MAP1LC3C

protein-coding

microtubule associated protein 1 light chain 3 gamma, the group of Autophagy related

Gene summary

Autophagy is a highly regulated bulk degradation process that plays an important role in cellular maintenance and development. MAP1LC3C is an ortholog of the yeast autophagosome protein Atg8 (He et al., 2003 [PubMed 12740394]).[supplied by OMIM, Nov 2010]

MANE transcript

NM_001004343.3

Inheritance

—

ClinVar variants

U:22B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.33

Max pathogenic AF

—

Genomic locus

chr1:241,995,490-241,999,098

External References & Databases

Ensembl (ENSG00000197769)

Transcript & Mutation Effects

hg38 • Region Span ~3.6 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 MAP1LC3C variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 23

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001004343.3. 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						0
missense			22 clinvar	1 clinvar		23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	1	0	23

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001004343.3	RefSeq	NP_001004343.1	4	MANE Select
ENST00000357246.4	Ensembl	ENSP00000349785.3	4	MANE Select
ENST00000943070.1	Ensembl	ENSP00000613129.1	4	Standard
ENST00001126938.1	Ensembl	ENSP00000796743.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ferroptosis - Homo sapiens (human)
Senescence and Autophagy in Cancer
Macroautophagy
Cellular responses to external stimuli

Biological Process

autophagosome assembly
autophagy of mitochondrion
cellular response to nitrogen starvation
cellular response to starvation
macroautophagy

Molecular Function

protein binding
microtubule binding
ubiquitin protein ligase binding

Cellular Component

autophagosome membrane
autophagosome
cytosol
microtubule
endomembrane system

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000357246
Coding exons: 4
Length: 3584
Individuals with no LoFs: 125706
Homozygous LoFs: 0
Heterozygous LoFs: 36
Defined: 125742
p: 0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.496	73	85.9	0.849	0.00000429	967
Missense (PolyPhen)		21	23.988	0.87545		305
Synonymous	-0.725	39	33.6	1.16	0.00000183	275
Loss of Function	-0.701	7	5.27	1.33	2.23e-7	64

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00074	0.00074	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Ubiquitin-like modifier that plays a crucial role in antibacterial autophagy (xenophagy) through the selective binding of CALCOCO2. Recruits all ATG8 family members to infecting bacteria such as S.Typhimurium (PubMed:23022382). May also play a role in aggrephagy, the macroautophagic degradation of ubiquitinated and aggregated proteins (PubMed:28404643). {ECO:0000269|PubMed:23022382, ECO:0000269|PubMed:28404643}.;

Recessive Scores

pRec: 0.0871

Intolerance Scores

LoFtool: 0.623
RVIS EVS: 0.06
RVIS percentile EVS: 58.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.716

Gene Damage Prediction

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