ZNF154

protein-coding

zinc finger protein 154, the group of Zinc fingers C2H2-type

Gene summary

This gene encodes a protein that belongs to the zinc finger Kruppel family of transcriptional regulators, whose members are thought to function in normal and abnormal cell growth and differentiation. Hypermethylation of this gene is associated with the recurrence of non muscle invasive bladder cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

MANE transcript

NM_001085384.3

Inheritance

—

ClinVar variants

U:59B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr19:57,696,275-57,709,204

External References & Databases

Ensembl (ENSG00000179909)

Transcript & Mutation Effects

hg38 • Region Span ~12.9 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 ZNF154 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 60

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001085384.3. 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			58 clinvar	2 clinvar		60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	59	2	0	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001085384.3	RefSeq	NP_001078853.1	3	MANE Select
ENST00000684351.1	Ensembl	ENSP00000507206.1	3	MANE Select
ENST00000451275.1	Ensembl	ENSP00000469633.1	3	Standard
ENST00000512439.6	Ensembl	ENSP00000421258.2	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, 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
DNA-binding transcription factor activity
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000512439
Coding exons: 3
Length: 11845
Individuals with no LoFs: 122970
Homozygous LoFs: 11
Heterozygous LoFs: 2667
Defined: 125648
p: 0.0107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.249	239	228	1.05	0.0000120	2911
Missense (PolyPhen)		90	82.097	1.0963		1119
Synonymous	-0.692	91	83.0	1.10	0.00000432	796
Loss of Function	0.899	12	15.9	0.757	9.38e-7	209

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0021	0.0020	notable
Latino/Admixed American	0.0037	0.0037	notable
Ashkenazi Jewish	0.015	0.015	notable
East Asian	0.0023	0.0023	notable
Finnish	0.016	0.016	notable
European (Non-Finnish)	0.013	0.013	notable
South Asian	0.014	0.013	notable
Other	0.010	0.010	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.597
RVIS EVS: 0.82
RVIS percentile EVS: 87.99

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0213

Gene Damage Prediction

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