ZFP1

ZFP1 zinc finger protein, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 16:75148494-75172236

Links

ENSG00000184517 ∙ NCBI:162239 ∙ OMIM:617230 ∙ HGNC:23328 ∙ Uniprot:Q6P2D0 ∙ 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 ZFP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFP1 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	18	2	0

Variants in ZFP1

This is a list of pathogenic ClinVar variants found in the ZFP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-75152957-C-T			Likely benign (Sep 01, 2022)
16-75166801-A-G		not specified	Uncertain significance (Feb 16, 2023)
16-75166821-G-C			Likely benign (Jan 01, 2023)
16-75166837-C-G		not specified	Uncertain significance (Feb 23, 2023)
16-75169254-A-C		not specified	Uncertain significance (Sep 06, 2023)
16-75169273-C-A		not specified	Uncertain significance (Feb 23, 2023)
16-75169334-A-G		not specified	Uncertain significance (May 25, 2022)
16-75169412-A-G		not specified	Uncertain significance (Jul 13, 2022)
16-75169439-A-G		not specified	Uncertain significance (Dec 18, 2023)
16-75169450-A-G		not specified	Uncertain significance (Feb 15, 2023)
16-75169462-G-C		not specified	Uncertain significance (Jun 05, 2023)
16-75169481-G-T		not specified	Uncertain significance (Feb 22, 2023)
16-75169505-A-G		not specified	Uncertain significance (Sep 16, 2021)
16-75169559-A-G		not specified	Uncertain significance (Jul 25, 2023)
16-75169577-C-T		not specified	Uncertain significance (May 05, 2023)
16-75169589-A-G		not specified	Uncertain significance (Mar 11, 2022)
16-75169621-A-G		not specified	Uncertain significance (Mar 31, 2024)
16-75169624-T-G		not specified	Uncertain significance (Jun 05, 2023)
16-75169873-C-T		not specified	Uncertain significance (Mar 20, 2024)
16-75170078-G-A		not specified	Uncertain significance (Apr 20, 2024)
16-75170090-G-A		not specified	Uncertain significance (May 16, 2024)
16-75170144-C-T		not specified	Uncertain significance (Mar 06, 2023)
16-75170174-C-A		not specified	Uncertain significance (May 28, 2024)
16-75170300-T-G		not specified	Uncertain significance (Feb 01, 2023)
16-75170320-G-A		not specified	Uncertain significance (Jul 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFP1	protein_coding	protein_coding	ENST00000393430	3	23745

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0139	0.980	125734	0	11	125745	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.907	250	213	1.18	0.0000104	2715
Missense in Polyphen		74	85.36	0.86692		1118
Synonymous	-3.85	124	80.1	1.55	0.00000440	697
Loss of Function	2.42	6	16.6	0.361	8.71e-7	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000446	0.0000440
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
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)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.395
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.310
• hipred: N
• hipred_score: 0.181
• ghis: 0.643

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp1

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