ZNF79

zinc finger protein 79, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 9:127424374-127445372

Links

ENSG00000196152 ∙ NCBI:7633 ∙ OMIM:194552 ∙ HGNC:13153 ∙ Uniprot:Q15937 ∙ 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 ZNF79 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF79 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			48	3		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	3	0

Variants in ZNF79

This is a list of pathogenic ClinVar variants found in the ZNF79 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-127428843-C-T		not specified	Uncertain significance (Jan 31, 2022)
9-127428855-C-G		not specified	Uncertain significance (Nov 08, 2022)
9-127428858-C-T		not specified	Uncertain significance (Nov 02, 2023)
9-127428918-C-T		not specified	Uncertain significance (Dec 22, 2023)
9-127435115-C-T		not specified	Uncertain significance (Nov 03, 2023)
9-127435121-C-G		not specified	Uncertain significance (Apr 25, 2022)
9-127435187-C-G		not specified	Uncertain significance (Dec 16, 2021)
9-127435961-G-T		not specified	Uncertain significance (Nov 16, 2021)
9-127435973-G-A		not specified	Uncertain significance (Nov 24, 2024)
9-127435979-G-A		not specified	Uncertain significance (Nov 15, 2021)
9-127435980-A-C		not specified	Uncertain significance (Jun 28, 2022)
9-127435989-G-A		not specified	Uncertain significance (May 25, 2022)
9-127435995-C-T		not specified	Uncertain significance (Aug 30, 2022)
9-127444133-A-G		not specified	Uncertain significance (Dec 21, 2022)
9-127444154-A-T		not specified	Uncertain significance (Jan 23, 2024)
9-127444155-A-G		not specified	Likely benign (Apr 23, 2024)
9-127444163-C-A		not specified	Uncertain significance (Nov 18, 2023)
9-127444173-C-G		not specified	Uncertain significance (Sep 30, 2021)
9-127444209-G-A		not specified	Likely benign (May 21, 2024)
9-127444215-G-A		not specified	Uncertain significance (Nov 08, 2021)
9-127444245-C-T		not specified	Uncertain significance (Sep 16, 2021)
9-127444329-A-T		not specified	Uncertain significance (Jan 30, 2024)
9-127444370-A-G		not specified	Uncertain significance (Sep 07, 2022)
9-127444383-A-G		not specified	Uncertain significance (Feb 01, 2025)
9-127444443-C-A		not specified	Uncertain significance (Mar 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF79	protein_coding	protein_coding	ENST00000342483	5	20991

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00696	0.990	125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.206	271	281	0.965	0.0000162	3304
Missense in Polyphen		97	93.46	1.0379		1162
Synonymous	-0.854	125	113	1.10	0.00000798	904
Loss of Function	2.57	7	19.2	0.365	9.90e-7	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000329	0.000329
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000369	0.000369
Middle Eastern	0.000381	0.000381
South Asian	0.00122	0.00121
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: 0.201

Intolerance Scores

• loftool: 0.812
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.57

Haploinsufficiency Scores

• pHI: 0.343
• hipred: N
• hipred_score: 0.132
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0800

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;biological_process
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;DNA binding;protein binding;metal ion binding