RABL3

RAB, member of RAS oncogene family like 3, the group of RAB like GTPases

Basic information

Region (hg38): 3:120684937-120742993

Links

ENSG00000144840 ∙ NCBI:285282 ∙ OMIM:618542 ∙ HGNC:18072 ∙ Uniprot:Q5HYI8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• pancreatic cancer, susceptibility to, 5 (Limited), mode of inheritance: AD
• familial pancreatic carcinoma (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Pancreatic cancer, susceptibility to, 5	AD	Oncologic	Individuals are reported to be at increased risk of pancreatic cancer (as well as other neoplasms), and awareness may allow early diagnosis and management	Oncologic	31406347

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RABL3 gene.

• RABL3-related condition (4 variants)
• Inborn genetic diseases (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RABL3 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in RABL3

This is a list of pathogenic ClinVar variants found in the RABL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-120689896-C-G		RABL3-related disorder	Benign (Jan 03, 2020)
3-120694160-A-G		not specified	Uncertain significance (Aug 04, 2023)
3-120694183-A-C		not specified	Uncertain significance (Oct 05, 2021)
3-120694208-C-T		RABL3-related disorder	Likely benign (Aug 12, 2022)
3-120698483-A-G		RABL3-related disorder	Benign (Nov 19, 2019)
3-120698500-G-C		RABL3-related disorder	Uncertain significance (Oct 01, 2022)
3-120698576-G-A		RABL3-related disorder	Likely benign (May 09, 2022)
3-120706004-T-A		RABL3-related disorder	Uncertain significance (Sep 08, 2022)
3-120706028-C-T		RABL3-related disorder	Uncertain significance (Oct 04, 2022)
3-120706090-G-A		RABL3-related disorder	Uncertain significance (Apr 25, 2023)
3-120706104-G-A		RABL3-related disorder	Likely benign (Dec 20, 2023)
3-120709774-T-C		RABL3-related disorder	Benign (Nov 05, 2019)
3-120709787-G-A		RABL3-related disorder	Benign/Likely benign (Jan 01, 2024)
3-120709797-A-G		not specified	Uncertain significance (Aug 09, 2021)
3-120709856-T-C		RABL3-related disorder	Likely benign (Dec 04, 2023)
3-120730695-C-T		RABL3-related disorder	Uncertain significance (Dec 26, 2023)
3-120730727-G-T		Pancreatic cancer, susceptibility to, 5	risk factor (Nov 26, 2019)
3-120730738-C-T		RABL3-related disorder	Likely benign (Mar 02, 2022)
3-120730761-G-A		not specified	Uncertain significance (Sep 20, 2023)
3-120742456-G-A		RABL3-related disorder	Likely benign (Feb 22, 2022)
3-120742488-A-C		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RABL3	protein_coding	protein_coding	ENST00000273375	8	56313

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000802	0.936	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.432	115	129	0.893	0.00000675	1530
Missense in Polyphen		35	44.737	0.78236		535
Synonymous	-0.134	48	46.8	1.02	0.00000237	448
Loss of Function	1.65	7	13.5	0.517	5.70e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000332	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.511
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.380
• ghis: 0.642

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rabl3

Gene ontology

• Biological process: intracellular protein transport;Rab protein signal transduction
• Cellular component: cell
• Molecular function: GTPase activity;GTP binding