ZNF662

zinc finger protein 662, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 3:42906142-42919334

Links

ENSG00000182983 ∙ NCBI:389114 ∙ ∙ HGNC:31930 ∙ Uniprot:Q6ZS27 ∙ 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 ZNF662 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF662 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			30	3		33
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	1		5
Total	0	0	34	5	0

Variants in ZNF662

This is a list of pathogenic ClinVar variants found in the ZNF662 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-42906406-C-T		not specified	Uncertain significance (Oct 05, 2023)
3-42906414-A-G			Likely benign (Oct 01, 2023)
3-42906418-C-T		not specified	Uncertain significance (Jun 23, 2023)
3-42906430-C-T		not specified	Uncertain significance (Mar 20, 2024)
3-42908049-G-C		not specified	Uncertain significance (May 13, 2024)
3-42908058-T-C		not specified	Uncertain significance (Jan 29, 2024)
3-42908094-A-G		not specified	Uncertain significance (Jul 06, 2021)
3-42908864-C-T		not specified	Uncertain significance (Sep 22, 2023)
3-42908895-G-T		not specified	Uncertain significance (Jun 27, 2022)
3-42908906-T-G		not specified	Uncertain significance (Jan 04, 2022)
3-42914356-T-C		not specified	Uncertain significance (Dec 21, 2022)
3-42914365-A-G		not specified	Uncertain significance (Aug 26, 2022)
3-42914407-T-G			Likely benign (Oct 01, 2023)
3-42914410-A-C		not specified	Uncertain significance (May 26, 2024)
3-42914440-T-G		not specified	Uncertain significance (Dec 28, 2022)
3-42914463-A-C		not specified	Uncertain significance (Aug 08, 2023)
3-42914495-A-G		not specified	Uncertain significance (Oct 27, 2023)
3-42914509-C-T		not specified	Uncertain significance (Aug 17, 2022)
3-42914591-C-T		not specified	Uncertain significance (May 06, 2024)
3-42914600-A-G		not specified	Uncertain significance (Dec 22, 2023)
3-42914633-A-G		not specified	Likely benign (Dec 01, 2022)
3-42914648-A-G		not specified	Uncertain significance (Apr 25, 2022)
3-42914653-T-C		not specified	Uncertain significance (Jun 01, 2023)
3-42914654-G-A		not specified	Uncertain significance (Nov 27, 2023)
3-42914665-G-A		not specified	Likely benign (Apr 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF662	protein_coding	protein_coding	ENST00000328199	4	13603

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.67e-13	0.0363	125257	2	489	125748	0.00195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.252	260	249	1.04	0.0000130	2985
Missense in Polyphen		52	61.249	0.84899		795
Synonymous	0.665	85	93.2	0.912	0.00000515	838
Loss of Function	0.127	19	19.6	0.969	0.00000118	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00323	0.00323
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.00245	0.00180
Finnish	0.00139	0.00139
European (Non-Finnish)	0.00231	0.00229
Middle Eastern	0.00245	0.00180
South Asian	0.00199	0.00199
Other	0.00277	0.00277

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.949
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.88

Haploinsufficiency Scores

• pHI: 0.0743
• hipred: N
• hipred_score: 0.112
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.133

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