ZNF654

zinc finger protein 654, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 3:88059255-88144660

Links

ENSG00000175105 ∙ NCBI:55279 ∙ ∙ HGNC:25612 ∙ Uniprot:Q8IZM8 ∙ 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 ZNF654 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF654 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			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in ZNF654

This is a list of pathogenic ClinVar variants found in the ZNF654 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-88139375-A-C		not specified	Uncertain significance (Jul 12, 2023)
3-88139396-T-C		not specified	Uncertain significance (Jul 05, 2023)
3-88139477-T-C		not specified	Uncertain significance (Feb 15, 2023)
3-88139584-G-C		not specified	Uncertain significance (Jan 22, 2024)
3-88139600-C-T		not specified	Uncertain significance (Apr 12, 2022)
3-88139605-T-C		not specified	Uncertain significance (Dec 22, 2023)
3-88139639-A-G		not specified	Uncertain significance (Apr 17, 2024)
3-88139699-T-C		not specified	Uncertain significance (Feb 17, 2024)
3-88139836-G-A		not specified	Likely benign (Jul 12, 2023)
3-88139848-A-G		not specified	Uncertain significance (Aug 08, 2023)
3-88139986-A-G		not specified	Uncertain significance (Jun 11, 2024)
3-88140019-T-G		not specified	Uncertain significance (Mar 01, 2023)
3-88140089-A-G		not specified	Uncertain significance (Dec 20, 2023)
3-88140403-G-T		not specified	Uncertain significance (Dec 22, 2023)
3-88140430-T-A		not specified	Uncertain significance (Nov 29, 2021)
3-88140449-G-A		not specified	Uncertain significance (Dec 17, 2023)
3-88140458-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-88140469-A-G		not specified	Uncertain significance (Sep 27, 2021)
3-88140515-C-T		not specified	Uncertain significance (Dec 18, 2023)
3-88140553-G-A		not specified	Uncertain significance (Jan 08, 2024)
3-88140557-T-C		not specified	Uncertain significance (May 02, 2024)
3-88140596-T-C		not specified	Uncertain significance (Jun 09, 2022)
3-88140647-C-T		not specified	Uncertain significance (Mar 08, 2024)
3-88140744-G-C		not specified	Uncertain significance (Oct 04, 2022)
3-88140811-G-A		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF654	protein_coding	protein_coding	ENST00000309495	2	5562

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00247	124332	0	3	124335	0.0000121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	245	300	0.816	0.0000143	3918
Missense in Polyphen		45	101.96	0.44137		1324
Synonymous	0.726	95	104	0.910	0.00000531	1035
Loss of Function	3.89	0	17.6	0.00	8.19e-7	263

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.00000890	0.00000889
Middle Eastern	0.0000557	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.

Intolerance Scores

• loftool: 0.151
• rvis_EVS: 0.68
• rvis_percentile_EVS: 85.04

Haploinsufficiency Scores

• pHI: 0.511
• hipred: Y
• hipred_score: 0.553
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.207

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp654

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