ZNF462

zinc finger protein 462, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 9:106863166-107013634

Links

ENSG00000148143 ∙ NCBI:58499 ∙ OMIM:617371 ∙ HGNC:21684 ∙ Uniprot:Q96JM2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Weiss-Kruszka syndrome (Moderate), mode of inheritance: AD
• Weiss-Kruszka syndrome (Definitive), mode of inheritance: AD
• Weiss-Kruszka syndrome (Definitive), mode of inheritance: AD
• Weiss-Kruszka syndrome (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Weiss-Kruszka syndrome	AD	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic	28513610; 31361404

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF462 gene.

• not_provided (295 variants)
• Inborn_genetic_diseases (285 variants)
• Weiss-Kruszka_syndrome (115 variants)
• ZNF462-related_disorder (69 variants)
• not_specified (35 variants)
• Craniosynostosis_syndrome (3 variants)
• Intellectual_disability,_autosomal_dominant (3 variants)
• Familial_cancer_of_breast (2 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
• Premature_ovarian_failure (1 variants)
• Cleft_lip (1 variants)
• See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF462 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021224.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous	1		3	83	6	93
missense	1	4	437	85	3	530
nonsense	19	11	3			33
start loss						0
frameshift	34	17	3			54
splice donor/acceptor (+/-2bp)	3		4			7
Total	58	32	450	168	9

Highest pathogenic variant AF is 0.00037252673

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF462	protein_coding	protein_coding	ENST00000277225	12	150538

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.35	1058	1.41e+3	0.749	0.0000831	16669
Missense in Polyphen		340	626.49	0.5427		7441
Synonymous	-1.40	601	559	1.08	0.0000354	4759
Loss of Function	8.56	3	91.2	0.0329	0.00000554	1120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000265	0.0000264
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: Mesodermal Commitment Pathway (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.413
• rvis_EVS: -2.81
• rvis_percentile_EVS: 0.64

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.369

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: chromatin organization;regulation of gene expression;negative regulation of DNA binding;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;histone methyltransferase complex
• Molecular function: RNA polymerase II core promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding