ZNF687

zinc finger protein 687, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 1:151281618-151292176

Links

ENSG00000143373 ∙ NCBI:57592 ∙ OMIM:610568 ∙ HGNC:29277 ∙ Uniprot:Q8N1G0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Paget disease of bone 6 (Limited), mode of inheritance: AD
• Paget disease of bone 6 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Paget disease of bone 6	AD	Oncologic	The condition can involve malignant giant cell tumors (GCT) of the bone arising from within the Paget bone lesions, and awareness may allow early detection and management	Musculoskeletal; Oncologic	26849110

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF687 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF687 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	105	10	116
missense			230	8	7	245
nonsense			2			2
start loss						0
frameshift			4			4
inframe indel			8		1	9
splice donor/acceptor (+/-2bp)						0
splice region			5	6	1	12
non coding				20	2	22
Total	0	0	245	133	20

Variants in ZNF687

This is a list of pathogenic ClinVar variants found in the ZNF687 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151286307-A-G		not specified	Uncertain significance (Oct 12, 2021)
1-151286308-C-A		not specified	Uncertain significance (Aug 12, 2021)
1-151286309-C-T			Likely benign (Jan 30, 2025)
1-151286360-G-A			Likely benign (Apr 21, 2023)
1-151286367-G-A		not specified	Uncertain significance (Mar 22, 2023)
1-151286378-T-C			Likely benign (May 16, 2023)
1-151286430-G-A			Uncertain significance (Oct 17, 2022)
1-151286458-C-T		not specified	Uncertain significance (Apr 07, 2023)
1-151286499-T-G		not specified	Uncertain significance (Mar 04, 2023)
1-151286502-G-T		not specified	Uncertain significance (Dec 17, 2021)
1-151286510-C-T			Likely benign (May 09, 2024)
1-151286515-C-T		not specified	Uncertain significance (Nov 08, 2024)
1-151286516-A-G		ZNF687-related disorder	Likely benign (Dec 27, 2023)
1-151286518-C-T		not specified	Uncertain significance (Apr 03, 2023)
1-151286519-G-A			Likely benign (Feb 22, 2023)
1-151286535-G-T			Uncertain significance (Mar 12, 2024)
1-151286538-A-T		not specified	Uncertain significance (May 24, 2023)
1-151286567-C-T		ZNF687-related disorder	Benign (Jan 31, 2024)
1-151286576-T-C			Likely benign (Jan 15, 2023)
1-151286579-GG-AC			Uncertain significance (Mar 12, 2024)
1-151286607-G-A			Uncertain significance (Dec 07, 2022)
1-151286612-C-T			Likely benign (Dec 10, 2022)
1-151286625-G-A			Uncertain significance (Jul 12, 2022)
1-151286637-G-A			Benign/Likely benign (Jan 07, 2024)
1-151286655-C-T			Uncertain significance (Nov 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF687	protein_coding	protein_coding	ENST00000324048	8	10563

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.971	0.0290	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.81	609	748	0.814	0.0000443	7961
Missense in Polyphen		149	257.17	0.57939		2750
Synonymous	-1.37	325	295	1.10	0.0000168	2716
Loss of Function	4.52	5	33.0	0.152	0.00000164	411

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000970	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000104	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Disease: DISEASE: Paget disease of bone 6 (PDB6) [MIM:616833]: An autosomal dominant form of Paget disease, a disorder of bone remodeling characterized by increased bone turnover affecting one or more sites throughout the skeleton, primarily the axial skeleton. Osteoclastic overactivity followed by compensatory osteoblastic activity leads to a structurally disorganized mosaic of bone (woven bone), which is mechanically weaker, larger, less compact, more vascular, and more susceptible to fracture than normal adult lamellar bone. PDB6 is characterized by adult onset of bone pain associated with polyostotic bone lesions primarily affecting the axial skeleton. In some cases, the pagetic tissue undergoes neoplastic transformation, resulting in osteosarcoma and, less frequently, in giant cell tumor of bone. {ECO:0000269|PubMed:26849110}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.382
• rvis_EVS: -0.81
• rvis_percentile_EVS: 12.08

Haploinsufficiency Scores

• pHI: 0.331
• hipred: Y
• hipred_score: 0.572
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp687

Gene ontology

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