ZNF879

zinc finger protein 879, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 5:179023803-179035064

Links

ENSG00000234284 ∙ NCBI:345462 ∙ ∙ HGNC:37273 ∙ Uniprot:B4DU55 ∙ 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 ZNF879 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF879 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	3		27
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	3	0

Variants in ZNF879

This is a list of pathogenic ClinVar variants found in the ZNF879 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-179027479-G-C		not specified	Uncertain significance (Oct 10, 2023)
5-179027531-T-C		not specified	Uncertain significance (Apr 12, 2022)
5-179027548-G-A		not specified	Likely benign (Nov 30, 2021)
5-179032355-G-C		not specified	Uncertain significance (Dec 03, 2021)
5-179032358-T-G		not specified	Uncertain significance (Apr 07, 2023)
5-179032406-G-A		not specified	Likely benign (Feb 27, 2024)
5-179032418-G-T		not specified	Uncertain significance (Nov 08, 2022)
5-179032454-C-T		not specified	Uncertain significance (Nov 05, 2021)
5-179032460-T-C		not specified	Uncertain significance (Feb 14, 2023)
5-179032495-C-A		not specified	Uncertain significance (Mar 14, 2023)
5-179032498-C-T		not specified	Uncertain significance (May 30, 2024)
5-179032499-G-A		not specified	Likely benign (May 05, 2023)
5-179032549-C-T		not specified	Uncertain significance (Dec 20, 2021)
5-179032788-A-C		not specified	Uncertain significance (Dec 19, 2022)
5-179032829-G-C		not specified	Uncertain significance (Sep 01, 2021)
5-179032861-A-G		not specified	Uncertain significance (Jan 16, 2024)
5-179032933-T-G		not specified	Uncertain significance (May 02, 2023)
5-179032992-G-C		not specified	Uncertain significance (Aug 06, 2021)
5-179033031-G-C		not specified	Uncertain significance (Apr 06, 2022)
5-179033150-C-A		not specified	Uncertain significance (Mar 25, 2024)
5-179033240-A-G		not specified	Uncertain significance (Oct 27, 2022)
5-179033273-G-T		not specified	Uncertain significance (May 28, 2024)
5-179033315-A-G		not specified	Uncertain significance (Nov 13, 2023)
5-179033372-G-A		not specified	Uncertain significance (Feb 13, 2024)
5-179033459-G-T		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF879	protein_coding	protein_coding	ENST00000444149	4	11313

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.67e-7	0.877	125708	0	18	125726	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.61	203	278	0.729	0.0000138	3692
Missense in Polyphen		64	120.29	0.53204		1586
Synonymous	1.16	85	99.7	0.853	0.00000511	988
Loss of Function	1.58	13	20.8	0.626	0.00000108	303

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000105	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000361	0.000326

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.56

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.227

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp879

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