ZFP69

ZFP69 zinc finger protein, the group of SCAN domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 1:40477290-40496343

Previous symbols: [ "ZNF642" ]

Links

ENSG00000187815 ∙ NCBI:339559 ∙ OMIM:617939 ∙ HGNC:24708 ∙ Uniprot:Q49AA0 ∙ 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 ZFP69 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFP69 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				1		1
missense			44	2	1	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	44	3	1

Variants in ZFP69

This is a list of pathogenic ClinVar variants found in the ZFP69 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-40479374-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-40479420-A-G		not specified	Uncertain significance (Mar 06, 2025)
1-40479437-G-A		not specified	Uncertain significance (Aug 28, 2023)
1-40481838-C-T		not specified	Likely benign (Aug 16, 2021)
1-40489093-G-T		not specified	Uncertain significance (Jan 18, 2023)
1-40489109-A-G		not specified	Uncertain significance (Mar 25, 2024)
1-40489110-T-C		not specified	Uncertain significance (Aug 13, 2021)
1-40489115-A-G		not specified	Likely benign (Jun 23, 2023)
1-40489116-T-C		not specified	Uncertain significance (Aug 26, 2024)
1-40489137-G-T		not specified	Uncertain significance (Jan 02, 2025)
1-40489173-G-A		not specified	Uncertain significance (Oct 20, 2023)
1-40489205-G-C			Benign (Aug 03, 2017)
1-40489531-T-C		not specified	Uncertain significance (Apr 25, 2022)
1-40489555-A-T		not specified	Uncertain significance (Oct 26, 2024)
1-40489556-T-C		not specified	Uncertain significance (Aug 27, 2024)
1-40494986-T-C		not specified	Uncertain significance (Jan 05, 2022)
1-40495008-G-A		not specified	Uncertain significance (Sep 01, 2024)
1-40495115-A-C		not specified	Uncertain significance (Jun 16, 2023)
1-40495122-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-40495125-A-C		not specified	Uncertain significance (May 29, 2024)
1-40495133-A-G		not specified	Uncertain significance (Oct 10, 2023)
1-40495134-G-T		not specified	Uncertain significance (Aug 17, 2022)
1-40495215-A-G		not specified	Uncertain significance (Dec 02, 2022)
1-40495229-C-T		not specified	Uncertain significance (Dec 19, 2022)
1-40495241-A-G		not specified	Uncertain significance (Oct 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFP69	protein_coding	protein_coding	ENST00000372706	5	19129

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.55e-8	0.619	125501	1	246	125748	0.000983

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	229	287	0.798	0.0000140	3517
Missense in Polyphen		75	112.2	0.66843		1396
Synonymous	1.42	84	102	0.821	0.00000544	922
Loss of Function	1.19	15	20.9	0.718	9.59e-7	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000607	0.000604
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000109	0.000109
Finnish	0.000510	0.000508
European (Non-Finnish)	0.00185	0.00183
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.000822	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative transcription factor that appears to regulate lipid metabolism. {ECO:0000250|UniProtKB:A2A761}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0932

Intolerance Scores

• rvis_EVS: 0.87
• rvis_percentile_EVS: 88.8

Haploinsufficiency Scores

• pHI: 0.168
• hipred: N
• hipred_score: 0.112
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp69

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;lipid metabolic process;regulation of lipid metabolic process
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding