FYCO1

FYVE and coiled-coil domain autophagy adaptor 1, the group of Zinc fingers FYVE-type|GOLD domain containing

Basic information

Region (hg38): 3:45917903-45995824

Links

ENSG00000163820 ∙ NCBI:79443 ∙ OMIM:607182 ∙ HGNC:14673 ∙ Uniprot:Q9BQS8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cataract 18 (Definitive), mode of inheritance: AR
• cataract 18 (Strong), mode of inheritance: AR
• early-onset nuclear cataract (Supportive), mode of inheritance: AD
• total early-onset cataract (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cataract 18	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	11519376; 21636066

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FYCO1 gene.

• Cataract 18 (11 variants)
• not provided (3 variants)
• FYCO1-related disorder (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FYCO1 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			7	29	9	45
missense			138	22	19	179
nonsense	8	4				12
start loss						0
frameshift	7	1	1			9
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1	1				2
splice region			1	3		4
non coding			61	21	72	154
Total	16	6	208	72	100

Highest pathogenic variant AF is 0.000105

Variants in FYCO1

This is a list of pathogenic ClinVar variants found in the FYCO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-45918023-A-T		Cataract 18	Benign (Jan 12, 2018)
3-45918040-T-C		Cataract 18	Likely benign (Jan 13, 2018)
3-45918074-T-G		Cataract 18	Uncertain significance (Jan 12, 2018)
3-45918182-G-A		Cataract 18	Uncertain significance (Jan 13, 2018)
3-45918205-G-T		Cataract 18	Likely benign (Jan 12, 2018)
3-45918238-C-T		Cataract 18	Uncertain significance (Jan 12, 2018)
3-45918253-A-T		Cataract 18	Uncertain significance (Jan 12, 2018)
3-45918263-T-A		Cataract 18	Uncertain significance (Jan 12, 2018)
3-45918267-T-C		Cataract 18	Benign (Jan 13, 2018)
3-45918326-T-A		Cataract 18	Benign (Jan 12, 2018)
3-45918399-A-C		Cataract 18	Uncertain significance (Jan 13, 2018)
3-45918439-C-T		Cataract 18	Uncertain significance (Jan 12, 2018)
3-45918482-C-T		Cataract 18	Uncertain significance (Jan 13, 2018)
3-45918487-C-T		Cataract 18	Uncertain significance (Jan 13, 2018)
3-45918507-TA-T		Developmental cataract	Benign (Jun 14, 2016)
3-45918574-C-T		Cataract 18	Uncertain significance (Jan 12, 2018)
3-45918587-C-A		Cataract 18	Benign (Jan 12, 2018)
3-45918702-C-T		Cataract 18	Uncertain significance (Jan 12, 2018)
3-45918708-C-T		Cataract 18	Uncertain significance (Jan 13, 2018)
3-45918759-C-T		Cataract 18	Uncertain significance (Jan 13, 2018)
3-45918876-G-T		Cataract 18	Uncertain significance (Jan 13, 2018)
3-45918914-G-A		Cataract 18	Likely benign (Jan 13, 2018)
3-45918928-G-C		Cataract 18	Benign (Jan 13, 2018)
3-45918994-T-C		Cataract 18	Uncertain significance (Jan 13, 2018)
3-45919008-G-T		Cataract 18	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FYCO1	protein_coding	protein_coding	ENST00000296137	17	77921

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.41e-27	0.353	125563	1	184	125748	0.000736

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.174	764	778	0.982	0.0000476	9657
Missense in Polyphen		227	232.17	0.97772		3099
Synonymous	0.723	319	336	0.950	0.0000203	2871
Loss of Function	2.18	52	71.9	0.723	0.00000383	804

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00138	0.00138
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000816	0.000816
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000951	0.000950
Middle Eastern	0.000816	0.000816
South Asian	0.000523	0.000523
Other	0.00114	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May mediate microtubule plus end-directed vesicle transport. {ECO:0000269|PubMed:20100911}.

Recessive Scores

• pRec: 0.0949

Intolerance Scores

• loftool: 0.913
• rvis_EVS: 3.05
• rvis_percentile_EVS: 99.24

Haploinsufficiency Scores

• pHI: 0.0784
• hipred: N
• hipred_score: 0.384
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.643

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fyco1

Gene ontology

• Biological process: plus-end-directed vesicle transport along microtubule;positive regulation of autophagosome maturation
• Cellular component: lysosome;late endosome;autophagosome;Golgi apparatus;membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding;metal ion binding