ZNF469

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

Basic information

Region (hg38): 16:88382959-88440757

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
• aortic disorder (Limited), mode of inheritance: AD

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 (3282 variants)
• not_provided (3241 variants)
• Brittle_cornea_syndrome_1 (406 variants)
• not_specified (386 variants)
• Ehlers-Danlos_syndrome (214 variants)
• ZNF469-related_disorder (153 variants)
• Keratoconus_1 (33 variants)
• Spontaneous_hematomas (3 variants)
• Soft_skin (3 variants)
• Myopia (3 variants)
• Poor_wound_healing (3 variants)
• Gastroesophageal_reflux (3 variants)
• Joint_hypermobility (3 variants)
• Striae_distensae (3 variants)
• Thoracic_scoliosis (3 variants)
• Brittle_cornea_syndrome (1 variants)
• Keratoconus (1 variants)
• Connective_tissue_disorder (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. These statistics are base on transcript: NM_001367624.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous		2	11	1996	4	2013
missense	6	1	2112	623	12	2754
nonsense	26	7	4			37
start loss			1			1
frameshift	98	30	15			143
splice donor/acceptor (+/-2bp)						0
Total	130	40	2143	2619	16

Highest pathogenic variant AF is 0.000159384

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