RUFY2

RUN and FYVE domain containing 2, the group of Zinc fingers FYVE-type

Basic information

Region (hg38): 10:68341107-68407294

Links

ENSG00000204130 ∙ NCBI:55680 ∙ OMIM:610328 ∙ HGNC:19761 ∙ Uniprot:Q8WXA3 ∙ 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 RUFY2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RUFY2 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	21	0	0

Variants in RUFY2

This is a list of pathogenic ClinVar variants found in the RUFY2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-68341629-G-A		not specified	Uncertain significance (May 03, 2023)
10-68341679-G-C		not specified	Uncertain significance (Apr 01, 2024)
10-68345860-C-T		not specified	Uncertain significance (Mar 30, 2024)
10-68346059-T-G		not specified	Uncertain significance (Jan 23, 2023)
10-68363653-T-A		not specified	Uncertain significance (Jan 23, 2023)
10-68364090-T-G		not specified	Uncertain significance (Mar 29, 2022)
10-68376946-A-C		not specified	Uncertain significance (Jan 16, 2024)
10-68379478-C-T		not specified	Uncertain significance (Sep 26, 2022)
10-68379494-T-C		not specified	Uncertain significance (Aug 16, 2022)
10-68383812-A-G		not specified	Uncertain significance (Nov 08, 2021)
10-68383841-T-C		not specified	Uncertain significance (Oct 26, 2022)
10-68383859-C-T		not specified	Uncertain significance (Nov 01, 2022)
10-68383874-T-C		not specified	Uncertain significance (Jun 16, 2023)
10-68383905-C-T		not specified	Uncertain significance (Apr 18, 2023)
10-68386127-T-G		not specified	Uncertain significance (May 04, 2022)
10-68393193-T-C		not specified	Uncertain significance (Mar 20, 2024)
10-68394089-A-C		not specified	Uncertain significance (Oct 06, 2021)
10-68401638-C-T		not specified	Uncertain significance (Dec 07, 2023)
10-68401657-C-G		not specified	Uncertain significance (Mar 03, 2022)
10-68401668-G-A		not specified	Uncertain significance (Dec 02, 2022)
10-68404730-T-C		not specified	Uncertain significance (Jun 03, 2022)
10-68406766-G-A		not specified	Uncertain significance (Nov 15, 2021)
10-68406780-C-A		not specified	Uncertain significance (Oct 18, 2021)
10-68406841-A-C		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RUFY2	protein_coding	protein_coding	ENST00000388768	18	66188

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000678	0.999	124763	0	30	124793	0.000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.68	233	317	0.735	0.0000155	4222
Missense in Polyphen		40	80.243	0.49849		1036
Synonymous	-0.736	123	113	1.09	0.00000564	1117
Loss of Function	4.17	14	43.8	0.320	0.00000240	521

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000228	0.000223
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000560	0.0000556
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000179	0.000177
Middle Eastern	0.0000560	0.0000556
South Asian	0.0000661	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0992

Intolerance Scores

• loftool: 0.677
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.136
• hipred: Y
• hipred_score: 0.663
• ghis: 0.660

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.826

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rufy2

Gene ontology

• Biological process: biological_process;regulation of endocytosis
• Cellular component: nucleus;cytoplasm;endosome
• Molecular function: SH3 domain binding;metal ion binding