ZNF462

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

Basic information

Region (hg38): 9:106863165-107013634

Links

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

Phenotypes

GenCC

Source: genCC

• weiss-kruszka syndrome (Strong), mode of inheritance: AD
• weiss-kruszka syndrome (Strong), mode of inheritance: AD
• weiss-kruszka syndrome (Definitive), mode of inheritance: AD
• weiss-kruszka syndrome (Moderate), mode of inheritance: AD
• weiss-kruszka syndrome (Definitive), 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.

• Weiss-kruszka syndrome (18 variants)
• not provided (13 variants)
• Inborn genetic diseases (2 variants)
• not specified (1 variants)
• ZNF462-related disorder (1 variants)
• Craniosynostosis syndrome;Intellectual disability, autosomal dominant (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.

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				58	11	69
missense		2	189	49	9	249
nonsense	13	5				18
start loss						0
frameshift	17	6	1			24
inframe indel			6		1	7
splice donor/acceptor (+/-2bp)	1		1			2
splice region			1			1
non coding			3		1	4
Total	31	13	200	107	22

Highest pathogenic variant AF is 0.000337

Variants in ZNF462

This is a list of pathogenic ClinVar variants found in the ZNF462 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-106863999-G-C		Weiss-kruszka syndrome	Uncertain significance (Mar 25, 2024)
9-106923425-G-A		not specified	Likely benign (Apr 15, 2024)
9-106923467-G-A		ZNF462-related disorder	Likely benign (Jul 20, 2022)
9-106923483-A-G		Inborn genetic diseases	Likely benign (Apr 19, 2024)
9-106923501-A-G		ZNF462-related disorder	Likely benign (Jan 18, 2023)
9-106923505-T-C		ZNF462-related disorder	Uncertain significance (Dec 20, 2023)
9-106923527-C-T			Likely benign (Nov 01, 2022)
9-106923528-G-A		Inborn genetic diseases	Likely benign (Feb 15, 2023)
9-106923556-A-C			Uncertain significance (Apr 07, 2022)
9-106923561-T-C		Inborn genetic diseases	Uncertain significance (Sep 14, 2023)
9-106923564-T-A			Uncertain significance (Sep 01, 2023)
9-106923602-A-G			Uncertain significance (Dec 19, 2022)
9-106923604-G-A		Weiss-kruszka syndrome	Pathogenic (Sep 20, 2021)
9-106924142-C-A		Inborn genetic diseases	Uncertain significance (Oct 30, 2023)
9-106924149-A-T		ZNF462-related disorder	Likely benign (Oct 28, 2019)
9-106924150-T-C		ZNF462-related disorder	Benign/Likely benign (Jan 01, 2024)
9-106924176-C-A		Inborn genetic diseases	Uncertain significance (Apr 25, 2022)
9-106924184-G-C		Inborn genetic diseases	Uncertain significance (Jun 05, 2023)
9-106924225-A-G		Inborn genetic diseases	Uncertain significance (Sep 21, 2023)
9-106924300-G-C			Uncertain significance (Mar 30, 2022)
9-106924322-G-A		Inborn genetic diseases	Likely benign (Jan 22, 2024)
9-106924326-T-A		Inborn genetic diseases	Uncertain significance (Nov 05, 2021)
9-106924353-C-A		ZNF462-related disorder	Benign/Likely benign (Mar 01, 2023)
9-106924377-C-T		ZNF462-related disorder	Likely benign (Jun 06, 2019)
9-106924378-G-A		Inborn genetic diseases	Uncertain significance (Apr 25, 2023)

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
1.00	3.84e-13	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

Haploinsufficiency Scores

• pHI: 0.441
• hipred: Y
• hipred_score: 0.729
• ghis: 0.541

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

Mouse Genome Informatics

• Gene name: Zfp462
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

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