ZNF669

zinc finger protein 669, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 1:247099962-247104372

Links

ENSG00000188295 ∙ NCBI:79862 ∙ ∙ HGNC:25736 ∙ Uniprot:Q96BR6 ∙ 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 ZNF669 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF669 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			35			35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	0	0

Variants in ZNF669

This is a list of pathogenic ClinVar variants found in the ZNF669 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-247100388-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-247100396-C-A		not specified	Uncertain significance (Jun 11, 2021)
1-247100402-A-G		not specified	Uncertain significance (Mar 29, 2023)
1-247100432-C-T		not specified	Uncertain significance (Jan 16, 2024)
1-247100451-G-A		not specified	Uncertain significance (Apr 12, 2024)
1-247100478-T-C		not specified	Uncertain significance (Dec 13, 2023)
1-247100483-C-T		not specified	Uncertain significance (Mar 16, 2024)
1-247100604-G-A		not specified	Uncertain significance (Nov 12, 2021)
1-247100634-T-G		not specified	Uncertain significance (Oct 20, 2023)
1-247100651-C-T		not specified	Uncertain significance (Aug 31, 2022)
1-247100687-G-C		not specified	Uncertain significance (Jan 03, 2024)
1-247100705-A-C		not specified	Uncertain significance (Apr 07, 2022)
1-247100720-C-T		not specified	Uncertain significance (Nov 19, 2022)
1-247100750-T-A		not specified	Uncertain significance (Sep 26, 2023)
1-247100769-A-G		not specified	Uncertain significance (Dec 08, 2023)
1-247100813-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-247100882-T-C		not specified	Uncertain significance (Sep 22, 2023)
1-247100894-G-T		not specified	Uncertain significance (Dec 15, 2023)
1-247100898-C-T		not specified	Uncertain significance (Jun 30, 2022)
1-247100940-G-C		not specified	Uncertain significance (Aug 26, 2022)
1-247100961-T-C		not specified	Uncertain significance (Aug 17, 2021)
1-247100969-C-T		not specified	Uncertain significance (Sep 22, 2023)
1-247101040-C-T		not specified	Uncertain significance (May 26, 2023)
1-247101128-T-C		not specified	Uncertain significance (Jan 23, 2023)
1-247101199-T-A		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF669	protein_coding	protein_coding	ENST00000343381	4	4411

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00145	0.689	125694	0	50	125744	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.670	283	253	1.12	0.0000132	3017
Missense in Polyphen		78	62.952	1.239		811
Synonymous	-1.45	112	94.1	1.19	0.00000512	883
Loss of Function	0.737	5	7.12	0.702	3.07e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000830	0.000783
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000239	0.000211
Middle Eastern	0.00	0.00
South Asian	0.000101	0.0000980
Other	0.000368	0.000326

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: 0.950
• rvis_EVS: 0.98
• rvis_percentile_EVS: 90.38

Haploinsufficiency Scores

• pHI: 0.0555
• hipred: N
• hipred_score: 0.132
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.851

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp963

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