FEZF2

FEZ family zinc finger 2, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 3:62369681-62374324

Previous symbols: [ "ZNF312" ]

Links

ENSG00000153266 ∙ NCBI:55079 ∙ OMIM:607414 ∙ HGNC:13506 ∙ Uniprot:Q8TBJ5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FEZF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FEZF2 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			18			18
nonsense						0
start loss						0
frameshift			1			1
inframe indel				1	2	3
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	2

Variants in FEZF2

This is a list of pathogenic ClinVar variants found in the FEZF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-62370112-T-C		not specified	Uncertain significance (Feb 21, 2024)
3-62370139-T-C		not specified	Uncertain significance (Jan 11, 2023)
3-62370157-CAT-C			Uncertain significance (Dec 15, 2023)
3-62370197-G-C		Neurodevelopmental disorder	Likely pathogenic (Oct 09, 2024)
3-62370205-C-T		not specified	Uncertain significance (Dec 27, 2023)
3-62370206-G-T			Uncertain significance (Dec 07, 2022)
3-62370292-A-C			Uncertain significance (Jun 07, 2023)
3-62371226-GA-G			Uncertain significance (Jun 24, 2022)
3-62371247-C-T		FEZF2-related disorder	Uncertain significance (Dec 01, 2023)
3-62371260-C-G		FEZF2-related disorder	Uncertain significance (Jun 01, 2024)
3-62371307-G-A			Uncertain significance (Oct 25, 2023)
3-62371316-C-CT			Uncertain significance (Dec 09, 2022)
3-62371330-T-C		not specified	Uncertain significance (Dec 16, 2023)
3-62371576-C-A		FEZF2-related disorder	Uncertain significance (Feb 07, 2024)
3-62371669-T-A			Uncertain significance (May 19, 2022)
3-62372058-C-G		not specified	Uncertain significance (Aug 08, 2023)
3-62372066-C-CCT		Neurodevelopmental phenotype	Likely pathogenic (Oct 28, 2024)
3-62372118-C-A		not specified	Uncertain significance (Feb 13, 2024)
3-62372119-CGA-C			Uncertain significance (Jan 04, 2024)
3-62372201-G-A		not specified	Uncertain significance (May 25, 2022)
3-62372271-C-T		not specified	Uncertain significance (Oct 08, 2024)
3-62372370-C-T		not specified	Uncertain significance (Jul 16, 2024)
3-62372376-C-T		not specified	Uncertain significance (Mar 22, 2023)
3-62372505-C-T			Uncertain significance (Nov 08, 2023)
3-62372510-A-C		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FEZF2	protein_coding	protein_coding	ENST00000283268	4	4644

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.989	0.0114	112048	0	1	112049	0.00000446

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.07	156	248	0.629	0.0000113	2930
Missense in Polyphen		16	51.777	0.30902		537
Synonymous	-1.51	131	111	1.18	0.00000543	942
Loss of Function	3.40	0	13.5	0.00	5.73e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000329	0.0000329
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription repressor. Required for the specification of corticospinal motor neurons and other subcerebral projection neurons. May play a role in layer and neuronal subtype-specific patterning of subcortical projections and axonal fasciculation. Controls the development of dendritic arborization and spines of large layer V pyramidal neurons. May be involved in innate immunity (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.149

Intolerance Scores

• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• pHI: 0.532
• hipred: Y
• hipred_score: 0.789
• ghis: 0.643

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.630

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fezf2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; taste/olfaction phenotype; craniofacial phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: fezf2
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: dead

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;axon guidance;axonal fasciculation;locomotory behavior;negative regulation of cell population proliferation;dendrite development;dentate gyrus development;forebrain anterior/posterior pattern specification;cerebral cortex GABAergic interneuron migration;commitment of neuronal cell to specific neuron type in forebrain;cell dedifferentiation;negative regulation of neuron differentiation;positive regulation of neuron differentiation;positive regulation of transcription by RNA polymerase II;neuron fate determination;regulation of axon guidance
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;chromatin DNA binding;sequence-specific DNA binding;metal ion binding