ZNF480

zinc finger protein 480, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:52297169-52325922

Links

ENSG00000198464 ∙ NCBI:147657 ∙ OMIM:613910 ∙ HGNC:23305 ∙ Uniprot:Q8WV37 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Schizophrenia	AD	General	Evidence or clinical applicability unclear	Neurologic	21743468

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF480 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF480 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			28			28
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	1

Variants in ZNF480

This is a list of pathogenic ClinVar variants found in the ZNF480 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-52300416-CTG-C		not specified	Benign (Mar 29, 2016)
19-52300425-G-A		not specified	Uncertain significance (Jul 05, 2022)
19-52314188-C-A		not specified	Uncertain significance (Dec 15, 2022)
19-52314196-C-A		not specified	Likely benign (Apr 12, 2024)
19-52314198-G-A		not specified	Uncertain significance (Oct 28, 2023)
19-52314219-G-A		not specified	Uncertain significance (Nov 10, 2024)
19-52314224-G-C		not specified	Uncertain significance (Dec 02, 2024)
19-52314246-A-G		not specified	Uncertain significance (Oct 05, 2021)
19-52315840-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-52315849-A-G		not specified	Uncertain significance (Sep 17, 2021)
19-52315854-A-G		not specified	Uncertain significance (Jun 30, 2022)
19-52315867-T-C		not specified	Uncertain significance (Dec 20, 2021)
19-52315904-T-G		not specified	Uncertain significance (Jun 09, 2022)
19-52315949-A-T		not specified	Uncertain significance (Oct 26, 2022)
19-52315951-G-T		not specified	Uncertain significance (May 30, 2023)
19-52321583-C-G		not specified	Uncertain significance (Dec 12, 2023)
19-52321620-A-G		not specified	Uncertain significance (Feb 10, 2022)
19-52321738-C-T		not specified	Uncertain significance (Sep 27, 2022)
19-52321762-C-T		not specified	Uncertain significance (Apr 20, 2024)
19-52321764-T-A		not specified	Uncertain significance (Jun 13, 2023)
19-52321857-T-C		not specified	Uncertain significance (Oct 12, 2021)
19-52321936-A-C		not specified	Uncertain significance (Apr 18, 2023)
19-52321975-G-A		not specified	Uncertain significance (May 23, 2023)
19-52322167-A-G		not specified	Uncertain significance (Jul 15, 2021)
19-52322317-C-T		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF480	protein_coding	protein_coding	ENST00000595962	4	28746

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0356	0.840	125718	0	3	125721	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.350	264	281	0.941	0.0000133	3558
Missense in Polyphen		81	97.203	0.83331		1248
Synonymous	-0.381	104	99.2	1.05	0.00000482	947
Loss of Function	1.23	3	6.32	0.474	2.67e-7	79

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)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in transcriptional regulation as an activator. {ECO:0000269|PubMed:15219843}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.870
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.57

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.148
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.115

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;nucleoplasm;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;nucleic acid binding;metal ion binding