FEZ1

fasciculation and elongation protein zeta 1

Basic information

Region (hg38): 11:125442880-125592568

Links

ENSG00000149557 ∙ NCBI:9638 ∙ OMIM:604825 ∙ HGNC:3659 ∙ Uniprot:Q99689 ∙ 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 FEZ1 gene.

• Inborn genetic diseases (13 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FEZ1 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			8		1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding			5			5
Total	0	0	13	0	2

Variants in FEZ1

This is a list of pathogenic ClinVar variants found in the FEZ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-125446118-C-T			Benign (May 15, 2018)
11-125452348-T-C		not specified	Uncertain significance (Jan 03, 2024)
11-125452358-C-G			Benign (Jun 11, 2018)
11-125452365-G-A			Benign (May 15, 2018)
11-125452382-T-G		not specified	Uncertain significance (Nov 09, 2023)
11-125454123-C-T			Benign (Jun 13, 2018)
11-125454209-C-T		not specified	Uncertain significance (Oct 24, 2023)
11-125455863-A-G		not specified	Uncertain significance (Nov 06, 2023)
11-125455866-C-T		not specified	Uncertain significance (Mar 06, 2023)
11-125455867-G-A		not specified	Uncertain significance (Jun 24, 2022)
11-125455891-T-C		not specified	Uncertain significance (Jul 06, 2021)
11-125455902-C-G		not specified	Uncertain significance (Feb 28, 2024)
11-125456007-C-T		not specified	Uncertain significance (Sep 14, 2021)
11-125460503-T-C		not specified	Uncertain significance (Jan 23, 2024)
11-125460567-C-T		not specified	Uncertain significance (Dec 22, 2023)
11-125460654-T-C		not specified	Uncertain significance (Feb 22, 2023)
11-125481566-C-T		not specified	Uncertain significance (Mar 06, 2023)
11-125481572-T-G		not specified	Uncertain significance (Jan 08, 2024)
11-125489474-C-T		not specified	Uncertain significance (Feb 24, 2022)
11-125489485-T-G		not specified	Uncertain significance (May 09, 2023)
11-125489630-A-C		not specified	Uncertain significance (Dec 22, 2023)
11-125489670-G-T		not specified	Uncertain significance (Aug 28, 2023)
11-125572568-G-A		not specified	Uncertain significance (Aug 20, 2023)
11-125577510-C-T		not specified	Uncertain significance (Nov 10, 2022)
11-125578163-C-T		not specified	Uncertain significance (Jun 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FEZ1	protein_coding	protein_coding	ENST00000278919	9	50568

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.750	0.250	125740	0	5	125745	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.38	163	221	0.739	0.0000124	2614
Missense in Polyphen		51	83.998	0.60716		978
Synonymous	0.225	86	88.7	0.970	0.00000547	706
Loss of Function	3.57	4	22.1	0.181	0.00000109	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000271	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in axonal outgrowth as component of the network of molecules that regulate cellular morphology and axon guidance machinery. Able to restore partial locomotion and axonal fasciculation to C.elegans unc-76 mutants in germline transformation experiments. May participate in the transport of mitochondria and other cargos along microtubules. {ECO:0000269|PubMed:20812761, ECO:0000269|PubMed:22354037}.
• Pathway: Prader-Willi and Angelman Syndrome (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.287
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.557
• hipred: Y
• hipred_score: 0.837
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.768

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fez1
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: cell adhesion;nervous system development;axon guidance;negative regulation of autophagosome assembly
• Cellular component: cytoplasm;Golgi apparatus;microtubule organizing center;microtubule;plasma membrane;axon
• Molecular function: protein binding