ZNF273

protein-coding

zinc finger protein 273, the group of Zinc fingers C2H2-type

Gene summary

This gene is a member of the krueppel C2H2-type zinc-finger protein family and encodes a protein with 13 C2H2-type zinc fingers and a KRAB domain. This nuclear protein is involved in transcriptional regulation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

MANE transcript

NM_021148.3

Inheritance

—

ClinVar variants

U:76B:4

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr7:64,870,172-64,930,981

External References & Databases

Ensembl (ENSG00000198039)

Transcript & Mutation Effects

hg38 • Region Span ~60.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF273 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 78

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021148.3. 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
missense			76 clinvar	3 clinvar		79
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	4	0	80

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021148.3	RefSeq	NP_066971.2	4	MANE Select
ENST00000476120.2	Ensembl	ENSP00000418719.1	4	MANE Select
NM_001385643.1	RefSeq	NP_001372572.1	3	Standard
NM_001385644.1	RefSeq	NP_001372573.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000476120
Coding exons: 4
Length: 60795
Individuals with no LoFs: 122623
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 122626
p: 0.0000122

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.384	269	287	0.936	0.0000129	3740
Missense (PolyPhen)		88	115.47	0.76208		1535
Synonymous	0.142	98	99.8	0.982	0.00000448	1023
Loss of Function	1.05	3	5.71	0.526	2.41e-7	69

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000057	0.000057	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Recessive Scores

pRec: 0.0920

Intolerance Scores

LoFtool: 0.919
RVIS EVS: 0.53
RVIS percentile EVS: 80.88

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.850

Gene Damage Prediction

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