ZNF417

zinc finger protein 417, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57900296-57916610

Links

ENSG00000173480 ∙ NCBI:147687 ∙ ∙ HGNC:20646 ∙ Uniprot:Q8TAU3 ∙ 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 ZNF417 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF417 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				3	1	4
missense			39	1	2	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	4	3

Variants in ZNF417

This is a list of pathogenic ClinVar variants found in the ZNF417 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57908563-C-T		not specified	Uncertain significance (Sep 21, 2023)
19-57908572-G-A		not specified	Uncertain significance (Jul 12, 2022)
19-57908587-A-G		not specified	Uncertain significance (Mar 15, 2024)
19-57908594-T-G		not specified	Uncertain significance (Jan 23, 2024)
19-57908695-G-A		not specified	Uncertain significance (Jun 24, 2022)
19-57908761-G-A		not specified	Uncertain significance (Aug 09, 2021)
19-57908765-A-G		not specified	Uncertain significance (Sep 28, 2021)
19-57908774-G-T		not specified	Uncertain significance (May 17, 2023)
19-57908806-G-A		not specified	Uncertain significance (May 01, 2022)
19-57908853-A-G			Benign (Dec 31, 2019)
19-57908866-T-G		not specified	Uncertain significance (Jan 23, 2023)
19-57908884-G-A		not specified	Uncertain significance (Nov 10, 2021)
19-57908885-C-T		not specified	Uncertain significance (Jan 07, 2022)
19-57908921-C-T		not specified	Uncertain significance (Nov 29, 2023)
19-57908933-A-G		not specified	Uncertain significance (Jun 05, 2023)
19-57908986-G-A		not specified	Uncertain significance (Jul 15, 2021)
19-57909000-G-A			Likely benign (Feb 01, 2023)
19-57909076-C-T		not specified	Uncertain significance (Dec 16, 2023)
19-57909118-T-C		not specified	Uncertain significance (Jan 23, 2023)
19-57909120-T-C			Likely benign (Feb 01, 2023)
19-57909134-A-G		not specified	Uncertain significance (Jun 22, 2021)
19-57909164-G-A		not specified	Uncertain significance (Mar 06, 2023)
19-57909176-T-C		not specified	Uncertain significance (May 11, 2022)
19-57909188-T-C		not specified	Uncertain significance (Apr 19, 2024)
19-57909191-G-C		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF417	protein_coding	protein_coding	ENST00000312026	3	16315

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00675	0.537	125182	0	563	125745	0.00224

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.296	307	293	1.05	0.0000149	3777
Missense in Polyphen		89	86.368	1.0305		1227
Synonymous	0.607	97	105	0.925	0.00000558	1030
Loss of Function	0.0398	3	3.08	0.976	1.31e-7	33

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00336	0.00336
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.00	0.00
Finnish	0.000326	0.000323
European (Non-Finnish)	0.00386	0.00380
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00335	0.00326

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: 0.0790

Intolerance Scores

• loftool: 0.953
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.19

Haploinsufficiency Scores

• pHI: 0.0980
• hipred: N
• hipred_score: 0.187
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.408

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