RUFY1

RUN and FYVE domain containing 1, the group of Zinc fingers FYVE-type

Basic information

Region (hg38): 5:179550554-179610012

Links

ENSG00000176783 ∙ NCBI:80230 ∙ OMIM:610327 ∙ HGNC:19760 ∙ Uniprot:Q96T51 ∙ 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 RUFY1 gene.

• not_specified (99 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RUFY1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000025158.5. 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	1		2
missense			103	3		106
nonsense						0
start loss						0
frameshift			2			2
splice donor/acceptor (+/-2bp)			8			8
Total	0	0	114	4	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RUFY1	protein_coding	protein_coding	ENST00000319449	18	59469

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.12e-8	1.00	125702	0	45	125747	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.525	330	358	0.922	0.0000195	4606
Missense in Polyphen		114	147.66	0.77204		1813
Synonymous	-0.298	144	140	1.03	0.00000793	1305
Loss of Function	3.20	20	42.5	0.471	0.00000213	502

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000450	0.000449
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000239	0.000229
Middle Eastern	0.0000544	0.0000544
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds phospholipid vesicles containing phosphatidylinositol 3-phosphate and participates in early endosomal trafficking. {ECO:0000269|PubMed:14617813}.
• Pathway: Endocytosis - Homo sapiens (human);Metabolism of lipids;Metabolism;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Intolerance Scores

• loftool: 0.786
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.65

Haploinsufficiency Scores

• pHI: 0.245
• hipred: Y
• hipred_score: 0.621
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.870

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rufy1

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;endocytosis;protein transport;regulation of endocytosis
• Cellular component: nucleus;cytoplasm;endosome;cytosol;nuclear speck;early endosome membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding;lipid binding;protein transporter activity;SH3 domain binding;SH2 domain binding;metal ion binding