ZNF460

zinc finger protein 460, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57280051-57294069

Previous symbols: [ "ZNF272" ]

Links

ENSG00000197714 ∙ NCBI:10794 ∙ OMIM:604755 ∙ HGNC:21628 ∙ Uniprot:Q14592 ∙ 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 ZNF460 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF460 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			14	3		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	14	3	0

Variants in ZNF460

This is a list of pathogenic ClinVar variants found in the ZNF460 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57284555-C-G		not specified	Uncertain significance (Jan 19, 2024)
19-57284665-C-A		not specified	Uncertain significance (Jun 17, 2024)
19-57290713-C-T		not specified	Uncertain significance (Mar 29, 2022)
19-57290767-C-T		not specified	Uncertain significance (Aug 20, 2023)
19-57290807-A-G		not specified	Uncertain significance (Dec 21, 2022)
19-57290824-G-A		not specified	Uncertain significance (Sep 14, 2022)
19-57290878-C-T		not specified	Uncertain significance (Jun 29, 2023)
19-57290892-A-T		not specified	Likely benign (Dec 26, 2023)
19-57291068-T-C		not specified	Uncertain significance (Apr 26, 2023)
19-57291092-T-C		not specified	Uncertain significance (May 17, 2023)
19-57291209-C-T		not specified	Uncertain significance (Jul 26, 2022)
19-57291272-G-A		not specified	Uncertain significance (May 11, 2022)
19-57291344-C-G		not specified	Uncertain significance (Dec 26, 2023)
19-57291356-G-A		not specified	Uncertain significance (Apr 22, 2024)
19-57291752-G-T		not specified	Uncertain significance (Jan 04, 2022)
19-57291776-A-G		not specified	Likely benign (Sep 16, 2021)
19-57291985-G-A		not specified	Uncertain significance (Mar 21, 2024)
19-57292054-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-57292074-C-G		not specified	Likely benign (Feb 28, 2023)
19-57292075-G-A		not specified	Uncertain significance (Jun 05, 2024)
19-57292157-C-T		not specified	Uncertain significance (Feb 22, 2024)
19-57292172-C-T		not specified	Uncertain significance (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF460	protein_coding	protein_coding	ENST00000360338	3	13519

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.682	0.300	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.55	196	325	0.603	0.0000183	3739
Missense in Polyphen		30	112.03	0.2678		1354
Synonymous	-0.835	135	123	1.10	0.00000711	1050
Loss of Function	1.79	0	3.74	0.00	1.61e-7	37

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
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)

Intolerance Scores

• loftool: 0.140
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.33

Haploinsufficiency Scores

• pHI: 0.0705
• hipred: N
• hipred_score: 0.459
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.454

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: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding