ZNF219

protein-coding

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

Gene summary

This gene is a member of the Kruppel-like zinc finger gene family. The encoded protein functions as a transcriptional repressor of the high mobility group nucleosome binding domain 1 protein, which is associated with transcriptionally active chromatin. [provided by RefSeq, Apr 2017]

MANE transcript

NM_016423.3

Inheritance

ClinVar variants

U:111B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr14:21,090,077-21,104,722

External References & Databases

Ensembl (ENSG00000165804)

Transcript & Mutation Effects

hg38 • Region Span ~14.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

microphthalmiaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0021129

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF219 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 109

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016423.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			108 clinvar	2 clinvar		110
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	111	3	0	114

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 62 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016423.3	RefSeq	NP_057507.2	4	MANE Select
ENST00000360947.8	Ensembl	ENSP00000354206.3	4	MANE Select
NM_001101672.2	RefSeq	NP_001095142.1	4	Standard
NM_001102454.2	RefSeq	NP_001095924.1	4	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
znf219	Danio rerio	Structure: whole organism Quality: curved abnormal

Gene / Model

Organism

Observed Phenotype

znf219

Danio rerio

Structure: whole organism

Quality: curved

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ectoderm Differentiation

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

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

Cellular Component

nucleus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360947
Coding exons: 4
Length: 14677
Individuals with no LoFs: 119899
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 119900
p: 0.00000417

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.92	271	444	0.610	0.0000321	4379
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0946

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.852

Gene Damage Prediction

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