ZNF219

zinc finger protein 219, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 14:21090077-21104722

Links

ENSG00000165804 ∙ ∙ OMIM:605036 ∙ HGNC:13011 ∙ Uniprot:Q9P2Y4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• microphthalmia (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF219 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF219 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			43			43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	1	0

Variants in ZNF219

This is a list of pathogenic ClinVar variants found in the ZNF219 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-21090553-C-T		not specified	Uncertain significance (Jul 02, 2024)
14-21090588-C-A		not specified	Uncertain significance (Jan 03, 2024)
14-21090610-G-A		not specified	Uncertain significance (May 20, 2024)
14-21090690-C-T		not specified	Uncertain significance (Aug 28, 2024)
14-21090691-G-A		not specified	Uncertain significance (Jan 29, 2024)
14-21090844-C-T		not specified	Uncertain significance (Jun 17, 2024)
14-21090888-C-G		not specified	Uncertain significance (Nov 14, 2023)
14-21090934-C-T		not specified	Likely benign (Jun 18, 2024)
14-21090961-G-A		not specified	Uncertain significance (Nov 15, 2021)
14-21090966-G-T		not specified	Uncertain significance (Oct 25, 2024)
14-21090987-G-A		not specified	Uncertain significance (Oct 20, 2023)
14-21091015-G-A		not specified	Uncertain significance (Feb 14, 2024)
14-21091036-C-T		not specified	Uncertain significance (Dec 19, 2023)
14-21091082-G-C			Likely benign (Nov 01, 2022)
14-21091505-T-G		not specified	Uncertain significance (Feb 03, 2022)
14-21091886-C-A		not specified	Uncertain significance (Jul 12, 2023)
14-21091887-C-A		not specified	Uncertain significance (Jul 12, 2023)
14-21091897-G-A		not specified	Uncertain significance (Mar 02, 2023)
14-21091915-C-T		not specified	Uncertain significance (Apr 26, 2023)
14-21091961-G-T		not specified	Uncertain significance (Jul 15, 2021)
14-21091969-C-A		not specified	Uncertain significance (Jul 08, 2022)
14-21092005-T-A		not specified	Uncertain significance (Nov 07, 2022)
14-21092021-G-T		not specified	Uncertain significance (Mar 29, 2023)
14-21092029-G-A		not specified	Uncertain significance (May 10, 2024)
14-21092053-G-A		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF219	protein_coding	protein_coding	ENST00000360947	4	14677

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000228	119899	0	1	119900	0.00000417

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.92	271	444	0.610	0.0000321	4379
Missense in Polyphen		137	262.5	0.5219		2552
Synonymous	1.58	168	196	0.856	0.0000144	1601
Loss of Function	4.54	0	24.0	0.00	0.00000154	236

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
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: Transcriptional regulator (PubMed:14621294, PubMed:19549071). Recognizes and binds 2 copies of the core DNA sequence motif 5'-GGGGG-3' (PubMed:14621294). Binds to the HMGN1 promoter and may repress HMGN1 expression (PubMed:14621294). Regulates SNCA expression in primary cortical neurons (PubMed:19549071). Binds to the COL2A1 promoter and activates COL2A1 expression, as part of a complex with SOX9 (By similarity). Plays a role in chondrocyte differentiation (By similarity). {ECO:0000250|UniProtKB:Q6IQX8, ECO:0000269|PubMed:14621294, ECO:0000269|PubMed:19549071}.
• Pathway: Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.0946

Haploinsufficiency Scores

• pHI: 0.312
• hipred: Y
• hipred_score: 0.572
• ghis: 0.631

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.852

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp219
• Phenotype: homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: znf219
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: curved

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of neurotransmitter levels;transcription, DNA-templated;regulation of transcription, DNA-templated;G protein-coupled receptor signaling pathway;positive regulation of chondrocyte differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;limb bud formation
• Cellular component: nucleus;integral component of membrane
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;histamine receptor activity;protein binding;metal ion binding