ZNF415

zinc finger protein 415, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:53107879-53133077

Links

ENSG00000170954 ∙ NCBI:55786 ∙ OMIM:619506 ∙ HGNC:20636 ∙ Uniprot:Q09FC8 ∙ 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 ZNF415 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF415 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			50	3		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	54	3	0

Variants in ZNF415

This is a list of pathogenic ClinVar variants found in the ZNF415 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-53108387-T-C		not specified	Uncertain significance (Feb 28, 2024)
19-53108396-T-G		not specified	Uncertain significance (Apr 01, 2024)
19-53108405-G-C		not specified	Uncertain significance (Feb 26, 2024)
19-53108415-T-C		not specified	Uncertain significance (Jan 11, 2023)
19-53108416-T-G		not specified	Uncertain significance (Jul 07, 2024)
19-53108439-G-A		not specified	Uncertain significance (Dec 06, 2024)
19-53108493-G-A		not specified	Uncertain significance (Jun 11, 2021)
19-53108543-C-T		not specified	Uncertain significance (Jan 19, 2025)
19-53108591-G-A		not specified	Uncertain significance (May 11, 2022)
19-53108624-C-A		not specified	Uncertain significance (Sep 22, 2023)
19-53108696-C-A		not specified	Uncertain significance (Mar 10, 2025)
19-53108713-C-G		not specified	Uncertain significance (Jun 21, 2021)
19-53108723-T-C		not specified	Uncertain significance (Sep 16, 2021)
19-53108734-C-A		not specified	Uncertain significance (Sep 29, 2022)
19-53108744-T-C		not specified	Uncertain significance (Feb 07, 2023)
19-53108795-C-T		not specified	Uncertain significance (May 10, 2022)
19-53108837-C-G		not specified	Uncertain significance (Jul 19, 2022)
19-53108880-A-T		not specified	Uncertain significance (Jul 02, 2024)
19-53108898-G-T		not specified	Uncertain significance (Nov 08, 2022)
19-53108916-T-C		not specified	Uncertain significance (May 23, 2023)
19-53108942-G-T		not specified	Uncertain significance (Sep 04, 2024)
19-53108949-T-C		not specified	Uncertain significance (Sep 16, 2021)
19-53108957-T-C		not specified	Uncertain significance (Jun 23, 2023)
19-53108973-A-G		not specified	Uncertain significance (Jul 15, 2021)
19-53108994-T-C		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF415	protein_coding	protein_coding	ENST00000500065	3	25199

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.217	0.658	100833	0	2	100835	0.00000992

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.784	261	299	0.872	0.0000153	3704
Missense in Polyphen		73	86.65	0.84247		1183
Synonymous	0.361	100	105	0.955	0.00000532	982
Loss of Function	1.07	1	2.99	0.335	1.28e-7	32

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000126	0.000126
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000126	0.000126
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in transcriptional regulation. Transcriptional activity differed among the various isoforms. All isoforms except isoform 3 seem to suppresses the transcriptional activities of AP- 1 and p53/TP53. {ECO:0000269|PubMed:17055453}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0892

Intolerance Scores

• loftool: 0.900
• rvis_EVS: 1.56
• rvis_percentile_EVS: 95.66

Haploinsufficiency Scores

• pHI: 0.0868
• hipred: N
• hipred_score: 0.112
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0945

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
• Cellular component: fibrillar center;nucleus;cytoplasm;microtubule cytoskeleton
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding