ZNF253

protein-coding

zinc finger protein 253, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF411

MANE transcript

NM_021047.3

Inheritance

—

ClinVar variants

U:62B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr19:19,865,882-19,894,674

External References & Databases

Ensembl (ENSG00000256771)

Transcript & Mutation Effects

hg38 • Region Span ~28.8 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 ZNF253 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021047.3. 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			62 clinvar	2 clinvar	1 clinvar	65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	62	3	1	66

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021047.3	RefSeq	NP_066385.2	4	MANE Select
ENST00000589717.2	Ensembl	ENSP00000468720.1	4	MANE Select
NM_001331133.1	RefSeq	NP_001318062.1	2	Standard
NM_001331134.1	RefSeq	NP_001318063.1	1	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, DNA-templated
regulation of transcription by RNA polymerase II
negative regulation of transcription, DNA-templated

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000589717
Coding exons: 4
Length: 28789
Individuals with no LoFs: 125454
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125463
p: 0.0000359

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.569	231	257	0.900	0.0000117	3295
Missense (PolyPhen)		78	101.96	0.76504		1349
Synonymous	-0.373	92	87.6	1.05	0.00000406	886
Loss of Function	0.458	4	5.12	0.782	2.17e-7	62

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000063	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function as a transcription factor. Seem to have a transcriptional repression activity.;

Recessive Scores

pRec: 0.0899

Intolerance Scores

LoFtool: 0.629
RVIS EVS: -0.36
RVIS percentile EVS: 29.16

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.341

Gene Damage Prediction

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