ATG2B

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

Basic information

Region (hg38): 14:96279195-96363341

Previous symbols: [ "C14orf103" ]

Links

ENSG00000066739 ∙ NCBI:55102 ∙ OMIM:616226 ∙ HGNC:20187 ∙ Uniprot:Q96BY7 ∙ 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 ATG2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATG2B 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	11	12	24
missense			105	11	12	128
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	4	3	8
non coding				1	67	68
Total	0	0	106	23	91

Variants in ATG2B

This is a list of pathogenic ClinVar variants found in the ATG2B region.

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

Position	Type	Phenotype	Significance	ClinVar
14-96285787-C-T		not specified	Uncertain significance (Dec 14, 2021)
14-96285824-G-A		not specified • ATG2B-related disorder	Likely benign (Jul 22, 2021)
14-96285835-C-G		not specified	Uncertain significance (Jun 11, 2024)
14-96285835-C-T		not specified	Uncertain significance (Jun 21, 2022)
14-96285842-C-T		ATG2B-related disorder	Likely benign (May 21, 2019)
14-96285886-G-C		not specified	Uncertain significance (Aug 02, 2022)
14-96285894-C-T		not specified	Uncertain significance (Jan 10, 2022)
14-96285963-G-C		not specified	Uncertain significance (May 10, 2022)
14-96286218-C-T			Benign (Jul 09, 2018)
14-96286247-G-A			Benign (Jul 09, 2018)
14-96289382-G-A			Benign (Jul 09, 2018)
14-96289472-A-G			Benign (Jul 05, 2018)
14-96289678-T-C		not specified	Uncertain significance (Jul 30, 2023)
14-96289721-G-C		ATG2B-related disorder	Likely benign (Feb 27, 2023)
14-96289730-G-A		not specified	Uncertain significance (Sep 19, 2022)
14-96289733-A-C		not specified	Uncertain significance (Nov 17, 2022)
14-96289757-T-C			Benign (Apr 16, 2018)
14-96289988-A-T			Benign (Jul 10, 2018)
14-96290457-G-T		not specified	Uncertain significance (Mar 01, 2024)
14-96290487-C-T		not specified	Likely benign (Sep 01, 2022)
14-96290533-C-T		not specified	Uncertain significance (Dec 21, 2022)
14-96290636-T-C			Benign (Jul 10, 2018)
14-96290832-G-A		not specified	Uncertain significance (Jul 05, 2022)
14-96290904-C-A		not specified	Uncertain significance (Mar 19, 2024)
14-96290925-C-T		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATG2B	protein_coding	protein_coding	ENST00000359933	42	82613

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.02e-8	1.00	125658	0	90	125748	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	984	1.09e+3	0.904	0.0000567	13570
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000773	0.000759
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000344	0.000326
Finnish	0.000325	0.000323
European (Non-Finnish)	0.000378	0.000369
Middle Eastern	0.000344	0.000326
South Asian	0.000480	0.000425
Other	0.000513	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for both autophagosome formation and regulation of lipid droplet morphology and dispersion. {ECO:0000269|PubMed:22219374}.
• Pathway: Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.835
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.38

Haploinsufficiency Scores

• pHI: 0.316
• hipred: N
• hipred_score: 0.414
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.826

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atg2b

Gene ontology

• Biological process: autophagosome assembly;autophagy of mitochondrion
• Cellular component: phagophore assembly site;nucleoplasm;lipid droplet;extrinsic component of membrane;phagophore assembly site membrane