EPG5

ectopic P-granules 5 autophagy tethering factor

Basic information

Region (hg38): 18:45800581-45967329

Previous symbols: [ "KIAA1632" ]

Links

ENSG00000152223 ∙ NCBI:57724 ∙ OMIM:615068 ∙ HGNC:29331 ∙ Uniprot:Q9HCE0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Vici syndrome (Strong), mode of inheritance: AR
• Vici syndrome (Definitive), mode of inheritance: AR
• Vici syndrome (Definitive), mode of inheritance: AR
• Vici syndrome (Strong), mode of inheritance: AR
• Vici syndrome (Supportive), mode of inheritance: AR
• Vici syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Vici syndrome	AR	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular	Antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial; Surveillance for cardiomyopathy (eg, including echocardiogram) may allow early management; Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Dermatologic; Musculoskeletal; Neurologic; Ophthalmologic	20186778; 23222957; 27343256; 28168853

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EPG5 gene.

• Vici_syndrome (2227 variants)
• Inborn_genetic_diseases (362 variants)
• not_provided (236 variants)
• EPG5-related_disorder (81 variants)
• not_specified (39 variants)
• NEURODEVELOPMENTAL_DISORDER_WITH_PARKINSONISM_OR_OTHER_MOVEMENT_ABNORMALITIES (4 variants)
• Microcephaly (3 variants)
• Limb-girdle_muscular_dystrophy (2 variants)
• Syndromic_retinitis_pigmentosa (2 variants)
• Intellectual_disability (2 variants)
• Global_developmental_delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPG5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020964.3. 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		1	7	744	17	769
missense	2	9	919	58	12	1000
nonsense	67	22	7			96
start loss		1	1			2
frameshift	71	14	5			90
splice donor/acceptor (+/-2bp)	8	25	9			42
Total	148	72	948	802	29

Highest pathogenic variant AF is 0.000028214687

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPG5	protein_coding	protein_coding	ENST00000282041	44	119667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124715	0	112	124827	0.000449

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	1233	1.34e+3	0.917	0.0000699	16923
Missense in Polyphen		598	690.76	0.86571		9074
Synonymous	-0.950	548	520	1.05	0.0000282	4979
Loss of Function	6.88	48	134	0.358	0.00000684	1556

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00131	0.00124
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000564	0.000556
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000454	0.000450
Middle Eastern	0.000564	0.000556
South Asian	0.000327	0.000327
Other	0.000496	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in autophagy. May play a role in a late step of autophagy, such as clearance of autophagosomal cargo. {ECO:0000269|PubMed:20550938, ECO:0000269|PubMed:23222957}.
• Disease: DISEASE: Vici syndrome (VICIS) [MIM:242840]: A rare congenital multisystem disorder characterized by agenesis of the corpus callosum, cataracts, pigmentary defects, progressive cardiomyopathy, and variable immunodeficiency. Affected individuals also have profound psychomotor retardation and hypotonia due to a myopathy. {ECO:0000269|PubMed:23222957}. Note=The disease is caused by mutations affecting the gene represented in this entry. Affected individuals show homozygosity or compound heterozygosity for truncating mutations, aberrant splicing and/or missense mutations. Parental studies suggest recessive inheritance with no carrier manifestation (PubMed:23222957). {ECO:0000269|PubMed:23222957}.

Recessive Scores

• pRec: 0.0999

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.31

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: autophagy;autophagosome maturation
• Cellular component: cytoplasm