ZNF688

zinc finger protein 688, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 16:30569671-30572734

Links

ENSG00000229809 ∙ NCBI:146542 ∙ ∙ HGNC:30489 ∙ Uniprot:P0C7X2 ∙ 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 ZNF688 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF688 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in ZNF688

This is a list of pathogenic ClinVar variants found in the ZNF688 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30569971-C-T		not specified	Uncertain significance (May 08, 2023)
16-30570104-C-G		not specified	Uncertain significance (Jun 21, 2022)
16-30570175-C-T		not specified	Uncertain significance (May 06, 2024)
16-30570203-G-T		not specified	Uncertain significance (Oct 26, 2022)
16-30570235-A-G		not specified	Uncertain significance (Dec 22, 2023)
16-30570259-G-A		not specified	Uncertain significance (May 08, 2023)
16-30570286-G-C		not specified	Uncertain significance (Aug 03, 2022)
16-30570307-G-A		not specified	Uncertain significance (Oct 14, 2023)
16-30570341-C-T		not specified	Uncertain significance (Feb 03, 2023)
16-30571015-C-T		not specified	Uncertain significance (Oct 25, 2022)
16-30571074-A-C		not specified	Uncertain significance (Mar 13, 2023)
16-30571076-T-C		not specified	Uncertain significance (May 12, 2024)
16-30571081-T-G		not specified	Uncertain significance (Apr 26, 2024)
16-30571490-T-G		not specified	Uncertain significance (Jul 11, 2023)
16-30571571-C-A		not specified	Uncertain significance (Oct 26, 2021)
16-30571587-C-T		not specified	Uncertain significance (May 18, 2022)
16-30571604-A-C		not specified	Uncertain significance (Jun 18, 2021)
16-30571616-G-C		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF688	protein_coding	protein_coding	ENST00000223459	3	3389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000700	0.297	125691	0	26	125717	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.848	150	182	0.823	0.0000123	1745
Missense in Polyphen		46	72.576	0.63381		711
Synonymous	1.58	56	73.1	0.766	0.00000476	588
Loss of Function	0.107	8	8.33	0.960	3.55e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000324	0.000323
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000958	0.0000924
European (Non-Finnish)	0.0000905	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000981	0.0000980
Other	0.00	0.00

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: 0.740
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.180
• ghis: 0.627

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.786

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp688

Gene ontology

• Biological process: regulation of transcription, DNA-templated;biological_process
• Cellular component: cellular_component;nucleus
• Molecular function: molecular_function;DNA binding;metal ion binding