ZNF709

zinc finger protein 709, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:12461183-12513854

Links

ENSG00000242852 ∙ NCBI:163051 ∙ ∙ HGNC:20629 ∙ Uniprot:Q8N972 ∙ 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 ZNF709 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF709 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			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in ZNF709

This is a list of pathogenic ClinVar variants found in the ZNF709 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12464042-C-T		not specified	Uncertain significance (Dec 18, 2023)
19-12464165-T-C		not specified	Uncertain significance (Feb 09, 2023)
19-12464303-G-T		not specified	Uncertain significance (Dec 17, 2023)
19-12464349-T-A		not specified	Uncertain significance (Apr 01, 2024)
19-12464447-C-T		not specified	Likely benign (Nov 22, 2022)
19-12464549-C-G		not specified	Uncertain significance (Mar 20, 2023)
19-12464664-G-A		not specified	Likely benign (Dec 27, 2022)
19-12464771-C-T		not specified	Uncertain significance (Apr 25, 2023)
19-12464807-G-C		not specified	Uncertain significance (Jan 08, 2024)
19-12464873-C-T		not specified	Uncertain significance (Dec 15, 2022)
19-12465117-T-C		not specified	Uncertain significance (Mar 28, 2024)
19-12465179-C-A		not specified	Uncertain significance (Apr 12, 2024)
19-12465227-G-A		not specified	Uncertain significance (Jan 09, 2024)
19-12465275-C-G		not specified	Uncertain significance (Apr 25, 2022)
19-12465279-T-C		not specified	Uncertain significance (May 06, 2024)
19-12465455-C-T		not specified	Uncertain significance (Nov 14, 2023)
19-12465494-T-C		not specified	Uncertain significance (Jul 14, 2021)
19-12465512-T-C		not specified	Uncertain significance (Aug 28, 2023)
19-12465527-T-A		not specified	Uncertain significance (Jun 24, 2022)
19-12465590-T-C		not specified	Uncertain significance (Dec 19, 2023)
19-12465711-A-G		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF709	protein_coding	protein_coding	ENST00000397732	4	52671

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000284	0.355	125702	0	6	125708	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.91	240	339	0.708	0.0000162	4290
Missense in Polyphen		86	154.54	0.55647		1871
Synonymous	0.929	92	104	0.884	0.00000471	1067
Loss of Function	-0.206	5	4.53	1.10	1.92e-7	53

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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: 0.0978

Intolerance Scores

• loftool: 0.864
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.59

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.259
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

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: transcription regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;metal ion binding