ZZEF1

zinc finger ZZ-type and EF-hand domain containing 1, the group of Zinc fingers ZZ-type|EF-hand domain containing

Basic information

Region (hg38): 17:4004445-4143030

Links

ENSG00000074755 ∙ NCBI:23140 ∙ OMIM:619459 ∙ HGNC:29027 ∙ Uniprot:O43149 ∙ 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 ZZEF1 gene.

• not_specified (406 variants)
• not_provided (8 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZZEF1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015113.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				6		6
missense			387	20		407
nonsense				1		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	387	27	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZZEF1	protein_coding	protein_coding	ENST00000381638	55	138576

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.835	0.165	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	1534	1.65e+3	0.928	0.0000954	19343
Missense in Polyphen		459	608.09	0.75482		7365
Synonymous	-1.29	703	661	1.06	0.0000401	5783
Loss of Function	8.92	33	151	0.218	0.00000786	1738

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000395	0.000394
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000109	0.000109
Finnish	0.000202	0.000185
European (Non-Finnish)	0.000258	0.000255
Middle Eastern	0.000109	0.000109
South Asian	0.000294	0.000294
Other	0.000174	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.550
• rvis_EVS: -3.38
• rvis_percentile_EVS: 0.39

Haploinsufficiency Scores

• pHI: 0.388
• hipred: N
• hipred_score: 0.462
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.708

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Zzef1
• Phenotype: homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; hematopoietic system phenotype

Gene ontology

• Molecular function: calcium ion binding;zinc ion binding