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.

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.

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						0
missense			41 clinvar	1 clinvar		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	41	1	0

Variants in RUFY1

This is a list of pathogenic ClinVar variants found in the RUFY1 region.

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

Position	Phenotype	Significance	ClinVar
5-179550582-G-A	not specified	Uncertain significance (Mar 20, 2024)	3315772
5-179550595-C-T	not specified	Uncertain significance (Sep 29, 2022)	2224556
5-179550616-T-G	not specified	Uncertain significance (Sep 14, 2021)	2398393
5-179550667-G-A	not specified	Uncertain significance (Apr 26, 2023)	2512995
5-179550781-G-T	not specified	Uncertain significance (Jun 07, 2023)	2511098
5-179550799-T-C	not specified	Uncertain significance (Dec 08, 2023)	3157146
5-179550801-T-C	not specified	Uncertain significance (Aug 20, 2023)	2609041
5-179550837-G-A	not specified	Uncertain significance (Jul 06, 2021)	2234967
5-179550844-G-T	not specified	Uncertain significance (May 26, 2023)	2552057
5-179550846-G-A	not specified	Uncertain significance (Aug 14, 2023)	2599073
5-179550849-G-T	not specified	Uncertain significance (Dec 28, 2022)	2362075
5-179550864-G-A	not specified	Uncertain significance (Feb 28, 2023)	2490899
5-179550867-A-G	not specified	Likely benign (Jan 12, 2024)	3157147
5-179560088-A-G	not specified	Uncertain significance (Apr 05, 2023)	2532903
5-179560090-G-A	not specified	Uncertain significance (Feb 28, 2023)	2491574
5-179560103-C-T	not specified	Uncertain significance (Jan 05, 2022)	2270594
5-179562558-T-C	not specified	Uncertain significance (May 13, 2024)	3315773
5-179562631-T-C	not specified	Uncertain significance (Apr 04, 2023)	2532753
5-179562655-C-T	not specified	Uncertain significance (Feb 13, 2024)	3157148
5-179567556-T-G	not specified	Uncertain significance (May 15, 2024)	2261656
5-179569302-C-G	not specified	Uncertain significance (Jun 03, 2022)	2275430
5-179569302-C-T	not specified	Likely benign (May 23, 2023)	2521695
5-179569327-A-T	not specified	Uncertain significance (Dec 21, 2023)	3157149
5-179569376-A-G	not specified	Uncertain significance (Aug 22, 2023)	2598162
5-179577123-G-A	not specified	Uncertain significance (Oct 25, 2022)	2319121

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
Phenotype

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