ZNF664

zinc finger protein 664, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 12:123971844-124015439

Previous symbols: [ "ZNF176" ]

Links

ENSG00000179195 ∙ NCBI:144348 ∙ OMIM:617890 ∙ HGNC:25406 ∙ Uniprot:Q8N3J9 ∙ 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 ZNF664 gene.

• Inborn genetic diseases (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF664 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		1
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in ZNF664

This is a list of pathogenic ClinVar variants found in the ZNF664 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-124012355-A-G		not specified	Uncertain significance (Nov 21, 2022)
12-124012361-A-C		not specified	Uncertain significance (Feb 27, 2024)
12-124012681-G-A			Likely benign (Apr 01, 2023)
12-124012885-A-C		not specified	Uncertain significance (Dec 06, 2022)
12-124012925-A-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF664	protein_coding	protein_coding	ENST00000539644	1	43595

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00133	0.669	125677	0	59	125736	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.42	57	137	0.417	0.00000663	1773
Missense in Polyphen		17	50.793	0.33469		667
Synonymous	-1.64	63	48.4	1.30	0.00000266	420
Loss of Function	0.688	5	6.96	0.719	2.99e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00408	0.00408
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.424
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.250
• hipred: N
• hipred_score: 0.483
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.450

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp664

Gene ontology

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