ZNF254

protein-coding

zinc finger protein 254, the group of Zinc fingers C2H2-type

Gene summary

Zinc finger proteins have been shown to interact with nucleic acids and to have diverse functions. The zinc finger domain is a conserved amino acid sequence motif containing 2 specifically positioned cysteines and 2 histidines that are involved in coordinating zinc. Kruppel-related proteins form 1 family of zinc finger proteins. See ZFP93 (MIM 604749) for additional information on zinc finger proteins.[supplied by OMIM, Jul 2002]

Previous symbols:

ZNF91L
ZNF539

MANE transcript

NM_203282.4

Inheritance

—

ClinVar variants

U:137B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr19:24,033,405-24,129,968

External References & Databases

Ensembl (ENSG00000213096)

Transcript & Mutation Effects

hg38 • Region Span ~96.6 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 ZNF254 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 136

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_203282.4. 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			137 clinvar	2 clinvar		139
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	137	3	0	140

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 52 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_203282.4	RefSeq	NP_975011.3	4	MANE Select
ENST00000357002.5	Ensembl	ENSP00000349494.3	4	MANE Select
NM_001278661.2	RefSeq	NP_001265590.1	3	Standard
NM_001278662.2	RefSeq	NP_001265591.1	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

negative regulation of transcription by RNA polymerase II

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000357002
Coding exons: 4
Length: 96379
Individuals with no LoFs: 125696
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125713
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-3.15	489	328	1.49	0.0000150	4319
Missense (PolyPhen)		65	52.69	1.2336		796
Synonymous	-2.68	147	111	1.32	0.00000499	1131
Loss of Function	0.143	5	5.36	0.933	2.27e-7	64

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0.000099	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0746

Intolerance Scores

LoFtool: 0.901
RVIS EVS: 0.56
RVIS percentile EVS: 81.71

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0397

Gene Damage Prediction

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