RUFY3

RUN and FYVE domain containing 3, the group of Zinc fingers FYVE-type

Basic information

Region (hg38): 4:70704204-70808619

Links

ENSG00000018189 ∙ NCBI:22902 ∙ OMIM:611194 ∙ HGNC:30285 ∙ Uniprot:Q7L099 ∙ 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 RUFY3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RUFY3 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			36	1		37
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	37	2	1

Variants in RUFY3

This is a list of pathogenic ClinVar variants found in the RUFY3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-70705045-G-C		not specified	Uncertain significance (Sep 01, 2021)
4-70705075-C-T		not specified	Uncertain significance (Aug 17, 2021)
4-70705219-C-T		not specified	Uncertain significance (Oct 06, 2021)
4-70762515-G-T			Benign (Dec 31, 2019)
4-70762542-G-A		not specified	Uncertain significance (Mar 11, 2022)
4-70762558-T-C		not specified	Uncertain significance (Mar 07, 2024)
4-70763605-G-A		not specified	Uncertain significance (Feb 10, 2022)
4-70763628-C-T			Likely benign (Dec 31, 2019)
4-70763629-G-A		not specified	Uncertain significance (Jan 26, 2022)
4-70764548-G-A		not specified	Uncertain significance (Oct 25, 2022)
4-70773581-A-G			Benign (Dec 31, 2019)
4-70775171-C-CG		not specified	Uncertain significance (Nov 12, 2015)
4-70775181-A-G		not specified	Uncertain significance (Dec 16, 2023)
4-70783135-G-A		not specified	Uncertain significance (Feb 06, 2024)
4-70783139-C-G		not specified	Uncertain significance (Dec 13, 2023)
4-70783140-G-A		not specified	Uncertain significance (Jan 26, 2022)
4-70783165-A-G		not specified	Uncertain significance (Dec 04, 2023)
4-70783179-G-A		not specified	Uncertain significance (Dec 06, 2023)
4-70784875-G-A		not specified	Uncertain significance (Sep 16, 2021)
4-70788863-A-G		not specified	Uncertain significance (Aug 04, 2023)
4-70788917-C-T		not specified	Uncertain significance (Jul 27, 2022)
4-70788951-A-G		not specified	Uncertain significance (Apr 07, 2022)
4-70789573-A-G		not specified	Uncertain significance (Mar 01, 2023)
4-70793790-G-A		not specified	Uncertain significance (Mar 01, 2023)
4-70793793-A-G		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RUFY3	protein_coding	protein_coding	ENST00000381006	18	103112

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0206	0.979	125714	0	31	125745	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.48	202	329	0.615	0.0000167	4112
Missense in Polyphen		50	131.42	0.38047		1718
Synonymous	0.683	107	116	0.919	0.00000597	1117
Loss of Function	4.22	11	39.7	0.277	0.00000212	466

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000666	0.000662
Ashkenazi Jewish	0.00	0.00
East Asian	0.000335	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000535	0.0000527
Middle Eastern	0.000335	0.000326
South Asian	0.0000699	0.0000653
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the generation of neuronal polarity formation and axon growth (By similarity). Implicated in the formation of a single axon by developing neurons (By similarity). May inhibit the formation of additional axons by inhibition of PI3K in minor neuronal processes (By similarity). Plays a role in the formation of F-actin-enriched protrusive structures at the cell periphery (PubMed:25766321). Plays a role in cytoskeletal organization by regulating the subcellular localization of FSCN1 and DBN1 at axonal growth cones (By similarity). Promotes gastric cancer cell migration and invasion in a PAK1-dependent manner (PubMed:25766321). {ECO:0000250|UniProtKB:Q5FVJ0, ECO:0000250|UniProtKB:Q9D394, ECO:0000269|PubMed:25766321}.

Recessive Scores

• pRec: 0.0840

Intolerance Scores

• loftool: 0.591
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.18

Haploinsufficiency Scores

• pHI: 0.861
• hipred: Y
• hipred_score: 0.527
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rufy3
• Phenotype: homeostasis/metabolism 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); digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: actin filament organization;positive regulation of cell migration;positive regulation of axon extension;regulation of axonogenesis;negative regulation of axonogenesis;positive regulation of intracellular protein transport;regulation of establishment of cell polarity
• Cellular component: cytoplasm;cytosol;endomembrane system;membrane;lamellipodium;cell junction;filopodium;axon;dendrite;growth cone;neuronal cell body;perikaryon;invadopodium
• Molecular function: protein binding