ZNF804A

protein-coding

zinc finger protein 804A, the group of Zinc fingers C2H2-type

Gene summary

The protein encoded by this gene is a zinc finger binding protein. Polymorphisms in this gene, especially rs1344706, are thought to confer increased susceptibility to schizophrenia, bipolar disorder, and heroin addiciton. [provided by RefSeq, Nov 2015]

Previous symbols:

C2orf10

MANE transcript

NM_194250.2

Inheritance

ClinVar variants

U:161B:27

Top phenotype

ZNF804A-related disorder

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr2:184,598,529-184,939,492

External References & Databases

Ensembl (ENSG00000170396)

Transcript & Mutation Effects

hg38 • Region Span ~341.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF804A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 168

ZNF804A-related disorderTotal: 14

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_194250.2. 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	3 clinvar	5 clinvar	9
missense			158 clinvar	18 clinvar	1 clinvar	177
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	161	21	6	188

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_194250.2	RefSeq	NP_919226.1	4	MANE Select
ENST00000302277.7	Ensembl	ENSP00000303252.6	4	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of gene expression
regulation of neuron projection development
positive regulation of neuron projection development
positive regulation of dendritic spine maintenance

Molecular Function

molecular_function
nucleic acid binding
metal ion binding

Cellular Component

nucleus
cytoplasm
plasma membrane
growth cone
neuronal cell body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000302277
Coding exons: 4
Length: 341127
Individuals with no LoFs: 125715
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 125748
p: 0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.451	630	599	1.05	0.0000281	7994
Missense (PolyPhen)		202	221.8	0.91072		3008
Synonymous	-0.199	223	219	1.02	0.0000106	2248
Loss of Function	4.16	12	40.6	0.296	0.00000210	582

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00015	0.00014	rare
South Asian	0.000099	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0920

Intolerance Scores

LoFtool: 0.460
RVIS EVS: 1.3
RVIS percentile EVS: 93.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.119

Gene Damage Prediction

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