VEZF1

vascular endothelial zinc finger 1, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 17:57971547-57988259

Previous symbols: [ "ZNF161" ]

Links

ENSG00000136451 ∙ NCBI:7716 ∙ OMIM:606747 ∙ HGNC:12949 ∙ Uniprot:Q14119 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autism spectrum disorder (Limited), mode of inheritance: AD
• cardiomyopathy, dilated, 100 (Limited), mode of inheritance: AD
• cardiomyopathy, dilated, 100 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cardiomyopathy, dilated, 1OO	AD	Cardiovascular	The condition may involve increased risk of cardiomyopathy, and awareness may allow early identification and management of cardiac disease	Cardiovascular	36657711

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VEZF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VEZF1 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				2		2
missense			19			19
nonsense						0
start loss						0
frameshift				2		2
inframe indel			1	3	1	5
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	7	1

Variants in VEZF1

This is a list of pathogenic ClinVar variants found in the VEZF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-57974543-T-C		not specified	Uncertain significance (Jan 06, 2023)
17-57974567-G-T		not specified	Uncertain significance (Jun 03, 2022)
17-57974595-T-C		not specified	Uncertain significance (Dec 27, 2022)
17-57974721-T-C		not specified	Uncertain significance (Jun 29, 2023)
17-57974727-T-C		not specified	Uncertain significance (May 04, 2022)
17-57974841-G-A		not specified	Uncertain significance (Oct 20, 2023)
17-57974843-G-C		not specified	Uncertain significance (Nov 10, 2022)
17-57974847-T-C		not specified	Uncertain significance (May 31, 2023)
17-57974850-G-C		not specified	Uncertain significance (Dec 07, 2021)
17-57974895-C-A		not specified	Uncertain significance (Mar 01, 2024)
17-57979243-T-C			Likely benign (Jul 17, 2018)
17-57979243-TTGCTGCTGC-T		VEZF1-related disorder	Likely benign (Jun 16, 2022)
17-57979243-TTGCTGCTGCTGC-T		not specified	Uncertain significance (May 04, 2022)
17-57979243-TTGCTGCTGCTGCTGC-T		VEZF1-related disorder	Likely benign (Jun 01, 2024)
17-57979243-T-TTGCTGCTGC		VEZF1-related disorder	Likely benign (Mar 23, 2023)
17-57979243-T-TTGTTGTTGC		not specified	Benign (May 04, 2022)
17-57979245-GC-G		VEZF1-related disorder	Likely benign (Apr 11, 2023)
17-57979247-TGC-T		VEZF1-related disorder	Likely benign (Apr 11, 2023)
17-57979249-C-T			Likely benign (Sep 01, 2023)
17-57982738-T-C		not specified	Uncertain significance (Oct 13, 2021)
17-57982741-G-C		not specified	Uncertain significance (Jan 24, 2023)
17-57982756-T-G		VEZF1-related disorder	Uncertain significance (Jun 09, 2023)
17-57982904-C-G		not specified	Uncertain significance (May 16, 2024)
17-57982937-T-A		Cardiomyopathy, dilated, 100	Pathogenic (Feb 15, 2023)
17-57982955-G-T		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VEZF1	protein_coding	protein_coding	ENST00000581208	6	16711

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00577	125656	18	48	125722	0.000263

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.92	148	287	0.515	0.0000149	3426
Missense in Polyphen		29	84.158	0.34459		1018
Synonymous	-1.38	126	108	1.17	0.00000584	1041
Loss of Function	3.91	1	19.7	0.0507	0.00000108	230

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00195	0.00114
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000163
Finnish	0.000609	0.000277
European (Non-Finnish)	0.000278	0.000141
Middle Eastern	0.000223	0.000163
South Asian	0.00146	0.000719
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible transcription factor. Specifically binds to the CT/GC-rich region of the interleukin-3 promoter and mediates tax transactivation of IL-3. {ECO:0000269|PubMed:8035792}.

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.246
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.36

Haploinsufficiency Scores

• pHI: 0.880
• hipred: Y
• hipred_score: 0.662
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.646

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vezf1
• Phenotype: growth/size/body region phenotype; craniofacial phenotype; immune system phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: angiogenesis;endothelial cell development;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;cellular defense response;positive regulation of endothelial cell differentiation;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;metal ion binding