RUFY4

RUN and FYVE domain containing 4, the group of Zinc fingers FYVE-type

Basic information

Region (hg38): 2:218034960-218090584

Links

ENSG00000188282 ∙ NCBI:285180 ∙ ∙ HGNC:24804 ∙ Uniprot:Q6ZNE9 ∙ 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 RUFY4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RUFY4 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				1		1
missense			32	8		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	9	0

Variants in RUFY4

This is a list of pathogenic ClinVar variants found in the RUFY4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-218070609-G-A		not specified	Uncertain significance (Oct 06, 2021)
2-218070755-G-A			Likely benign (Apr 01, 2022)
2-218070771-T-C		not specified	Uncertain significance (Mar 07, 2024)
2-218070818-G-A		not specified	Uncertain significance (Mar 21, 2024)
2-218072408-C-A		not specified	Uncertain significance (Dec 01, 2022)
2-218072411-G-C		not specified	Uncertain significance (Aug 30, 2021)
2-218072449-C-T		not specified	Uncertain significance (May 10, 2024)
2-218072464-A-G		not specified	Uncertain significance (Sep 30, 2022)
2-218072816-G-A		not specified	Uncertain significance (Dec 02, 2022)
2-218072831-G-T		not specified	Uncertain significance (Sep 01, 2021)
2-218072846-A-T		not specified	Uncertain significance (Nov 21, 2022)
2-218072878-C-G		not specified	Uncertain significance (Dec 19, 2022)
2-218073254-G-C		not specified	Uncertain significance (Sep 22, 2023)
2-218073284-G-A		not specified	Uncertain significance (Sep 17, 2021)
2-218073334-G-A		not specified	Uncertain significance (Jan 11, 2023)
2-218073335-A-T		not specified	Uncertain significance (Apr 23, 2024)
2-218073336-G-T		not specified	Likely benign (Jul 05, 2022)
2-218073357-C-G		not specified	Uncertain significance (Nov 27, 2023)
2-218073838-C-G		not specified	Uncertain significance (Jun 29, 2023)
2-218075094-T-G		not specified	Uncertain significance (Jul 25, 2023)
2-218075111-G-A		not specified	Likely benign (Dec 07, 2021)
2-218075129-A-G		not specified	Uncertain significance (Apr 07, 2023)
2-218075168-G-A		not specified	Uncertain significance (Nov 04, 2022)
2-218075256-G-T		not specified	Uncertain significance (Jan 04, 2024)
2-218075281-G-C			Likely benign (Apr 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RUFY4	protein_coding	protein_coding	ENST00000374155	11	55622

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.07e-14	0.0982	124522	1	123	124646	0.000498

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0655	317	314	1.01	0.0000170	3860
Missense in Polyphen		78	75.475	1.0335		988
Synonymous	0.317	115	119	0.963	0.00000610	1190
Loss of Function	0.765	23	27.3	0.842	0.00000126	328

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00224	0.00219
Ashkenazi Jewish	0.00	0.00
East Asian	0.000128	0.000111
Finnish	0.000924	0.000836
European (Non-Finnish)	0.000274	0.000230
Middle Eastern	0.000128	0.000111
South Asian	0.0000330	0.0000327
Other	0.00107	0.000991

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positively regulates macroautophagy in primary dendritic cells. Increases autophagic flux, probably by stimulating both autophagosome formation and facilitating tethering with lysosomes. Binds to phosphatidylinositol 3-phosphate (PtdIns3P) through its FYVE-type zinc finger. {ECO:0000269|PubMed:26416964}.

Haploinsufficiency Scores

• pHI: 0.0311
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0199

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rufy4

Gene ontology

• Biological process: autophagosome assembly;positive regulation of macroautophagy;cellular response to interleukin-4
• Cellular component: autophagosome;cytoplasmic vesicle
• Molecular function: protein binding;phosphatidylinositol-3-phosphate binding;metal ion binding