ZNF880

zinc finger protein 880, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:52369917-52385795

Links

ENSG00000221923 ∙ NCBI:400713 ∙ ∙ HGNC:37249 ∙ Uniprot:Q6PDB4 ∙ 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 ZNF880 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF880 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				2		2
missense			54	2		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	4	0

Variants in ZNF880

This is a list of pathogenic ClinVar variants found in the ZNF880 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-52369969-C-G		not specified	Uncertain significance (Jan 26, 2022)
19-52373139-T-C		not specified	Uncertain significance (Oct 07, 2024)
19-52373141-G-A		not specified	Uncertain significance (Feb 06, 2023)
19-52373151-A-G		not specified	Uncertain significance (May 05, 2023)
19-52373173-C-A		not specified	Uncertain significance (Aug 22, 2023)
19-52373210-G-A		not specified	Uncertain significance (Jan 22, 2024)
19-52374302-T-C		not specified	Uncertain significance (Feb 17, 2022)
19-52374310-C-T		not specified	Uncertain significance (Apr 09, 2022)
19-52374355-C-T		not specified	Likely benign (Feb 27, 2023)
19-52374361-C-G		not specified	Uncertain significance (May 05, 2023)
19-52374423-C-T			Likely benign (Oct 01, 2022)
19-52383960-A-G		not specified	Uncertain significance (Apr 18, 2023)
19-52383983-G-A		not specified	Uncertain significance (Feb 07, 2023)
19-52384035-G-C		not specified	Likely benign (May 09, 2023)
19-52384061-T-C		not specified	Uncertain significance (Oct 26, 2022)
19-52384126-A-C		not specified	Uncertain significance (Jul 17, 2024)
19-52384127-C-T		not specified	Uncertain significance (Nov 18, 2023)
19-52384141-T-G		not specified	Uncertain significance (Jan 30, 2024)
19-52384148-G-A		not specified	Uncertain significance (May 15, 2024)
19-52384197-A-C		not specified	Uncertain significance (Nov 14, 2024)
19-52384206-A-G		not specified	Uncertain significance (Dec 13, 2023)
19-52384208-A-C		not specified	Uncertain significance (Dec 23, 2024)
19-52384220-T-A		not specified	Uncertain significance (Mar 21, 2023)
19-52384232-G-A		not specified	Uncertain significance (Dec 28, 2023)
19-52384259-C-A		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF880	protein_coding	protein_coding	ENST00000422689	4	15879

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00291	0.598	125707	0	13	125720	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.239	272	283	0.960	0.0000131	3781
Missense in Polyphen		74	86.611	0.85439		1207
Synonymous	1.35	81	98.0	0.827	0.00000467	974
Loss of Function	0.396	4	4.95	0.808	2.09e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000494	0.000493
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000913	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.784
• rvis_EVS: 1.95
• rvis_percentile_EVS: 97.53

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.148
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
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;nucleic acid binding;metal ion binding