ZNF418

zinc finger protein 418, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57921882-57935402

Links

ENSG00000196724 ∙ NCBI:147686 ∙ OMIM:619509 ∙ HGNC:20647 ∙ Uniprot:Q8TF45 ∙ 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 ZNF418 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF418 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			56	4		60
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	5	0

Variants in ZNF418

This is a list of pathogenic ClinVar variants found in the ZNF418 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57926182-T-C		not specified	Uncertain significance (Mar 19, 2024)
19-57926188-G-A		not specified	Uncertain significance (Aug 21, 2023)
19-57926205-C-G		not specified	Uncertain significance (Jan 03, 2022)
19-57926208-C-T		not specified	Uncertain significance (Jan 03, 2022)
19-57926235-C-A		not specified	Uncertain significance (May 23, 2023)
19-57926238-T-A		not specified	Uncertain significance (Jul 30, 2024)
19-57926311-A-G		not specified	Uncertain significance (Nov 18, 2022)
19-57926337-C-T		not specified	Uncertain significance (Oct 21, 2024)
19-57926343-T-C		not specified	Uncertain significance (Feb 14, 2025)
19-57926380-T-G		not specified	Uncertain significance (Jul 30, 2024)
19-57926386-T-C		not specified	Uncertain significance (Feb 20, 2025)
19-57926401-T-A		not specified	Uncertain significance (Apr 06, 2024)
19-57926403-C-T		not specified	Uncertain significance (Feb 07, 2025)
19-57926424-G-A		Moyamoya angiopathy	Likely pathogenic (-)
19-57926595-C-T		not specified	Likely benign (Nov 21, 2024)
19-57926598-T-C		not specified	Uncertain significance (Jan 23, 2024)
19-57926601-C-T		not specified	Uncertain significance (Dec 12, 2023)
19-57926614-A-G		not specified	Uncertain significance (Jul 16, 2024)
19-57926642-A-T		not specified	Uncertain significance (Jan 17, 2025)
19-57926686-C-T		not specified	Likely benign (Apr 19, 2023)
19-57926722-A-G		not specified	Uncertain significance (Feb 07, 2023)
19-57926770-C-T		not specified	Uncertain significance (May 25, 2022)
19-57926817-T-G		not specified	Uncertain significance (Feb 10, 2025)
19-57926844-C-T		not specified	Uncertain significance (Sep 29, 2023)
19-57926862-T-C		not specified	Uncertain significance (Aug 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF418	protein_coding	protein_coding	ENST00000396147	3	13510

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00e-9	0.0916	125594	1	152	125747	0.000609

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.368	367	348	1.06	0.0000181	4467
Missense in Polyphen		127	119.6	1.0619		1519
Synonymous	-0.587	129	121	1.07	0.00000621	1218
Loss of Function	0.0659	14	14.3	0.981	7.86e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00527	0.00510
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000331	0.000325
Middle Eastern	0.00	0.00
South Asian	0.000265	0.000261
Other	0.00168	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor. {ECO:0000269|Ref.1}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.963
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.16

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.112
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.724

Gene Damage Prediction

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

Gene ontology

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