ZNF416

zinc finger protein 416, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57571566-57578911

Links

ENSG00000083817 ∙ NCBI:55659 ∙ ∙ HGNC:20645 ∙ Uniprot:Q9BWM5 ∙ 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 ZNF416 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF416 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				1		1
missense			28	6		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	7	0

Variants in ZNF416

This is a list of pathogenic ClinVar variants found in the ZNF416 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57572144-T-C		not specified	Uncertain significance (Oct 22, 2024)
19-57572148-G-A		not specified	Likely benign (Apr 25, 2023)
19-57572195-T-G		not specified	Uncertain significance (Oct 12, 2022)
19-57572256-A-G		not specified	Uncertain significance (May 05, 2023)
19-57572371-T-A		not specified	Uncertain significance (Feb 12, 2025)
19-57572373-C-G		not specified	Likely benign (Jul 27, 2024)
19-57572398-A-C		not specified	Uncertain significance (Dec 17, 2024)
19-57572523-T-C		not specified	Uncertain significance (Mar 06, 2023)
19-57572712-C-A		not specified	Uncertain significance (Nov 14, 2024)
19-57572750-C-T		not specified	Uncertain significance (Feb 10, 2023)
19-57572786-T-C		not specified	Uncertain significance (Oct 11, 2024)
19-57572819-G-C		not specified	Uncertain significance (Apr 18, 2023)
19-57572870-C-G		not specified	Uncertain significance (Jul 05, 2024)
19-57572925-C-T		not specified	Uncertain significance (Apr 18, 2023)
19-57573038-C-T		not specified	Likely benign (Jul 12, 2023)
19-57573141-A-T		not specified	Uncertain significance (Feb 22, 2025)
19-57573171-T-A		not specified	Uncertain significance (Aug 28, 2023)
19-57573225-T-G		not specified	Uncertain significance (Jul 13, 2022)
19-57573286-C-G		not specified	Uncertain significance (Aug 04, 2024)
19-57573337-C-T			Likely benign (Jan 01, 2023)
19-57573363-G-C		not specified	Uncertain significance (Dec 27, 2023)
19-57573387-T-G		not specified	Uncertain significance (Jun 03, 2022)
19-57573420-A-G		not specified	Uncertain significance (Mar 01, 2024)
19-57573447-T-C		not specified	Likely benign (Jul 25, 2023)
19-57573461-G-C		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF416	protein_coding	protein_coding	ENST00000196489	4	7362

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.367	0.588	123203	0	1	123204	0.00000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.894	263	307	0.856	0.0000151	3951
Missense in Polyphen		47	82.088	0.57255		1117
Synonymous	-0.385	119	114	1.05	0.00000591	1082
Loss of Function	1.58	1	4.70	0.213	2.01e-7	52

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000907	0.00000907
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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)

Intolerance Scores

• loftool: 0.818
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.86

Haploinsufficiency Scores

• pHI: 0.0469
• hipred: N
• hipred_score: 0.112
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.248

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp418

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;metal ion binding