FEZ2

protein-coding

fasciculation and elongation protein zeta 2

Gene summary

This gene is an ortholog of the C. elegans unc-76 gene, which is necessary for normal axonal bundling and elongation within axon bundles. Other orthologs include the rat gene that encodes zygin II, which can bind to synaptotagmin. [provided by RefSeq, Jul 2008]

MANE transcript

NM_005102.3

Inheritance

—

ClinVar variants

U:95B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr2:36,531,805-36,646,087

External References & Databases

Ensembl (ENSG00000171055)

Transcript & Mutation Effects

hg38 • Region Span ~114.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FEZ2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 94

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005102.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			91 clinvar			91
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	95	1	0	96

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005102.3	RefSeq	NP_005093.2	8	MANE Select
ENST00000405912.8	Ensembl	ENSP00000385112.3	8	MANE Select
NM_001042548.2	RefSeq	NP_001036013.1	9	Standard
ENST00000305852.11	Ensembl	ENSP00000305843.7	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Prader-Willi and Angelman Syndrome

Biological Process

signal transduction
nervous system development
axon guidance
negative regulation of autophagosome assembly

Molecular Function

protein binding

Cellular Component

cytoplasm
axon

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379245
Coding exons: 9
Length: 94661
Individuals with no LoFs: 124602
Homozygous LoFs: 0
Heterozygous LoFs: 36
Defined: 124638
p: 0.000144

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.82	238	171	1.39	0.00000875	2428
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00019	0.00019	rare
South Asian	0.000065	0.000065	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in axonal outgrowth and fasciculation. {ECO:0000250}.;

Recessive Scores

pRec: 0.0973

Intolerance Scores

LoFtool: 0.961
RVIS EVS: -0.07
RVIS percentile EVS: 48.35

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.688

Gene Damage Prediction

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