ZNF804A

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

Basic information

Region (hg38): 2:184598528-184939492

Previous symbols: [ "C2orf10" ]

Links

ENSG00000170396 ∙ NCBI:91752 ∙ OMIM:612282 ∙ HGNC:21711 ∙ Uniprot:Q7Z570 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF804A gene.

• Inborn genetic diseases (35 variants)
• not provided (12 variants)
• not specified (1 variants)
• ZNF804A-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF804A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	4	6
missense			36	4	3	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	6	7

Variants in ZNF804A

This is a list of pathogenic ClinVar variants found in the ZNF804A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-184598973-A-G		not specified	Uncertain significance (Feb 17, 2022)
2-184598975-A-T		not specified	Uncertain significance (Feb 28, 2023)
2-184598990-A-T		not specified	Uncertain significance (Dec 04, 2023)
2-184866383-G-T		not specified	Uncertain significance (Aug 05, 2023)
2-184866467-G-A		ZNF804A-related disorder	Benign/Likely benign (May 24, 2019)
2-184933718-G-A		ZNF804A-related disorder	Likely benign (Aug 29, 2022)
2-184935829-A-G		not specified	Uncertain significance (Aug 17, 2022)
2-184935913-A-T		not specified	Uncertain significance (Oct 20, 2023)
2-184935926-C-T		not specified	Uncertain significance (Jan 26, 2022)
2-184935928-A-G		ZNF804A-related disorder	Likely benign (May 24, 2019)
2-184935995-T-A		not specified	Uncertain significance (Dec 26, 2023)
2-184936065-C-A		ZNF804A-related disorder	Likely benign (Jun 07, 2019)
2-184936126-A-G		not specified	Uncertain significance (Sep 17, 2021)
2-184936166-G-T		not specified	Uncertain significance (Jan 16, 2024)
2-184936178-A-T			Benign (Jul 14, 2020)
2-184936244-C-A			Uncertain significance (Oct 21, 2021)
2-184936268-T-C		not specified	Likely benign (Mar 04, 2024)
2-184936291-G-A		not specified	Uncertain significance (Dec 08, 2023)
2-184936297-A-T		not specified	Uncertain significance (Apr 05, 2023)
2-184936370-G-T		ZNF804A-related disorder	Likely benign (May 10, 2019)
2-184936373-A-T		not specified	Uncertain significance (Feb 15, 2023)
2-184936390-G-C		not specified	Uncertain significance (Mar 22, 2022)
2-184936513-C-A		not specified	Uncertain significance (Jan 31, 2022)
2-184936546-G-A		not specified	Uncertain significance (Oct 26, 2022)
2-184936584-C-T			Benign/Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF804A	protein_coding	protein_coding	ENST00000302277	4	341127

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00553	0.994	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.451	630	599	1.05	0.0000281	7994
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000220	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000151	0.000141
Middle Eastern	0.000220	0.000217
South Asian	0.0000986	0.0000980
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0920

Intolerance Scores

• loftool: 0.460
• rvis_EVS: 1.3
• rvis_percentile_EVS: 93.91

Haploinsufficiency Scores

• pHI: 0.328
• hipred: N
• hipred_score: 0.280
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.119

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp804a

Gene ontology

• Biological process: positive regulation of gene expression;regulation of neuron projection development;positive regulation of neuron projection development;positive regulation of dendritic spine maintenance
• Cellular component: nucleus;cytoplasm;plasma membrane;growth cone;neuronal cell body;dendritic spine;dendritic shaft;presynapse;postsynapse;dendritic microtubule
• Molecular function: molecular_function;nucleic acid binding;metal ion binding