ZNF394

protein-coding

zinc finger protein 394, the group of Zinc fingers C2H2-type|SCAN domain containing

Gene summary

The protein encoded by this gene is a zinc finger protein that inhibits the transcription of mitogen-activated protein kinase signaling pathways. The encoded protein may be involved in cardiac function. [provided by RefSeq, Sep 2016]

MANE transcript

NM_032164.4

Inheritance

—

ClinVar variants

U:83B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.6

Max pathogenic AF

—

Genomic locus

chr7:99,473,877-99,504,857

External References & Databases

Ensembl (ENSG00000160908)

Transcript & Mutation Effects

hg38 • Region Span ~31.0 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 ZNF394 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 83

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032164.4. 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						0
missense			82 clinvar	2 clinvar		84
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	83	2	0	85

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032164.4	RefSeq	NP_115540.2	3	MANE Select
ENST00000337673.7	Ensembl	ENSP00000337363.6	3	MANE Select
NM_001345967.2	RefSeq	NP_001332896.1	2	Standard
NM_001345968.2	RefSeq	NP_001332897.1	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: ENST00000337673
Coding exons: 3
Length: 13806
Individuals with no LoFs: 125699
Homozygous LoFs: 0
Heterozygous LoFs: 47
Defined: 125746
p: 0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.211	310	321	0.967	0.0000173	3712
Missense (PolyPhen)		72	84.688	0.85018		1075
Synonymous	-0.856	141	129	1.10	0.00000711	1061
Loss of Function	1.65	12	19.9	0.602	8.61e-7	239

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00023	0.00022	rare
South Asian	0.00033	0.00029	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0931

Intolerance Scores

LoFtool: 0.737
RVIS EVS: -0.11
RVIS percentile EVS: 45.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.868

Gene Damage Prediction

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