ZNF556

zinc finger protein 556, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:2867335-2883445

Links

ENSG00000172000 ∙ NCBI:80032 ∙ ∙ HGNC:25669 ∙ Uniprot:Q9HAH1 ∙ 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 ZNF556 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF556 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			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	0

Variants in ZNF556

This is a list of pathogenic ClinVar variants found in the ZNF556 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-2873551-T-C		not specified	Uncertain significance (Jun 06, 2023)
19-2873572-A-G		not specified	Uncertain significance (Aug 21, 2023)
19-2873609-C-G		not specified	Uncertain significance (Sep 16, 2021)
19-2876125-A-C		not specified	Uncertain significance (Aug 12, 2021)
19-2876260-A-G		not specified	Uncertain significance (Feb 21, 2024)
19-2877298-T-C		not specified	Uncertain significance (Sep 29, 2023)
19-2877323-G-A		not specified	Uncertain significance (Mar 22, 2023)
19-2877358-C-T		not specified	Uncertain significance (Apr 16, 2024)
19-2877368-G-A		not specified	Uncertain significance (May 30, 2024)
19-2877395-G-A		not specified	Uncertain significance (Dec 26, 2023)
19-2877515-G-A		not specified	Uncertain significance (Apr 17, 2024)
19-2877520-T-G		not specified	Uncertain significance (Nov 14, 2023)
19-2877521-C-T		not specified	Uncertain significance (Jun 03, 2022)
19-2877566-A-G		not specified	Uncertain significance (Feb 16, 2023)
19-2877583-G-A		not specified	Uncertain significance (Jul 16, 2021)
19-2877698-G-A		not specified	Uncertain significance (Jul 12, 2022)
19-2877746-A-G		not specified	Uncertain significance (Jan 04, 2022)
19-2877815-C-A		not specified	Uncertain significance (Feb 06, 2023)
19-2877830-A-T		not specified	Uncertain significance (Aug 12, 2021)
19-2877884-A-G		not specified	Uncertain significance (Nov 14, 2023)
19-2877902-A-G		not specified	Uncertain significance (Nov 19, 2022)
19-2877925-G-C		not specified	Uncertain significance (Apr 01, 2022)
19-2877934-T-C		not specified	Uncertain significance (Dec 17, 2023)
19-2877959-C-T		not specified	Likely benign (Aug 21, 2023)
19-2877965-C-T		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF556	protein_coding	protein_coding	ENST00000307635	4	11183

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000925	0.354	124989	1	757	125747	0.00302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.776	294	259	1.14	0.0000148	2994
Missense in Polyphen		89	68.754	1.2945		871
Synonymous	-2.23	132	103	1.28	0.00000697	844
Loss of Function	-0.0193	6	5.95	1.01	2.52e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00164	0.00161
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000886	0.000878
European (Non-Finnish)	0.00577	0.00554
Middle Eastern	0.0000544	0.0000544
South Asian	0.00226	0.00190
Other	0.00264	0.00228

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: 0.697
• rvis_EVS: 1.45
• rvis_percentile_EVS: 95.14

Haploinsufficiency Scores

• pHI: 0.0464
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.948

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;metal ion binding