ZNF260

zinc finger protein 260, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:36510687-36528271

Links

ENSG00000254004 ∙ NCBI:339324 ∙ OMIM:613749 ∙ HGNC:13499 ∙ Uniprot:Q3ZCT1 ∙ 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 ZNF260 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF260 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in ZNF260

This is a list of pathogenic ClinVar variants found in the ZNF260 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-36514160-T-C		not specified	Uncertain significance (Oct 05, 2023)
19-36514187-A-T		not specified	Uncertain significance (Jan 04, 2024)
19-36514217-A-T		not specified	Uncertain significance (Apr 22, 2024)
19-36514229-C-T		not specified	Uncertain significance (Mar 24, 2023)
19-36514328-T-C		not specified	Uncertain significance (May 26, 2023)
19-36514349-A-G		not specified	Uncertain significance (Dec 19, 2023)
19-36514520-C-T		not specified	Uncertain significance (Oct 03, 2022)
19-36514536-G-C		not specified	Uncertain significance (May 11, 2022)
19-36514539-T-C		not specified	Uncertain significance (Jan 27, 2022)
19-36514554-A-G		not specified	Uncertain significance (Apr 01, 2024)
19-36514746-C-T		not specified	Uncertain significance (Mar 14, 2023)
19-36514770-T-C		not specified	Uncertain significance (Mar 16, 2022)
19-36514790-T-C		not specified	Uncertain significance (Apr 24, 2023)
19-36514818-A-T		not specified	Uncertain significance (Sep 26, 2023)
19-36514826-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-36514838-T-G		not specified	Uncertain significance (Jan 09, 2024)
19-36514862-T-A		not specified	Uncertain significance (Jul 05, 2023)
19-36514893-C-G		not specified	Uncertain significance (Nov 14, 2023)
19-36514902-A-C		not specified	Uncertain significance (Feb 11, 2022)
19-36514916-T-C		not specified	Uncertain significance (Sep 29, 2022)
19-36514950-T-C		not specified	Uncertain significance (Dec 18, 2023)
19-36514967-G-T		not specified	Uncertain significance (Mar 31, 2024)
19-36515006-G-A		not specified	Uncertain significance (Feb 13, 2024)
19-36515120-T-G		not specified	Uncertain significance (May 15, 2024)
19-36515124-T-C		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF260	protein_coding	protein_coding	ENST00000523638	1	17966

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000602	0.722	125707	0	29	125736	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.612	179	204	0.879	0.00000939	2771
Missense in Polyphen		74	88.689	0.83438		1266
Synonymous	-0.0353	69	68.6	1.01	0.00000329	702
Loss of Function	1.01	8	11.7	0.683	6.56e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000456	0.000456
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000106
Middle Eastern	0.000163	0.000163
South Asian	0.0000980	0.0000980
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that acts as a cardiac regulator and an effector of alpha1-adrenergic signaling. Binds to PE response elements (PERE) present in the promoter of genes such as ANF/NPPA and acts as a direct transcriptional activator of NPPA. Also acts as a cofactor with GATA4, a key cardiac regulator (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.590
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.262
• hipred: N
• hipred_score: 0.248
• ghis: 0.645

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp260
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;multicellular organism development
• Cellular component: nucleoplasm;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding