ZNF546

zinc finger protein 546, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:39984133-40021038

Previous symbols: [ "ZNF49" ]

Links

ENSG00000187187 ∙ NCBI:339327 ∙ ∙ HGNC:28671 ∙ Uniprot:Q86UE3 ∙ 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 ZNF546 gene.

• Inborn genetic diseases (20 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF546 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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	0

Variants in ZNF546

This is a list of pathogenic ClinVar variants found in the ZNF546 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-39998374-T-G		not specified	Uncertain significance (Oct 05, 2023)
19-40006099-C-T		not specified	Likely benign (Nov 14, 2023)
19-40006132-G-A		not specified	Uncertain significance (Dec 19, 2022)
19-40007329-G-T		not specified	Uncertain significance (Sep 29, 2023)
19-40008478-A-G		not specified	Uncertain significance (Dec 01, 2022)
19-40008500-C-A		not specified	Uncertain significance (Mar 24, 2023)
19-40008513-A-T		not specified	Uncertain significance (Apr 17, 2023)
19-40008526-T-C		not specified	Uncertain significance (Jul 12, 2023)
19-40013677-A-G		not specified	Uncertain significance (Mar 29, 2023)
19-40014061-A-T		not specified	Uncertain significance (Mar 31, 2023)
19-40014075-G-C		not specified	Uncertain significance (Jan 16, 2024)
19-40014104-T-G		not specified	Uncertain significance (Mar 04, 2024)
19-40014127-A-G		not specified	Uncertain significance (Dec 06, 2022)
19-40014178-G-A		not specified	Uncertain significance (Dec 12, 2023)
19-40014345-T-C		not specified	Uncertain significance (Dec 17, 2023)
19-40014565-G-A		not specified	Likely benign (Apr 08, 2022)
19-40014598-G-A		not specified	Uncertain significance (Jan 19, 2024)
19-40014607-G-A		not specified	Uncertain significance (Dec 21, 2023)
19-40014613-A-G		not specified	Uncertain significance (Nov 03, 2023)
19-40014637-T-C		not specified	Uncertain significance (Apr 26, 2023)
19-40014915-T-C		not specified	Uncertain significance (Oct 26, 2021)
19-40014951-G-T		not specified	Uncertain significance (Mar 01, 2024)
19-40014988-G-A		not specified	Uncertain significance (Oct 03, 2022)
19-40015026-T-C		not specified	Uncertain significance (Dec 22, 2023)
19-40015048-G-A		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF546	protein_coding	protein_coding	ENST00000347077	5	33474

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.02e-12	0.798	125226	0	521	125747	0.00207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.282	449	466	0.963	0.0000242	5580
Missense in Polyphen		45	52.613	0.8553		495
Synonymous	1.15	133	151	0.881	0.00000776	1467
Loss of Function	1.75	23	34.0	0.676	0.00000203	439

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00345	0.00344
Ashkenazi Jewish	0.00913	0.00917
East Asian	0.000840	0.000816
Finnish	0.000185	0.000185
European (Non-Finnish)	0.00199	0.00199
Middle Eastern	0.000840	0.000816
South Asian	0.00206	0.00206
Other	0.00311	0.00310

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.883
• rvis_EVS: 0.61
• rvis_percentile_EVS: 82.93

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.112
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0671

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp11

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;metal ion binding