FEZ2

fasciculation and elongation protein zeta 2

Basic information

Region (hg38): 2:36531805-36646087

Links

ENSG00000171055 ∙ NCBI:9637 ∙ OMIM:604826 ∙ HGNC:3660 ∙ Uniprot:Q9UHY8 ∙ 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 FEZ2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FEZ2 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			41			41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	1	0

Variants in FEZ2

This is a list of pathogenic ClinVar variants found in the FEZ2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-36537405-G-A		not specified	Uncertain significance (Dec 28, 2022)
2-36537420-G-A		not specified	Uncertain significance (Jun 22, 2023)
2-36537464-C-A		CRIM1-related disorder	Likely benign (Mar 01, 2023)
2-36537489-C-A		not specified	Uncertain significance (May 24, 2023)
2-36537489-C-T		CRIM1-related disorder	Likely benign (Dec 31, 2019)
2-36537490-C-T		not specified	Uncertain significance (Aug 17, 2021)
2-36537537-A-G		not specified	Uncertain significance (Oct 20, 2024)
2-36544403-T-C		not specified	Uncertain significance (Nov 28, 2023)
2-36544481-T-C		not specified	Uncertain significance (Sep 12, 2023)
2-36544482-C-T		CRIM1-related disorder	Benign (Dec 31, 2019)
2-36546976-T-C		CRIM1-related disorder	Likely benign (Mar 01, 2024)
2-36546989-G-T		not specified	Uncertain significance (Aug 12, 2024)
2-36546993-A-G		not specified	Uncertain significance (Dec 06, 2022)
2-36547073-C-T		not specified	Uncertain significance (Mar 31, 2023)
2-36547098-T-C		not specified	Uncertain significance (Sep 14, 2023)
2-36547104-C-T		not specified	Uncertain significance (May 06, 2024)
2-36547126-G-C		not specified	Uncertain significance (Nov 10, 2022)
2-36547166-A-G		CRIM1-related disorder	Likely benign (Mar 30, 2018)
2-36548548-A-C		CRIM1-related disorder	Likely benign (Feb 26, 2020)
2-36548576-A-G			Benign (Apr 18, 2018)
2-36548637-G-T		not specified	Uncertain significance (Jan 17, 2024)
2-36548651-A-G		not specified	Uncertain significance (Jun 22, 2021)
2-36548679-A-T		not specified	Uncertain significance (Mar 11, 2024)
2-36553176-A-G		not specified	Uncertain significance (Apr 04, 2023)
2-36553177-G-C		not specified	Uncertain significance (Aug 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FEZ2	protein_coding	protein_coding	ENST00000379245	9	94661

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.15e-11	0.0480	124602	0	36	124638	0.000144

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.82	238	171	1.39	0.00000875	2428
Missense in Polyphen		99	71.391	1.3867		955
Synonymous	-2.72	94	65.9	1.43	0.00000367	672
Loss of Function	0.0623	17	17.3	0.984	8.26e-7	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000111	0.000111
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000195	0.000195
Middle Eastern	0.000111	0.000111
South Asian	0.0000654	0.0000654
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in axonal outgrowth and fasciculation. {ECO:0000250}.
• Pathway: Prader-Willi and Angelman Syndrome (Consensus)

Recessive Scores

• pRec: 0.0973

Intolerance Scores

• loftool: 0.961
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.0768
• hipred: N
• hipred_score: 0.350
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.688

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fez2

Gene ontology

• Biological process: signal transduction;nervous system development;axon guidance;negative regulation of autophagosome assembly
• Cellular component: cytoplasm;axon
• Molecular function: protein binding