RAB41

protein-coding

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

Gene summary

This gene encodes a small GTP-binding protein that belongs to the largest family within the Ras superfamily. These proteins function as regulators of membrane trafficking. They cycle between inactive GDP-bound and activated GTP-bound states, which is controlled by GTP hydrolysis-activating proteins (GAPs). This family member can be activated by the GAP protein RN-Tre, and it is localized to the Golgi complex. [provided by RefSeq, May 2010]

MANE transcript

NM_001363807.1

Inheritance

—

ClinVar variants

U:46B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chrX:70,282,093-70,285,002

External References & Databases

Ensembl (ENSG00000147127)

Transcript & Mutation Effects

hg38 • Region Span ~2.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RAB41 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 31

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001363807.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	1 clinvar		5
missense			37 clinvar	2 clinvar		39
nonsense			1 clinvar			1
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	46	3	1	50

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001363807.1	RefSeq	NP_001350736.1	8	MANE Select
ENST00000374473.6	Ensembl	ENSP00000363597.2	8	MANE Select
NM_001032726.3	RefSeq	NP_001027898.2	8	Standard
ENST00000276066.4	Ensembl	ENSP00000276066.4	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Post-translational protein modification
Metabolism of proteins
Intra-Golgi traffic

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

Molecular Function

GTPase activity
protein binding
GTP binding

Cellular Component

Golgi membrane
Golgi apparatus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000276066
Coding exons: 8
Length: 2910
Individuals with no LoFs: 125718
Homozygous LoFs: 9
Heterozygous LoFs: 17
Defined: 125744
p: 0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.278	86	93.6	0.919	0.00000781	1458
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00015	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00027	0.00019	rare
South Asian	0.00010	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for normal Golgi ribbon organization and ER-to- Golgi trafficking. {ECO:0000269|PubMed:23936529}.;

Recessive Scores

pRec: 0.0846

Intolerance Scores

LoFtool: 0.599
RVIS EVS: -0.32
RVIS percentile EVS: 31.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0934

Gene Damage Prediction

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