ZNF468

zinc finger protein 468, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:52838010-52857649

Links

ENSG00000204604 ∙ NCBI:90333 ∙ OMIM:616841 ∙ HGNC:33105 ∙ Uniprot:Q5VIY5 ∙ 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 ZNF468 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF468 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				4		4
missense			47			47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	4	0

Variants in ZNF468

This is a list of pathogenic ClinVar variants found in the ZNF468 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-52840744-T-A		not specified	Uncertain significance (Oct 20, 2024)
19-52840763-C-T		not specified	Uncertain significance (Jul 19, 2023)
19-52840837-C-T		not specified	Uncertain significance (Jan 24, 2025)
19-52840838-G-A		not specified	Uncertain significance (Mar 25, 2022)
19-52840846-A-C		not specified	Uncertain significance (Jun 29, 2022)
19-52840864-C-A		not specified	Uncertain significance (May 23, 2023)
19-52840864-C-T		not specified	Uncertain significance (Jan 20, 2025)
19-52840886-T-C		not specified	Uncertain significance (Mar 01, 2023)
19-52840948-T-C		not specified	Uncertain significance (Jan 03, 2025)
19-52840970-T-G		not specified	Uncertain significance (Aug 27, 2024)
19-52841007-G-A			Likely benign (Nov 01, 2024)
19-52841016-C-A			Likely benign (Nov 01, 2024)
19-52841047-C-G		not specified	Uncertain significance (May 01, 2024)
19-52841162-T-C		not specified	Uncertain significance (Mar 18, 2024)
19-52841249-G-A		not specified	Uncertain significance (Jul 30, 2023)
19-52841270-G-C		not specified	Uncertain significance (Aug 05, 2024)
19-52841281-T-C		not specified	Uncertain significance (Nov 25, 2024)
19-52841338-C-T		not specified	Uncertain significance (Feb 23, 2025)
19-52841344-T-C		not specified	Uncertain significance (Jan 30, 2024)
19-52841378-T-C		not specified	Uncertain significance (Apr 12, 2022)
19-52841416-T-C		not specified	Uncertain significance (Dec 04, 2023)
19-52841419-A-G		not specified	Uncertain significance (Jan 03, 2025)
19-52841422-G-C		not specified	Uncertain significance (Jan 23, 2023)
19-52841432-T-G		not specified	Uncertain significance (May 17, 2023)
19-52841534-G-T		not specified	Uncertain significance (Feb 05, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF468	protein_coding	protein_coding	ENST00000595646	3	19642

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000100	0.209	125733	0	10	125743	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.37	334	271	1.23	0.0000141	3479
Missense in Polyphen		61	47.537	1.2832		600
Synonymous	-0.736	106	96.8	1.10	0.00000516	913
Loss of Function	-0.957	5	3.16	1.58	1.35e-7	34

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000625	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000163	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: 0.947
• rvis_EVS: 1.98
• rvis_percentile_EVS: 97.62

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.112
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.289

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;metal ion binding