RBSN

rabenosyn, RAB effector, the group of Zinc fingers FYVE-type

Basic information

Region (hg38): 3:15070069-15099163

Previous symbols: [ "ZFYVE20" ]

Links

ENSG00000131381 ∙ NCBI:64145 ∙ OMIM:609511 ∙ HGNC:20759 ∙ Uniprot:Q9H1K0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital neutropenia-myelofibrosis-nephromegaly syndrome (Supportive), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RBSN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBSN 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				4	4	8
missense			47	2		49
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	48	6	5

Variants in RBSN

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

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

Position	Type	Phenotype	Significance	ClinVar
3-15073789-G-C		not specified	Uncertain significance (Dec 08, 2023)
3-15073796-C-A		not specified	Uncertain significance (Sep 14, 2022)
3-15073815-G-A			Likely benign (Jul 01, 2022)
3-15073829-G-A		not specified	Uncertain significance (Nov 08, 2022)
3-15073852-A-G		not specified	Uncertain significance (Jun 22, 2023)
3-15073864-C-T		not specified	Uncertain significance (May 08, 2023)
3-15073865-G-A		not specified	Uncertain significance (Jul 05, 2024)
3-15073869-G-A			Benign/Likely benign (Jan 01, 2023)
3-15073908-G-C		not specified	Uncertain significance (Sep 30, 2022)
3-15073949-C-G		not specified	Uncertain significance (Aug 05, 2024)
3-15073972-A-G		not specified	Uncertain significance (Oct 20, 2023)
3-15074003-C-T		not specified	Uncertain significance (May 23, 2023)
3-15074026-G-A		not specified	Uncertain significance (Dec 06, 2022)
3-15074055-G-A			Benign (Dec 31, 2019)
3-15074077-G-A		not specified	Uncertain significance (Oct 10, 2023)
3-15074099-T-A		not specified	Uncertain significance (Aug 12, 2021)
3-15074130-C-G		not specified	Uncertain significance (Nov 20, 2023)
3-15074132-C-T		not specified	Uncertain significance (Apr 07, 2023)
3-15074146-A-G		not specified	Uncertain significance (Jan 23, 2024)
3-15074153-T-C		not specified	Uncertain significance (Sep 28, 2022)
3-15074165-G-C		not specified	Uncertain significance (May 31, 2022)
3-15074170-C-G		not specified	Uncertain significance (Jan 23, 2023)
3-15074171-G-A		not specified	Uncertain significance (Mar 21, 2024)
3-15074192-C-A		not specified	Uncertain significance (Oct 25, 2022)
3-15074275-T-G		not specified	Uncertain significance (Nov 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBSN	protein_coding	protein_coding	ENST00000253699	11	29091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0227	0.977	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	370	452	0.818	0.0000266	5145
Missense in Polyphen		107	135.95	0.78706		1553
Synonymous	1.61	145	172	0.844	0.00000949	1524
Loss of Function	4.25	11	40.0	0.275	0.00000244	430

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000163	0.000163
South Asian	0.000134	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Rab4/Rab5 effector protein acting in early endocytic membrane fusion and membrane trafficking of recycling endosomes. Required for endosome fusion either homotypically or with clathrin coated vesicles. Plays a role in the lysosomal trafficking of CTSD/cathepsin D from the Golgi to lysosomes. Also promotes the recycling of transferrin directly from early endosomes to the plasma membrane. Binds phospholipid vesicles containing phosphatidylinositol 3-phosphate (PtdInsP3) (PubMed:11062261, PubMed:11788822, PubMed:15020713). Plays a role in the recycling of transferrin receptor to the plasma membrane (PubMed:22308388). {ECO:0000269|PubMed:11062261, ECO:0000269|PubMed:11788822, ECO:0000269|PubMed:15020713, ECO:0000269|PubMed:22308388}.
• Pathway: Endocytosis - Homo sapiens (human);Toll Like Receptor 9 (TLR9) Cascade;Toll-Like Receptors Cascades;Factors involved in megakaryocyte development and platelet production;Innate Immune System;Immune System;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.73

Haploinsufficiency Scores

• pHI: 0.229
• hipred: Y
• hipred_score: 0.648
• ghis: 0.598

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Rbsn
• Phenotype: vision/eye 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); pigmentation phenotype

Gene ontology

• Biological process: blood coagulation;protein transport;endosomal transport;early endosome to Golgi transport;Golgi to lysosome transport;regulation of Golgi organization
• Cellular component: endosome;cytosol;plasma membrane;endosome membrane;early endosome membrane;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: nucleic acid binding;protein binding;zinc ion binding;Rab GTPase binding