ATG101

autophagy related 101, the group of Autophagy related

Basic information

Region (hg38): 12:52069245-52077495

Previous symbols: [ "C12orf44" ]

Links

ENSG00000123395 ∙ NCBI:60673 ∙ OMIM:615089 ∙ HGNC:25679 ∙ Uniprot:Q9BSB4 ∙ 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 ATG101 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATG101 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in ATG101

This is a list of pathogenic ClinVar variants found in the ATG101 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-52073674-G-A			Likely benign (Dec 09, 2017)
12-52073693-C-T		not specified	Uncertain significance (Mar 28, 2024)
12-52073711-A-T		not specified	Uncertain significance (Jun 01, 2023)
12-52073730-C-T		not specified	Uncertain significance (Mar 11, 2024)
12-52073836-C-A		not specified	Uncertain significance (Jun 12, 2023)
12-52073847-G-A		not specified	Uncertain significance (Nov 08, 2021)
12-52073895-A-C		not specified	Uncertain significance (May 16, 2024)
12-52076795-C-T		not specified	Uncertain significance (Dec 01, 2022)
12-52076825-A-G		not specified	Uncertain significance (Nov 19, 2022)
12-52076859-G-A		not specified	Uncertain significance (Feb 06, 2024)
12-52076870-T-G		not specified	Uncertain significance (Mar 20, 2023)
12-52076921-G-T		not specified	Uncertain significance (Mar 31, 2024)
12-52076931-C-T		not specified	Uncertain significance (May 05, 2023)
12-52076990-A-G		not specified	Uncertain significance (Feb 28, 2024)
12-52077033-A-G		not specified	Uncertain significance (Oct 25, 2022)
12-52077081-G-A		not specified	Uncertain significance (May 28, 2023)
12-52077158-C-T		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATG101	protein_coding	protein_coding	ENST00000336854	2	8249

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.606	0.386	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	107	142	0.754	0.00000944	1420
Missense in Polyphen		23	41.676	0.55188		447
Synonymous	0.301	55	57.9	0.950	0.00000378	449
Loss of Function	2.13	1	7.17	0.140	3.09e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000581	0.0000581
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Autophagy factor required for autophagosome formation. Stabilizes ATG13, protecting it from proteasomal degradation. {ECO:0000269|PubMed:19287211, ECO:0000269|PubMed:19597335}.
• Pathway: Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);Macroautophagy;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.0524
• hipred: Y
• hipred_score: 0.528
• ghis: 0.593

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Atg101

Gene ontology

• Biological process: autophagosome assembly;macroautophagy;regulation of macroautophagy
• Cellular component: phagophore assembly site;endoplasmic reticulum membrane;cytosol
• Molecular function: protein binding;identical protein binding;protein-containing complex binding