ZNF554

zinc finger protein 554, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:2819868-2836735

Links

ENSG00000172006 ∙ NCBI:115196 ∙ ∙ HGNC:26629 ∙ Uniprot:Q86TJ5 ∙ 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 ZNF554 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF554 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			43	1		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	2	0

Variants in ZNF554

This is a list of pathogenic ClinVar variants found in the ZNF554 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-2820089-C-G		not specified	Uncertain significance (May 21, 2024)
19-2820115-C-G		not specified	Uncertain significance (May 31, 2023)
19-2823042-C-T		not specified	Uncertain significance (Dec 22, 2023)
19-2823045-C-T		not specified	Uncertain significance (Mar 20, 2023)
19-2823077-A-G		not specified	Uncertain significance (Nov 26, 2024)
19-2823087-C-G		not specified	Uncertain significance (Feb 16, 2023)
19-2823102-G-C		not specified	Likely benign (Feb 12, 2025)
19-2827664-G-T		not specified	Uncertain significance (Aug 12, 2024)
19-2832312-A-C		not specified	Uncertain significance (Jun 22, 2023)
19-2832330-T-G		not specified	Uncertain significance (Oct 29, 2021)
19-2832383-C-T		not specified	Uncertain significance (Feb 22, 2025)
19-2832392-T-C		not specified	Uncertain significance (Oct 23, 2024)
19-2832426-C-T		not specified	Uncertain significance (Oct 02, 2023)
19-2833815-G-A		not specified	Uncertain significance (May 07, 2024)
19-2833876-A-G		not specified	Uncertain significance (Jan 29, 2024)
19-2833903-G-A		not specified	Uncertain significance (Feb 05, 2025)
19-2833915-A-G		not specified	Uncertain significance (Sep 16, 2021)
19-2833975-G-A		not specified	Uncertain significance (Feb 27, 2025)
19-2833984-A-G		not specified	Uncertain significance (Jan 16, 2024)
19-2834082-C-T		not specified	Uncertain significance (Nov 07, 2024)
19-2834095-A-C		not specified	Uncertain significance (Dec 24, 2024)
19-2834115-A-C		not specified	Uncertain significance (Feb 20, 2025)
19-2834116-A-G		not specified	Uncertain significance (May 31, 2023)
19-2834128-A-G		not specified	Uncertain significance (Jan 09, 2025)
19-2834157-G-A		not specified	Likely benign (Dec 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF554	protein_coding	protein_coding	ENST00000317243	5	15900

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.72e-10	0.324	125521	0	180	125701	0.000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.134	282	288	0.978	0.0000157	3526
Missense in Polyphen		85	98.409	0.86374		1122
Synonymous	0.319	113	117	0.963	0.00000733	989
Loss of Function	0.894	17	21.5	0.792	0.00000110	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00233	0.00231
Ashkenazi Jewish	0.00141	0.00139
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000644	0.000642
Middle Eastern	0.000110	0.000109
South Asian	0.000492	0.000457
Other	0.000825	0.000815

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: 0.715
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.24

Haploinsufficiency Scores

• pHI: 0.147
• 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: 0.225

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