RAB20

RAB20, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 13:110523065-110561722

Links

ENSG00000139832 ∙ NCBI:55647 ∙ ∙ HGNC:18260 ∙ Uniprot:Q9NX57 ∙ 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 RAB20 gene.

• Inborn genetic diseases (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB20 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in RAB20

This is a list of pathogenic ClinVar variants found in the RAB20 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-110523693-T-C		not specified	Uncertain significance (Apr 13, 2022)
13-110523805-T-C		not specified	Uncertain significance (Jan 03, 2024)
13-110523937-C-T		not specified	Uncertain significance (Apr 17, 2023)
13-110523952-G-A		not specified	Likely benign (Jul 26, 2022)
13-110523985-C-T		not specified	Uncertain significance (Dec 27, 2022)
13-110523999-G-A		not specified	Uncertain significance (Dec 18, 2023)
13-110524008-C-T		not specified	Uncertain significance (Aug 11, 2022)
13-110524071-T-C		not specified	Uncertain significance (May 17, 2023)
13-110524126-C-A		not specified	Uncertain significance (Feb 23, 2023)
13-110524129-C-A		not specified	Uncertain significance (Feb 09, 2023)
13-110524155-C-T		not specified	Uncertain significance (Dec 22, 2023)
13-110524158-C-T		not specified	Uncertain significance (Jun 27, 2022)
13-110524159-G-A		not specified	Uncertain significance (Sep 12, 2023)
13-110561447-A-G		not specified	Uncertain significance (May 25, 2022)
13-110561480-T-C		not specified	Uncertain significance (Mar 01, 2023)
13-110561480-T-G		not specified	Uncertain significance (Sep 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB20	protein_coding	protein_coding	ENST00000267328	2	38664

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00390	0.661	125739	0	6	125745	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.697	118	141	0.835	0.00000788	1529
Missense in Polyphen		51	72.597	0.70251		772
Synonymous	0.431	58	62.3	0.931	0.00000383	465
Loss of Function	0.580	4	5.46	0.732	2.31e-7	72

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000462	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in apical endocytosis/recycling. Plays a role in the maturation and acidification of phagosomes that engulf pathogens, such as S.aureus and M.tuberculosis. Plays a role in the fusion of phagosomes with lysosomes. {ECO:0000269|PubMed:21255211}.
• Pathway: Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.390
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.101

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab20
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: intracellular protein transport;endocytosis;regulation of endocytosis;Rab protein signal transduction;cellular response to interferon-gamma;phagosome acidification;phagosome-lysosome fusion
• Cellular component: endosome;early endosome;Golgi apparatus;plasma membrane;endocytic vesicle;phagocytic vesicle membrane;intracellular membrane-bounded organelle;phagocytic vesicle
• Molecular function: GTPase activity;GTP binding