RAB40B

RAB40B, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:82654973-82698698

Links

ENSG00000141542 ∙ NCBI:10966 ∙ OMIM:619550 ∙ HGNC:18284 ∙ Uniprot:Q12829 ∙ 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 RAB40B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB40B 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in RAB40B

This is a list of pathogenic ClinVar variants found in the RAB40B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-82657867-G-C		not specified	Uncertain significance (Sep 26, 2023)
17-82657906-C-T		not specified	Uncertain significance (Aug 10, 2021)
17-82657907-T-C		not specified	Uncertain significance (Dec 02, 2024)
17-82657916-G-T		not specified	Uncertain significance (Nov 05, 2021)
17-82657919-G-A		not specified	Uncertain significance (Feb 23, 2023)
17-82657937-G-A		not specified	Uncertain significance (Mar 02, 2023)
17-82657988-C-T		not specified	Uncertain significance (Aug 08, 2023)
17-82658009-G-C		not specified	Uncertain significance (Nov 07, 2023)
17-82658062-G-A		not specified	Uncertain significance (Nov 25, 2024)
17-82658086-G-C		not specified	Uncertain significance (Feb 28, 2024)
17-82658099-C-T		not specified	Uncertain significance (Dec 07, 2021)
17-82658107-C-T		not specified	Uncertain significance (Jul 09, 2024)
17-82658502-C-T		not specified	Uncertain significance (Sep 17, 2021)
17-82658578-T-C		not specified	Uncertain significance (Jul 14, 2021)
17-82658616-C-G		not specified	Uncertain significance (Apr 13, 2023)
17-82658616-C-T		not specified	Uncertain significance (Jan 24, 2024)
17-82658618-C-G		not specified	Uncertain significance (Dec 12, 2023)
17-82658701-C-T		not specified	Uncertain significance (Jan 25, 2023)
17-82658704-C-G		not specified	Uncertain significance (Aug 06, 2021)
17-82659585-C-T		not specified	Uncertain significance (Jul 20, 2021)
17-82659605-T-A		not specified	Uncertain significance (Jan 03, 2022)
17-82660992-C-T		not specified	Uncertain significance (May 08, 2024)
17-82660997-C-T		not specified	Uncertain significance (Oct 01, 2024)
17-82661009-C-T		not specified	Uncertain significance (Jul 14, 2024)
17-82661036-C-A		not specified	Uncertain significance (Jun 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB40B	protein_coding	protein_coding	ENST00000571995	6	43756

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000866	0.543	125726	0	20	125746	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.461	169	187	0.905	0.0000127	1784
Missense in Polyphen		73	89.226	0.81815		816
Synonymous	0.101	84	85.2	0.986	0.00000587	585
Loss of Function	0.731	9	11.7	0.769	5.66e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.000272	0.000272
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.487
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.0994
• hipred: N
• hipred_score: 0.180
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.232

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab40b

Gene ontology

• Biological process: intracellular protein transport;protein ubiquitination;Rab protein signal transduction;multi-organism toxin transport
• Cellular component: Golgi membrane;nuclear envelope;plasma membrane;perinuclear region of cytoplasm
• Molecular function: GTPase activity;GTP binding