ZNF555

zinc finger protein 555, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:2841437-2860471

Links

ENSG00000186300 ∙ NCBI:148254 ∙ ∙ HGNC:28382 ∙ Uniprot:Q8NEP9 ∙ 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 ZNF555 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF555 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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in ZNF555

This is a list of pathogenic ClinVar variants found in the ZNF555 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-2850609-T-C		not specified	Uncertain significance (May 30, 2024)
19-2850611-G-C		not specified	Uncertain significance (Feb 15, 2023)
19-2850692-T-C		not specified	Uncertain significance (Mar 31, 2022)
19-2851483-T-G		not specified	Uncertain significance (Dec 27, 2023)
19-2851555-C-T		not specified	Uncertain significance (Jan 16, 2024)
19-2851585-T-C		not specified	Uncertain significance (Mar 28, 2022)
19-2851620-G-T		not specified	Uncertain significance (Aug 21, 2023)
19-2852414-A-G		not specified	Uncertain significance (Sep 27, 2021)
19-2852451-A-G		not specified	Uncertain significance (Aug 02, 2021)
19-2852465-A-G		not specified	Uncertain significance (Aug 26, 2022)
19-2852510-G-A		not specified	Uncertain significance (Jul 20, 2021)
19-2852532-G-A		not specified	Likely benign (Dec 12, 2022)
19-2852681-G-C		not specified	Uncertain significance (Jun 10, 2024)
19-2852763-G-A		not specified	Uncertain significance (Apr 25, 2022)
19-2852952-C-G		not specified	Uncertain significance (Apr 17, 2023)
19-2852964-G-A		not specified	Uncertain significance (Jan 03, 2024)
19-2852967-G-A		not specified	Uncertain significance (Jan 17, 2024)
19-2852981-C-T		not specified	Uncertain significance (May 30, 2024)
19-2853006-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-2853216-G-A		not specified	Uncertain significance (Nov 27, 2023)
19-2853233-C-G		not specified	Uncertain significance (Oct 25, 2022)
19-2853244-G-C		not specified	Uncertain significance (Jan 23, 2023)
19-2853300-G-A		not specified	Uncertain significance (Nov 09, 2021)
19-2853306-A-G		not specified	Uncertain significance (Sep 27, 2022)
19-2853483-T-C		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF555	protein_coding	protein_coding	ENST00000334241	4	19050

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.74e-8	0.772	125651	0	97	125748	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.275	326	340	0.958	0.0000172	4159
Missense in Polyphen		116	144.36	0.80357		1801
Synonymous	0.518	116	123	0.941	0.00000663	1121
Loss of Function	1.38	14	20.8	0.673	0.00000127	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000572	0.000572
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.000326	0.000326
Finnish	0.00129	0.00129
European (Non-Finnish)	0.000273	0.000273
Middle Eastern	0.000326	0.000326
South Asian	0.000327	0.000327
Other	0.000652	0.000652

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: 0.966
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.67

Haploinsufficiency Scores

• pHI: 0.143
• hipred: N
• hipred_score: 0.112
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.611

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