ZNF469

zinc finger protein 469, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 16:88382958-88440757

Links

ENSG00000225614 ∙ NCBI:84627 ∙ OMIM:612078 ∙ HGNC:23216 ∙ Uniprot:Q96JG9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• brittle cornea syndrome 1 (Strong), mode of inheritance: AR
• brittle cornea syndrome 1 (Strong), mode of inheritance: AR
• brittle cornea syndrome (Supportive), mode of inheritance: AR
• brittle cornea syndrome 1 (Strong), mode of inheritance: AR
• brittle cornea syndrome 1 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Brittle cornea syndrome 1	AR	Ophthalmologic	Individuals are prone to ophthalmologic injury (such as corneal rupture) with minimal trauma, and protective measures may be beneficial	Musculoskeletal; Ophthalmologic	13627089; 14218178; 5755738; 4872990; 5775573; 4691558; 962660; 7387950; 2112090; 2363420; 14679583; 18452888; 19661234; 20938016

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF469 gene.

• Cardiovascular phenotype (2057 variants)
• not provided (1938 variants)
• Brittle cornea syndrome 1 (393 variants)
• Ehlers-Danlos syndrome (216 variants)
• not specified (203 variants)
• Inborn genetic diseases (137 variants)
• Keratoconus 1 (22 variants)
• ZNF469-related condition (9 variants)
• 8 conditions (3 variants)
• Brittle cornea syndrome (1 variants)
• Connective tissue disorder (1 variants)
• Keratoconus (1 variants)
• Joint laxity (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF469 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			14	1066	12	1092
missense		1	1519	164	16	1700
nonsense	10	4	2			16
start loss			1			1
frameshift	40	22	10			72
inframe indel			22	4		26
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			24	5	7	36
Total	50	27	1592	1239	35

Highest pathogenic variant AF is 0.0000131

Variants in ZNF469

This is a list of pathogenic ClinVar variants found in the ZNF469 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-88427453-C-A		not specified	Likely benign (Nov 16, 2017)
16-88427468-G-A		Cardiovascular phenotype	Uncertain significance (Nov 04, 2021)
16-88427469-C-T		Cardiovascular phenotype	Uncertain significance (Oct 01, 2020)
16-88427471-A-G			Uncertain significance (Dec 23, 2019)
16-88427473-GC-G			Pathogenic (Aug 07, 2023)
16-88427474-C-A			Uncertain significance (Jul 25, 2023)
16-88427475-C-T		Cardiovascular phenotype	Uncertain significance (May 10, 2021)
16-88427478-GGGAGCGCCCCCGA-G			Pathogenic (Dec 19, 2023)
16-88427483-C-T		Cardiovascular phenotype	Uncertain significance (Feb 22, 2024)
16-88427484-G-A		Ehlers-Danlos syndrome • Cardiovascular phenotype	Conflicting classifications of pathogenicity (Nov 22, 2023)
16-88427484-GC-G			Pathogenic (Sep 21, 2023)
16-88427485-C-A			Likely benign (Jan 02, 2024)
16-88427487-C-T			Uncertain significance (Aug 23, 2022)
16-88427488-C-G			Likely benign (Aug 18, 2023)
16-88427489-C-T		Brittle cornea syndrome 1 • Ehlers-Danlos syndrome • Cardiovascular phenotype	Conflicting classifications of pathogenicity (Jan 18, 2024)
16-88427490-G-A			Uncertain significance (Jun 24, 2022)
16-88427494-A-G		Cardiovascular phenotype	Likely benign (Nov 13, 2023)
16-88427496-C-T		Cardiovascular phenotype	Conflicting classifications of pathogenicity (Feb 28, 2024)
16-88427497-G-A		Cardiovascular phenotype	Likely benign (Jan 16, 2024)
16-88427500-G-A		Cardiovascular phenotype	Likely benign (Dec 29, 2023)
16-88427500-G-GC			Pathogenic (Jan 06, 2024)
16-88427502-C-T			Uncertain significance (Nov 25, 2021)
16-88427506-C-A		Cardiovascular phenotype	Likely benign (Jan 31, 2024)
16-88427506-C-G		Cardiovascular phenotype	Likely benign (Feb 04, 2024)
16-88427506-C-T		Cardiovascular phenotype	Likely benign (Feb 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF469	protein_coding	protein_coding	ENST00000437464	2	13287

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.719	0.281	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.774	2188	2.29e+3	0.955	0.000147	24895
Missense in Polyphen		326	355.28	0.91757		4145
Synonymous	1.38	1017	1.07e+3	0.946	0.0000804	8757
Loss of Function	4.63	8	39.3	0.203	0.00000213	446

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
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.

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.142

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp469

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