ATG2B

protein-coding

autophagy related 2B, the group of bridge-like lipid transfer protein family|Autophagy related

Gene summary

This gene encodes a protein required for autophagy. The encoded protein is involved in autophagosome formation. A germline duplication of a region that includes this gene is associated with predisposition to myeloid malignancies. [provided by RefSeq, Jul 2016]

Previous symbols:

C14orf103

MANE transcript

NM_018036.7

Inheritance

—

ClinVar variants

U:267B:50

Top phenotype

ATG2B-related disorder

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr14:96,279,195-96,363,341

External References & Databases

Ensembl (ENSG00000066739)

Transcript & Mutation Effects

hg38 • Region Span ~84.1 kb

Loading mutation effect viewer...

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 ATG2B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 279

not providedTotal: 39

ATG2B-related disorderTotal: 31

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018036.7. 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			3 clinvar	16 clinvar	7 clinvar	26
missense			260 clinvar	18 clinvar	9 clinvar	287
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	267	34	16	317

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018036.7	RefSeq	NP_060506.6	42	MANE Select
ENST00000359933.6	Ensembl	ENSP00000353010.4	42	MANE Select
ENST00000938845.1	Ensembl	ENSP00000608904.1	42	Standard
ENST00000938845.2	Ensembl	ENSP00000608904.1	42	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Autophagy - animal - Homo sapiens (human)
Autophagy - other - Homo sapiens (human)

Biological Process

autophagosome assembly
autophagy of mitochondrion

Cellular Component

phagophore assembly site
nucleoplasm
lipid droplet
extrinsic component of membrane
phagophore assembly site membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359933
Coding exons: 42
Length: 82613
Individuals with no LoFs: 125658
Homozygous LoFs: 0
Heterozygous LoFs: 90
Defined: 125748
p: 0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.12	984	1.09e+3	0.904	0.0000567	13570
Missense (PolyPhen)		424	508.93	0.83312		6298
Synonymous	-0.366	407	398	1.02	0.0000213	4007
Loss of Function	6.43	35	107	0.328	0.00000580	1324

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00044	0.00043	rare
Latino/Admixed American	0.00033	0.00032	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00034	0.00033	rare
Finnish	0.00033	0.00032	rare
European (Non-Finnish)	0.00038	0.00037	rare
South Asian	0.00048	0.00042	rare
Other	0.00051	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for both autophagosome formation and regulation of lipid droplet morphology and dispersion. {ECO:0000269|PubMed:22219374}.;

Intolerance Scores

LoFtool: 0.835
RVIS EVS: 0.49
RVIS percentile EVS: 79.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.826

Gene Damage Prediction

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