ATG101

protein-coding

autophagy related 101, the group of Autophagy related

Gene summary

Enables identical protein binding activity. Involved in autophagosome assembly; negative regulation of cell population proliferation; and regulation of protein lipidation. Located in phagophore assembly site. Biomarker of cholangiocarcinoma; colon cancer; and hepatocellular carcinoma. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C12orf44

MANE transcript

NM_021934.5

Inheritance

—

ClinVar variants

U:33B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr12:52,069,246-52,077,495

External References & Databases

Ensembl (ENSG00000123395)

Transcript & Mutation Effects

hg38 • Region Span ~8.2 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 ATG101 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 29

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021934.5. 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
missense			31 clinvar			31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	33	1	0	34

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021934.5	RefSeq	NP_068753.2	2	MANE Select
ENST00000336854.9	Ensembl	ENSP00000338990.4	2	MANE Select
NM_001098673.2	RefSeq	NP_001092143.1	2	Standard
ENST00000548915.1	Ensembl	ENSP00000449935.1	2	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)
Longevity regulating pathway - Homo sapiens (human)
Macroautophagy
Cellular responses to external stimuli

Biological Process

autophagosome assembly
macroautophagy
regulation of macroautophagy

Molecular Function

protein binding
identical protein binding
protein-containing complex binding

Cellular Component

phagophore assembly site
endoplasmic reticulum membrane
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000336854
Coding exons: 2
Length: 8249
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125747
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.04	107	142	0.754	0.00000944	1420
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

RVIS EVS: -0.43
RVIS percentile EVS: 25.15

Essentials

Essential (gene trap): N