487018-G-A		not specified	Uncertain significance (Nov 21, 2022)
7-99487034-A-G		not specified	Uncertain significance (May 23, 2023)
7-99487121-A-C		not specified	Uncertain significance (Jun 11, 2021)
7-99487171-G-T		not specified	Uncertain significance (Feb 16, 2023)
7-99487180-C-T		not specified	Uncertain significance (Jul 13, 2021)
7-99487222-C-T		not specified	Uncertain significance (Jan 02, 2024)
7-99487340-C-T		not specified	Uncertain significance (Feb 17, 2023)
7-99487415-G-A		not specified	Uncertain significance (Aug 02, 2023)
7-99487432-T-C		not specified	Uncertain significance (Feb 16, 2023)
7-99487448-T-C		not specified	Uncertain significance (Mar 16, 2022)
7-99493536-C-T		not specified	Uncertain significance (Oct 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF789	protein_coding	protein_coding	ENST00000331410	4	30810

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.92e-7	0.533	125671	0	76	125747	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.483	211	232	0.911	0.0000121	2855
Missense in Polyphen		48	60.192	0.79744		763
Synonymous	0.0838	83	84.0	0.988	0.00000465	727
Loss of Function	0.910	12	15.9	0.754	8.42e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00105	0.00105
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000264	0.000264
Middle Eastern	0.000163	0.000163
South Asian	0.000261	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Intolerance Scores

• loftool: 0.867
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.17

Haploinsufficiency Scores

• pHI: 0.0980
• hipred: N
• hipred_score: 0.146
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.933

Gene Damage Prediction

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

Gene ontology

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