ZNF660

zinc finger protein 660, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 3:44578222-44599694

Links

ENSG00000144792 ∙ NCBI:285349 ∙ ∙ HGNC:26720 ∙ Uniprot:Q6AZW8 ∙ 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 ZNF660 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF660 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in ZNF660

This is a list of pathogenic ClinVar variants found in the ZNF660 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-44594292-G-T		not specified	Uncertain significance (Feb 26, 2024)
3-44594320-G-C		not specified	Uncertain significance (Aug 20, 2023)
3-44594402-G-A		not specified	Uncertain significance (Feb 28, 2024)
3-44594521-G-C		not specified	Uncertain significance (Nov 07, 2022)
3-44594560-C-T		not specified	Uncertain significance (Jul 19, 2023)
3-44594627-G-A		not specified	Uncertain significance (Dec 07, 2021)
3-44594662-A-G		not specified	Uncertain significance (Jun 16, 2024)
3-44594686-A-G		not specified	Uncertain significance (Apr 24, 2024)
3-44594687-T-C		not specified	Uncertain significance (Aug 26, 2022)
3-44594730-A-C		not specified	Uncertain significance (Oct 12, 2021)
3-44594731-C-T		not specified	Uncertain significance (Nov 30, 2021)
3-44594776-T-C		not specified	Uncertain significance (Jan 04, 2024)
3-44594833-G-A		not specified	Uncertain significance (Jan 18, 2023)
3-44594842-C-G		not specified	Uncertain significance (Jul 26, 2022)
3-44594855-A-C		not specified	Uncertain significance (Oct 29, 2021)
3-44594857-G-A		not specified	Uncertain significance (Dec 22, 2023)
3-44594874-C-A		not specified	Uncertain significance (Dec 22, 2023)
3-44594914-C-T			Uncertain significance (May 03, 2020)
3-44594915-G-A		not specified	Uncertain significance (Nov 08, 2021)
3-44594973-C-G		not specified	Uncertain significance (May 17, 2023)
3-44595063-T-G		not specified	Uncertain significance (Dec 30, 2023)
3-44595179-A-C		not specified	Uncertain significance (Jun 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF660	protein_coding	protein_coding	ENST00000322734	1	21472

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.31e-7	0.222	124705	3	1039	125747	0.00415

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.451	161	178	0.905	0.00000907	2212
Missense in Polyphen		67	70.541	0.9498		879
Synonymous	-0.201	62	60.0	1.03	0.00000288	584
Loss of Function	0.136	10	10.5	0.955	6.70e-7	154

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00412	0.00412
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.000326	0.000272
Finnish	0.00278	0.00278
European (Non-Finnish)	0.00708	0.00707
Middle Eastern	0.000326	0.000272
South Asian	0.000490	0.000490
Other	0.00473	0.00473

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: 0.701
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.228
• hipred: N
• hipred_score: 0.168
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.136

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