RAB41

RAB41, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): X:70282092-70285002

Links

ENSG00000147127 ∙ NCBI:347517 ∙ ∙ HGNC:18293 ∙ Uniprot:Q5JT25 ∙ 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 RAB41 gene.

• not provided (4 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB41 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			2			2
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	2	2	1

Variants in RAB41

This is a list of pathogenic ClinVar variants found in the RAB41 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-70282242-G-C		not specified	Uncertain significance (Oct 27, 2023)
X-70282339-G-A		not specified	Uncertain significance (Feb 13, 2024)
X-70282348-G-A			Likely benign (Feb 01, 2023)
X-70282563-T-C		not specified	Uncertain significance (Dec 02, 2022)
X-70282837-G-A		not specified	Uncertain significance (Sep 30, 2021)
X-70283304-C-T		not specified	Uncertain significance (Dec 01, 2022)
X-70283553-C-T			Likely benign (May 01, 2023)
X-70284588-CG-C			Benign (May 03, 2018)
X-70284614-G-C		not specified	Uncertain significance (May 17, 2023)
X-70284647-C-T			Likely benign (Jan 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB41	protein_coding	protein_coding	ENST00000276066	8	2910

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000583	0.731	125718	9	17	125744	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.278	86	93.6	0.919	0.00000781	1458
Missense in Polyphen		27	34.378	0.7854		543
Synonymous	-0.479	38	34.4	1.10	0.00000311	398
Loss of Function	0.909	6	8.93	0.672	6.37e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000270	0.000193
Middle Eastern	0.00	0.00
South Asian	0.000105	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for normal Golgi ribbon organization and ER-to- Golgi trafficking. {ECO:0000269|PubMed:23936529}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Intra-Golgi traffic;RAB geranylgeranylation;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.0846

Intolerance Scores

• loftool: 0.599
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.0556
• hipred: N
• hipred_score: 0.123
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0934

Gene Damage Prediction

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

Gene ontology

• Biological process: intracellular protein transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;intra-Golgi vesicle-mediated transport;Rab protein signal transduction;retrograde transport, endosome to Golgi
• Cellular component: Golgi membrane;Golgi apparatus;cytosol
• Molecular function: GTPase activity;protein binding;GTP binding