ZNF19

zinc finger protein 19, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 16:71464554-71565089

Links

ENSG00000157429 ∙ NCBI:7567 ∙ OMIM:194525 ∙ HGNC:12981 ∙ Uniprot:P17023 ∙ 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 ZNF19 gene.

• Inborn genetic diseases (16 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF19 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in ZNF19

This is a list of pathogenic ClinVar variants found in the ZNF19 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-71475211-G-T		not specified	Uncertain significance (Sep 17, 2021)
16-71475270-G-A		not specified	Uncertain significance (Jul 25, 2023)
16-71475369-G-T		not specified	Uncertain significance (Sep 22, 2023)
16-71475576-G-A		not specified	Uncertain significance (Jul 05, 2022)
16-71475678-C-T		not specified	Uncertain significance (Oct 04, 2022)
16-71475738-T-A		not specified	Uncertain significance (Jul 25, 2023)
16-71475781-T-C		not specified	Uncertain significance (Mar 04, 2024)
16-71475834-A-G		not specified	Uncertain significance (May 17, 2023)
16-71475931-G-A		not specified	Uncertain significance (Dec 07, 2021)
16-71476015-T-C		not specified	Uncertain significance (Dec 19, 2022)
16-71476047-C-T		not specified	Uncertain significance (Aug 08, 2022)
16-71476068-G-C		not specified	Uncertain significance (Jun 28, 2022)
16-71476073-C-T			Likely benign (Jun 01, 2022)
16-71476108-T-A		not specified	Uncertain significance (Aug 12, 2022)
16-71476111-T-C		not specified	Uncertain significance (Dec 05, 2022)
16-71476168-T-C		not specified	Uncertain significance (Oct 14, 2023)
16-71476195-C-T		not specified	Uncertain significance (Nov 17, 2022)
16-71476216-T-C		not specified	Uncertain significance (Oct 25, 2022)
16-71478323-G-T		not specified	Uncertain significance (Jul 20, 2022)
16-71478990-C-T		not specified	Uncertain significance (Oct 05, 2022)
16-71482086-T-A		not specified	Uncertain significance (Feb 02, 2024)
16-71536745-T-A		not specified	Uncertain significance (Oct 12, 2022)
16-71536792-C-G		not specified	Likely benign (Nov 09, 2021)
16-71536802-G-A		not specified	Likely benign (Aug 12, 2021)
16-71536810-G-A		not specified	Uncertain significance (Aug 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF19	protein_coding	protein_coding	ENST00000288177	4	100540

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000431	0.634	125684	0	64	125748	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.125	249	243	1.02	0.0000117	3052
Missense in Polyphen		50	61.366	0.81478		814
Synonymous	-0.0436	86	85.5	1.01	0.00000404	833
Loss of Function	0.954	10	13.8	0.723	6.63e-7	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000724	0.000601
Ashkenazi Jewish	0.00	0.00
East Asian	0.00190	0.00190
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000705	0.0000703
Middle Eastern	0.00190	0.00190
South Asian	0.000131	0.000131
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)

Recessive Scores

• pRec: 0.0789

Intolerance Scores

• loftool: 0.780
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.343
• hipred: N
• hipred_score: 0.112
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0822

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