ZNF862

zinc finger protein 862, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 7:149838374-149867479

Links

ENSG00000106479 ∙ NCBI:643641 ∙ ∙ HGNC:34519 ∙ Uniprot:O60290 ∙ 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 ZNF862 gene.

• Inborn genetic diseases (69 variants)
• not provided (3 variants)
• Gingival fibromatosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF862 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				1	1	2
missense		1	64	5	1	71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	64	6	2

Highest pathogenic variant AF is 0.00000658

Variants in ZNF862

This is a list of pathogenic ClinVar variants found in the ZNF862 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-149844656-A-C		not specified	Uncertain significance (Jul 26, 2023)
7-149844664-C-G		not specified	Uncertain significance (Feb 28, 2023)
7-149844724-G-C		not specified	Uncertain significance (Apr 07, 2022)
7-149846160-T-C		not specified	Uncertain significance (May 23, 2023)
7-149846168-C-G		not specified	Uncertain significance (Dec 14, 2023)
7-149846193-G-A		not specified	Likely benign (Jan 03, 2022)
7-149846219-G-A		not specified	Uncertain significance (Jan 23, 2024)
7-149847740-A-G		not specified	Uncertain significance (Aug 12, 2021)
7-149847746-A-G		not specified	Uncertain significance (May 05, 2023)
7-149847770-G-A		not specified	Uncertain significance (Feb 22, 2023)
7-149847808-G-A			Benign (May 16, 2018)
7-149847869-T-C		not specified	Uncertain significance (Sep 12, 2023)
7-149847902-C-T		not specified	Uncertain significance (Aug 02, 2023)
7-149847903-G-A		not specified	Uncertain significance (Apr 13, 2022)
7-149847936-C-T		not specified	Uncertain significance (Aug 12, 2021)
7-149847948-T-C		not specified	Uncertain significance (Jul 06, 2021)
7-149847971-T-C		not specified	Uncertain significance (Mar 01, 2023)
7-149848011-A-G		not specified	Uncertain significance (Mar 01, 2024)
7-149848130-T-G		Long QT syndrome	Likely benign (-)
7-149848145-C-T		not specified	Uncertain significance (Jan 03, 2024)
7-149848146-G-A		not specified	Likely benign (Mar 23, 2022)
7-149848219-C-G		not specified	Likely benign (Sep 29, 2023)
7-149848227-C-A		not specified	Uncertain significance (Jun 01, 2023)
7-149848271-A-T		not specified	Uncertain significance (Aug 12, 2022)
7-149848299-G-A		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF862	protein_coding	protein_coding	ENST00000223210	8	29113

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.78e-12	0.958	124692	1	105	124798	0.000425

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.327	666	690	0.965	0.0000424	7555
Missense in Polyphen		204	230.99	0.88316		2549
Synonymous	-0.380	305	297	1.03	0.0000198	2348
Loss of Function	2.19	24	38.7	0.620	0.00000202	472

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00206	0.00195
Ashkenazi Jewish	0.00	0.00
East Asian	0.000672	0.000667
Finnish	0.0000468	0.0000464
European (Non-Finnish)	0.000260	0.000256
Middle Eastern	0.000672	0.000667
South Asian	0.000695	0.000621
Other	0.00101	0.000990

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.852
• rvis_EVS: -1.27
• rvis_percentile_EVS: 5.2

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

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, DNA-templated;biological_process
• Cellular component: cellular_component;nucleus
• Molecular function: molecular_function;nucleic acid binding;metal ion binding;protein dimerization activity