ZNF394

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

Basic information

Region (hg38): 7:99473877-99504857

Links

ENSG00000160908 ∙ NCBI:84124 ∙ OMIM:619300 ∙ HGNC:18832 ∙ Uniprot:Q53GI3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF394 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF394 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						0
missense			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	0

Variants in ZNF394

This is a list of pathogenic ClinVar variants found in the ZNF394 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-99476476-G-A		not specified	Uncertain significance (Dec 02, 2022)
7-99479689-T-C		not specified	Uncertain significance (Dec 19, 2022)
7-99479701-G-T		not specified	Uncertain significance (Jun 29, 2022)
7-99484102-C-T		not specified	Uncertain significance (May 24, 2023)
7-99486569-A-C		not specified	Uncertain significance (Oct 05, 2021)
7-99486598-C-G		not specified	Uncertain significance (Aug 22, 2023)
7-99486599-A-G		not specified	Uncertain significance (Sep 17, 2021)
7-99486647-G-C		not specified	Uncertain significance (Dec 19, 2022)
7-99486666-G-C		not specified	Uncertain significance (Oct 10, 2023)
7-99486748-A-G		not specified	Uncertain significance (Jul 25, 2023)
7-99486872-G-T		not specified	Uncertain significance (Jan 23, 2023)
7-99486880-T-C		not specified	Uncertain significance (Dec 06, 2021)
7-99486913-G-A		not specified	Uncertain significance (Sep 06, 2022)
7-99486991-G-A		not specified	Uncertain significance (Sep 20, 2023)
7-99487018-G-A		not specified	Uncertain significance (Nov 21, 2022)
7-99487034-A-G		not specified	Uncertain significance (May 23, 2023)
7-99487121-A-C		not specified	Uncertain significance (Jun 11, 2021)
7-99487171-G-T		not specified	Uncertain significance (Feb 16, 2023)
7-99487180-C-T		not specified	Uncertain significance (Jul 13, 2021)
7-99487222-C-T		not specified	Uncertain significance (Jan 02, 2024)
7-99487340-C-T		not specified	Uncertain significance (Feb 17, 2023)
7-99487415-G-A		not specified	Uncertain significance (Aug 02, 2023)
7-99487432-T-C		not specified	Uncertain significance (Feb 16, 2023)
7-99487448-T-C		not specified	Uncertain significance (Mar 16, 2022)
7-99493536-C-T		not specified	Uncertain significance (Oct 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF394	protein_coding	protein_coding	ENST00000337673	3	13806

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000224	0.908	125699	0	47	125746	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.211	310	321	0.967	0.0000173	3712
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000332	0.000328
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000170	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000229	0.000220
Middle Eastern	0.000170	0.000163
South Asian	0.000327	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0931

Intolerance Scores

• loftool: 0.737
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.49

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.322
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.868

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zkscan14
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding