ANKFY1

ankyrin repeat and FYVE domain containing 1, the group of Zinc fingers FYVE-type|Ankyrin repeat domain containing|BTB domain containing

Basic information

Region (hg38): 17:4163821-4263995

Links

ENSG00000185722 ∙ NCBI:51479 ∙ OMIM:607927 ∙ HGNC:20763 ∙ Uniprot:Q9P2R3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• familial idiopathic steroid-resistant nephrotic syndrome (Supportive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ANKFY1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKFY1 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				18	5	23
missense			64	5	1	70
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding				5	29	34
Total	0	0	64	28	35

Variants in ANKFY1

This is a list of pathogenic ClinVar variants found in the ANKFY1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4167769-G-A		ANKFY1-related disorder	Likely benign (Jun 18, 2020)
17-4167820-T-C		not specified	Uncertain significance (Nov 20, 2023)
17-4167856-T-C		not specified	Uncertain significance (Nov 17, 2022)
17-4167894-A-C		not specified	Uncertain significance (Feb 22, 2024)
17-4167951-C-T			Benign (May 10, 2021)
17-4168008-G-C			Benign (May 10, 2021)
17-4168032-C-G			Benign (May 10, 2021)
17-4169247-A-C		not specified	Uncertain significance (Mar 18, 2024)
17-4169261-C-G		not specified	Uncertain significance (Jan 31, 2023)
17-4169280-A-G		not specified	Uncertain significance (Mar 13, 2023)
17-4169413-G-A			Benign (May 11, 2021)
17-4169467-G-C			Benign (May 11, 2021)
17-4170784-T-C		not specified	Uncertain significance (May 11, 2022)
17-4170817-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-4170830-G-A		ANKFY1-related disorder	Likely benign (May 21, 2021)
17-4170870-C-A		ANKFY1-related disorder	Likely benign (Jun 23, 2020)
17-4170967-A-C			Benign (May 10, 2021)
17-4172571-C-T		not specified	Uncertain significance (May 17, 2023)
17-4172624-A-G		not specified	Uncertain significance (Dec 22, 2023)
17-4172670-G-C		not specified	Uncertain significance (Jan 10, 2023)
17-4172671-T-G		ANKFY1-related disorder	Likely benign (Aug 08, 2019)
17-4173320-C-T			Benign (May 11, 2021)
17-4173371-G-A		ANKFY1-related disorder	Likely benign (Jun 04, 2019)
17-4173371-G-C		ANKFY1-related disorder	Likely benign (Apr 26, 2021)
17-4173374-G-A			Benign (Apr 25, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKFY1	protein_coding	protein_coding	ENST00000570535	25	100074

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.956	0.0437	124792	0	22	124814	0.0000881

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.46	531	717	0.741	0.0000425	7906
Missense in Polyphen		157	270.48	0.58046		3015
Synonymous	1.02	283	306	0.926	0.0000204	2431
Loss of Function	5.74	11	58.3	0.189	0.00000316	653

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000241	0.000241
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.0000800	0.0000794
Middle Eastern	0.000111	0.000111
South Asian	0.0000686	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proposed effector of Rab5. Binds to phosphatidylinositol 3-phosphate (PI(3)P). Involved in homotypic early endosome fusion and to a lesser extent in heterotypic fusion of chlathrin-coated vesicles with early endosomes. Involved in macropinocytosis; the function is dependent on Rab5-GTP. Required for correct endosomal localization. Involved in the internalization and trafficking of activated tyrosine kinase receptors such as PDGFRB. Regulates the subcellular localization of the retromer complex in a EHD1- dependent manner. Involved in endosome-to-Golgi transport and biosynthetic transport to late endosomes and lysosomes indicative for a regulation of retromer complex-mediated retrograde transport. {ECO:0000269|PubMed:15328530, ECO:0000269|PubMed:22284051, ECO:0000269|PubMed:24102721}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.491
• rvis_EVS: -1.75
• rvis_percentile_EVS: 2.36

Haploinsufficiency Scores

• pHI: 0.0827
• hipred: Y
• hipred_score: 0.575
• ghis: 0.654

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.926

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ankfy1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: endocytosis;endosomal transport;endosomal vesicle fusion;retrograde transport, endosome to Golgi;positive regulation of pinocytosis;Golgi to lysosome transport
• Cellular component: lysosomal membrane;endosome;early endosome;cytosol;endosome membrane;membrane;retromer complex;intracellular membrane-bounded organelle;macropinosome;extracellular exosome
• Molecular function: protein binding;Rab GTPase binding;metal ion binding;phosphatidylinositol phosphate binding