ZNF486

zinc finger protein 486, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:20167214-20200488

Previous symbols: [ "KRBO2" ]

Links

ENSG00000256229 ∙ NCBI:90649 ∙ ∙ HGNC:20807 ∙ Uniprot:Q96H40 ∙ 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 ZNF486 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF486 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			60	2		62
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	60	3	0

Variants in ZNF486

This is a list of pathogenic ClinVar variants found in the ZNF486 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-20167335-C-T		not specified	Uncertain significance (Mar 06, 2025)
19-20184363-T-C		not specified	Uncertain significance (Feb 14, 2024)
19-20184393-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-20184404-T-A		not specified	Uncertain significance (Apr 23, 2024)
19-20184438-A-G		not specified	Uncertain significance (Jun 27, 2023)
19-20184443-G-A		not specified	Uncertain significance (May 24, 2023)
19-20184443-G-C		not specified	Uncertain significance (Jan 21, 2025)
19-20184449-A-G		not specified	Uncertain significance (Dec 28, 2024)
19-20185991-T-G		not specified	Uncertain significance (Sep 27, 2021)
19-20185999-C-G		not specified	Uncertain significance (Feb 20, 2025)
19-20186032-G-C		not specified	Uncertain significance (Sep 25, 2024)
19-20196966-G-A		not specified	Likely benign (Jun 22, 2023)
19-20197060-A-C		not specified	Uncertain significance (Jun 07, 2023)
19-20197066-A-G		not specified	Uncertain significance (May 03, 2023)
19-20197086-T-G		not specified	Uncertain significance (Jan 03, 2024)
19-20197105-G-C		not specified	Uncertain significance (Apr 19, 2024)
19-20197135-T-C		not specified	Uncertain significance (Mar 21, 2023)
19-20197140-C-A		not specified	Uncertain significance (Feb 05, 2024)
19-20197144-G-A		not specified	Uncertain significance (May 08, 2023)
19-20197180-G-A		not specified	Uncertain significance (Nov 27, 2024)
19-20197188-G-A		not specified	Uncertain significance (Jul 25, 2024)
19-20197194-G-A		not specified	Uncertain significance (Nov 07, 2022)
19-20197221-A-G		not specified	Uncertain significance (Aug 04, 2024)
19-20197252-C-T		not specified	Uncertain significance (Aug 04, 2023)
19-20197270-G-T		not specified	Uncertain significance (May 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF486	protein_coding	protein_coding	ENST00000335117	4	33263

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000679	0.163	125644	0	26	125670	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.58	349	237	1.47	0.0000110	3058
Missense in Polyphen		131	87.598	1.4955		1151
Synonymous	-3.64	126	83.6	1.51	0.00000418	796
Loss of Function	-0.613	7	5.45	1.28	2.31e-7	66

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000178
Ashkenazi Jewish	0.00	0.00
East Asian	0.000121	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000626	0.0000616
Middle Eastern	0.000121	0.000109
South Asian	0.000359	0.000359
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.778
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.58

Haploinsufficiency Scores

• pHI: 0.0653
• hipred: N
• hipred_score: 0.148
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

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: nucleus;extracellular exosome
• Molecular function: molecular_function;DNA binding;metal ion binding