ZNF419

zinc finger protein 419, the group of Zinc fingers C2H2-type|Minor histocompatibility antigens

Basic information

Region (hg38): 19:57487711-57496098

Previous symbols: [ "ZNF419A" ]

Links

ENSG00000105136 ∙ NCBI:79744 ∙ OMIM:617410 ∙ HGNC:20648 ∙ Uniprot:Q96HQ0 ∙ 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 ZNF419 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF419 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			30	2	1	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	2

Variants in ZNF419

This is a list of pathogenic ClinVar variants found in the ZNF419 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57487964-C-T		not specified	Uncertain significance (Jun 16, 2024)
19-57487969-A-G		not specified	Uncertain significance (Dec 15, 2022)
19-57491471-G-T		Malignant tumor of prostate	Uncertain significance (-)
19-57491486-G-C		not specified	Uncertain significance (Jul 13, 2022)
19-57491489-G-T		not specified	Uncertain significance (Mar 21, 2023)
19-57491527-G-T		not specified	Uncertain significance (Mar 29, 2024)
19-57491537-G-A		not specified	Likely benign (May 08, 2024)
19-57491553-A-C		not specified	Uncertain significance (Jul 14, 2021)
19-57491564-A-G		not specified	Uncertain significance (Oct 02, 2023)
19-57492134-A-G		not specified	Uncertain significance (Dec 12, 2022)
19-57492206-C-T		not specified	Uncertain significance (Mar 23, 2023)
19-57492888-C-T		not specified	Uncertain significance (Dec 09, 2023)
19-57492891-G-C		not specified	Uncertain significance (Oct 21, 2024)
19-57493012-T-A		not specified	Uncertain significance (Apr 25, 2022)
19-57493021-C-T		not specified	Uncertain significance (Feb 17, 2023)
19-57493051-G-A		not specified	Uncertain significance (Jul 11, 2022)
19-57493141-C-T		not specified	Uncertain significance (Mar 30, 2024)
19-57493231-A-G		not specified	Uncertain significance (Jan 31, 2024)
19-57493253-A-G			Benign (Jan 11, 2018)
19-57493257-A-G		not specified	Uncertain significance (Aug 12, 2024)
19-57493282-A-G		not specified	Uncertain significance (Jul 09, 2021)
19-57493283-T-G		not specified	Uncertain significance (Feb 10, 2022)
19-57493344-A-G		not specified	Likely benign (Dec 17, 2023)
19-57493365-C-T		not specified	Uncertain significance (Aug 02, 2022)
19-57493413-C-G		not specified	Uncertain significance (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF419	protein_coding	protein_coding	ENST00000424930	5	6970

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00533	0.726	125629	0	119	125748	0.000473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.79	345	263	1.31	0.0000125	3392
Missense in Polyphen		100	82.986	1.205		1082
Synonymous	-1.80	114	92.1	1.24	0.00000450	903
Loss of Function	0.772	4	6.05	0.661	2.57e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00390	0.00369
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000388	0.000387
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000500	0.000489

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: 0.0847

Intolerance Scores

• loftool: 0.994
• rvis_EVS: 1.58
• rvis_percentile_EVS: 95.77

Haploinsufficiency Scores

• pHI: 0.227
• hipred: N
• hipred_score: 0.112
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.516

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: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding