MAP1LC3C

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

Basic information

Region (hg38): 1:241995490-241999098

Links

ENSG00000197769 ∙ NCBI:440738 ∙ OMIM:609605 ∙ HGNC:13353 ∙ Uniprot:Q9BXW4 ∙ 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 MAP1LC3C gene.

• not_specified (21 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP1LC3C gene is commonly pathogenic or not. These statistics are base on transcript: NM_001004343.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			20	1		21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	20	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP1LC3C	protein_coding	protein_coding	ENST00000357246	4	3584

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000581	0.149	125706	0	36	125742	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.496	73	85.9	0.849	0.00000429	967
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000827	0.000826
Ashkenazi Jewish	0.00	0.00
East Asian	0.000169	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000169	0.000163
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Ferroptosis - Homo sapiens (human);Senescence and Autophagy in Cancer;Macroautophagy;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.0871

Intolerance Scores

• loftool: 0.623
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.26

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.492
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.716

Gene Damage Prediction

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

Gene ontology

• Biological process: autophagosome assembly;autophagy of mitochondrion;cellular response to nitrogen starvation;cellular response to starvation;macroautophagy;aggrephagy;autophagosome maturation
• Cellular component: autophagosome membrane;autophagosome;cytosol;microtubule;endomembrane system;organelle membrane;cytoplasmic vesicle;cytoplasmic ribonucleoprotein granule
• Molecular function: protein binding;microtubule binding;ubiquitin protein ligase binding